Starting phenix.real_space_refine on Fri Sep 27 12:53:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g04_3385/09_2024/5g04_3385_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g04_3385/09_2024/5g04_3385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g04_3385/09_2024/5g04_3385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g04_3385/09_2024/5g04_3385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g04_3385/09_2024/5g04_3385_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g04_3385/09_2024/5g04_3385_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 395 5.16 5 C 41859 2.51 5 N 11233 2.21 5 O 11991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 65481 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 10925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1437, 10925 Classifications: {'peptide': 1437} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'CIS': 10, 'PCIS': 3, 'PTRANS': 78, 'TRANS': 1345} Chain breaks: 20 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 494 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 239 Chain: "B" Number of atoms: 649 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 84, 644 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 84, 644 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 660 Chain: "C" Number of atoms: 4306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4306 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 509} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 450 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3923 Classifications: {'peptide': 498} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 482} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "G" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 213 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3853 Classifications: {'peptide': 483} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 5709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5709 Classifications: {'peptide': 730} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 706} Chain breaks: 3 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 Chain: "J" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4047 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 14, 'TRANS': 489} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "K" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3988 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1435 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 168} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 493 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain breaks: 1 Chain: "N" Number of atoms: 4837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4837 Classifications: {'peptide': 631} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'CIS': 16, 'PCIS': 3, 'PTRANS': 25, 'TRANS': 586} Chain breaks: 11 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 368 Unresolved non-hydrogen angles: 473 Unresolved non-hydrogen dihedrals: 295 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 8, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 195 Chain: "O" Number of atoms: 5395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5395 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 665} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "P" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 4039 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 477} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2855 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 348} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 370, 2855 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 348} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2912 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 72 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "W" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 213 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3767 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 468} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "Y" Number of atoms: 3859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3859 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 480} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11100 SG CYS B 23 133.409 44.914 147.281 1.00500.00 S ATOM 11118 SG CYS B 26 134.428 48.812 146.585 1.00500.00 S ATOM 11363 SG CYS B 59 131.086 49.075 148.592 1.00500.00 S ATOM 11472 SG CYS B 73 128.757 36.849 145.170 1.00500.00 S ATOM 11493 SG CYS B 76 128.523 32.926 143.600 1.00500.00 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ACYS R 388 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS R 388 " occ=0.50 residue: pdb=" N AMET R 451 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET R 451 " occ=0.50 Time building chain proxies: 27.56, per 1000 atoms: 0.42 Number of scatterers: 65481 At special positions: 0 Unit cell: (231.2, 186.32, 227.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 395 16.00 O 11991 8.00 N 11233 7.00 C 41859 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.47 Conformation dependent library (CDL) restraints added in 6.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1085 " pdb="ZN ZN B1085 " - pdb=" SG CYS B 23 " pdb="ZN ZN B1085 " - pdb=" SG CYS B 26 " pdb="ZN ZN B1085 " - pdb=" SG CYS B 59 " pdb="ZN ZN B1085 " - pdb=" ND1 HIS B 56 " pdb=" ZN B1086 " pdb="ZN ZN B1086 " - pdb=" ND1 HIS B 53 " pdb="ZN ZN B1086 " - pdb=" SG CYS B 73 " pdb="ZN ZN B1086 " - pdb=" SG CYS B 76 " pdb=" ZN B1087 " pdb="ZN ZN B1087 " - pdb=" ND1 HIS B 58 " Number of angles added : 3 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15920 Finding SS restraints... Secondary structure from input PDB file: 387 helices and 36 sheets defined 68.1% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.16 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 615 through 629 removed outlier: 3.809A pdb=" N LEU A 629 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 646 removed outlier: 3.761A pdb=" N GLN A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 669 removed outlier: 4.083A pdb=" N THR A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 775 removed outlier: 3.635A pdb=" N ILE A 762 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE A 764 " --> pdb=" O PRO A 760 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 790 Processing helix chain 'A' and resid 800 through 810 Processing helix chain 'A' and resid 843 through 854 Processing helix chain 'A' and resid 867 through 882 Processing helix chain 'A' and resid 924 through 937 removed outlier: 3.645A pdb=" N ASN A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 945 removed outlier: 3.760A pdb=" N GLU A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 965 Proline residue: A 954 - end of helix removed outlier: 3.571A pdb=" N ALA A 958 " --> pdb=" O PRO A 954 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 965 " --> pdb=" O HIS A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 978 removed outlier: 3.617A pdb=" N CYS A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 985 removed outlier: 3.782A pdb=" N LEU A 983 " --> pdb=" O ARG A 980 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 985 " --> pdb=" O ASP A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1032 through 1042 removed outlier: 3.961A pdb=" N ASP A1036 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1088 removed outlier: 3.802A pdb=" N GLU A1064 " --> pdb=" O HIS A1060 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A1065 " --> pdb=" O GLU A1061 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG A1076 " --> pdb=" O GLN A1072 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A1079 " --> pdb=" O GLN A1075 " (cutoff:3.500A) Proline residue: A1081 - end of helix removed outlier: 3.755A pdb=" N MET A1086 " --> pdb=" O VAL A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1146 removed outlier: 3.572A pdb=" N PHE A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A1146 " --> pdb=" O ALA A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1161 removed outlier: 3.758A pdb=" N ILE A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1183 removed outlier: 3.612A pdb=" N TYR A1172 " --> pdb=" O LEU A1168 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A1180 " --> pdb=" O LEU A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1188 Processing helix chain 'A' and resid 1189 through 1193 Processing helix chain 'A' and resid 1201 through 1217 removed outlier: 3.523A pdb=" N LEU A1210 " --> pdb=" O ILE A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1228 Processing helix chain 'A' and resid 1246 through 1261 removed outlier: 3.510A pdb=" N GLN A1250 " --> pdb=" O PRO A1246 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A1251 " --> pdb=" O HIS A1247 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA A1252 " --> pdb=" O ASN A1248 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A1253 " --> pdb=" O VAL A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1278 removed outlier: 3.681A pdb=" N GLU A1271 " --> pdb=" O ARG A1267 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A1278 " --> pdb=" O LEU A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1307 removed outlier: 3.823A pdb=" N TYR A1294 " --> pdb=" O ASP A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1331 Processing helix chain 'A' and resid 1359 through 1375 removed outlier: 3.965A pdb=" N THR A1363 " --> pdb=" O ASN A1359 " (cutoff:3.500A) Proline residue: A1365 - end of helix Processing helix chain 'A' and resid 1380 through 1387 removed outlier: 3.700A pdb=" N TRP A1386 " --> pdb=" O SER A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1399 removed outlier: 3.909A pdb=" N ASP A1397 " --> pdb=" O MET A1393 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A1398 " --> pdb=" O TYR A1394 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1415 removed outlier: 3.589A pdb=" N LEU A1405 " --> pdb=" O PRO A1401 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A1406 " --> pdb=" O GLU A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1429 removed outlier: 3.908A pdb=" N VAL A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A1429 " --> pdb=" O TRP A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1437 removed outlier: 3.556A pdb=" N ASN A1437 " --> pdb=" O ILE A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1476 Processing helix chain 'A' and resid 1481 through 1500 removed outlier: 3.599A pdb=" N LEU A1499 " --> pdb=" O PHE A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1508 Processing helix chain 'A' and resid 1508 through 1527 removed outlier: 3.705A pdb=" N CYS A1515 " --> pdb=" O ASN A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1546 removed outlier: 4.000A pdb=" N THR A1546 " --> pdb=" O LEU A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1566 Processing helix chain 'A' and resid 1567 through 1570 Processing helix chain 'A' and resid 1578 through 1588 removed outlier: 3.676A pdb=" N ALA A1582 " --> pdb=" O ASN A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1608 removed outlier: 3.615A pdb=" N LEU A1606 " --> pdb=" O LEU A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1613 removed outlier: 3.961A pdb=" N ALA A1613 " --> pdb=" O LEU A1609 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1609 through 1613' Processing helix chain 'A' and resid 1684 through 1693 removed outlier: 3.919A pdb=" N LYS A1688 " --> pdb=" O THR A1684 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A1693 " --> pdb=" O SER A1689 " (cutoff:3.500A) Processing helix chain 'A' and resid 1744 through 1755 removed outlier: 3.895A pdb=" N GLU A1752 " --> pdb=" O LEU A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1764 through 1781 removed outlier: 4.179A pdb=" N LEU A1768 " --> pdb=" O LYS A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1785 through 1803 removed outlier: 4.634A pdb=" N ALA A1789 " --> pdb=" O GLU A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1808 through 1822 removed outlier: 3.663A pdb=" N GLN A1813 " --> pdb=" O SER A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1844 through 1863 Processing helix chain 'A' and resid 1864 through 1873 removed outlier: 3.539A pdb=" N SER A1873 " --> pdb=" O HIS A1869 " (cutoff:3.500A) Processing helix chain 'A' and resid 1878 through 1893 removed outlier: 4.046A pdb=" N SER A1883 " --> pdb=" O GLU A1879 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N MET A1884 " --> pdb=" O SER A1880 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS A1887 " --> pdb=" O SER A1883 " (cutoff:3.500A) Processing helix chain 'A' and resid 1911 through 1920 removed outlier: 3.713A pdb=" N LEU A1915 " --> pdb=" O SER A1911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1925 through 1931 removed outlier: 3.546A pdb=" N ARG A1931 " --> pdb=" O ARG A1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 68 Processing helix chain 'C' and resid 29 through 47 Processing helix chain 'C' and resid 48 through 62 Processing helix chain 'C' and resid 77 through 97 removed outlier: 4.933A pdb=" N ASP C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ALA C 86 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 106 Processing helix chain 'C' and resid 112 through 137 removed outlier: 5.241A pdb=" N TYR C 118 " --> pdb=" O ALA C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 165 removed outlier: 3.759A pdb=" N VAL C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 182 removed outlier: 3.574A pdb=" N TYR C 173 " --> pdb=" O GLY C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 199 removed outlier: 3.672A pdb=" N ASP C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.671A pdb=" N TRP C 206 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 222 Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.815A pdb=" N PHE C 232 " --> pdb=" O TRP C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.725A pdb=" N LEU C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 removed outlier: 4.482A pdb=" N LYS C 261 " --> pdb=" O GLY C 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 258 through 261' Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 278 through 293 removed outlier: 3.819A pdb=" N ILE C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 310 Processing helix chain 'C' and resid 312 through 327 Processing helix chain 'C' and resid 330 through 344 Processing helix chain 'C' and resid 346 through 360 Processing helix chain 'C' and resid 365 through 378 removed outlier: 3.852A pdb=" N THR C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 414 through 427 removed outlier: 4.164A pdb=" N TYR C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR C 421 " --> pdb=" O TYR C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 439 removed outlier: 3.874A pdb=" N LEU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 447 Processing helix chain 'C' and resid 448 through 463 removed outlier: 3.501A pdb=" N ALA C 452 " --> pdb=" O GLN C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 480 removed outlier: 3.566A pdb=" N LYS C 472 " --> pdb=" O MET C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 500 Processing helix chain 'C' and resid 511 through 523 Processing helix chain 'C' and resid 525 through 540 Processing helix chain 'C' and resid 543 through 557 removed outlier: 4.192A pdb=" N LYS C 547 " --> pdb=" O ARG C 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 46 Processing helix chain 'E' and resid 52 through 92 removed outlier: 3.519A pdb=" N VAL E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU E 88 " --> pdb=" O GLY E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 removed outlier: 3.745A pdb=" N PHE E 96 " --> pdb=" O GLU E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 96' Processing helix chain 'E' and resid 98 through 103 Processing helix chain 'F' and resid 6 through 18 Processing helix chain 'F' and resid 20 through 36 Processing helix chain 'F' and resid 37 through 51 Processing helix chain 'F' and resid 53 through 64 Processing helix chain 'F' and resid 68 through 82 Processing helix chain 'F' and resid 84 through 94 removed outlier: 3.578A pdb=" N GLN F 90 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE F 91 " --> pdb=" O GLU F 87 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 113 through 129 Processing helix chain 'F' and resid 130 through 145 removed outlier: 3.722A pdb=" N GLU F 136 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 158 removed outlier: 4.026A pdb=" N PHE F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 478 removed outlier: 4.127A pdb=" N ALA F 458 " --> pdb=" O LEU F 454 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA F 459 " --> pdb=" O GLN F 455 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY F 461 " --> pdb=" O ALA F 457 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU F 462 " --> pdb=" O ALA F 458 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 465 " --> pdb=" O GLY F 461 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY F 472 " --> pdb=" O GLU F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 490 removed outlier: 3.615A pdb=" N HIS F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 513 Processing helix chain 'F' and resid 514 through 529 removed outlier: 3.505A pdb=" N GLU F 524 " --> pdb=" O ARG F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 546 removed outlier: 3.522A pdb=" N TYR F 539 " --> pdb=" O GLY F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 563 Processing helix chain 'F' and resid 566 through 580 removed outlier: 3.921A pdb=" N TRP F 570 " --> pdb=" O SER F 566 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE F 577 " --> pdb=" O ALA F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 597 removed outlier: 3.545A pdb=" N LYS F 588 " --> pdb=" O ASP F 584 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE F 589 " --> pdb=" O ILE F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 615 removed outlier: 4.221A pdb=" N TYR F 604 " --> pdb=" O TYR F 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 631 removed outlier: 3.762A pdb=" N ALA F 622 " --> pdb=" O ASP F 618 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS F 623 " --> pdb=" O LYS F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 648 removed outlier: 3.866A pdb=" N TRP F 638 " --> pdb=" O HIS F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 665 Processing helix chain 'F' and resid 668 through 683 Processing helix chain 'F' and resid 684 through 699 Processing helix chain 'F' and resid 702 through 716 Processing helix chain 'F' and resid 718 through 733 removed outlier: 3.767A pdb=" N GLU F 728 " --> pdb=" O GLN F 724 " (cutoff:3.500A) Processing helix chain 'F' and resid 736 through 751 removed outlier: 3.763A pdb=" N TYR F 740 " --> pdb=" O GLU F 736 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS F 749 " --> pdb=" O LYS F 745 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 767 Processing helix chain 'F' and resid 769 through 782 removed outlier: 3.793A pdb=" N ASN F 773 " --> pdb=" O LYS F 769 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS F 776 " --> pdb=" O ASN F 772 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE F 779 " --> pdb=" O ILE F 775 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP F 780 " --> pdb=" O LYS F 776 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 25 removed outlier: 3.771A pdb=" N GLU G 18 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE G 19 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 18 Processing helix chain 'H' and resid 20 through 36 Processing helix chain 'H' and resid 37 through 51 Processing helix chain 'H' and resid 53 through 64 Processing helix chain 'H' and resid 68 through 82 Processing helix chain 'H' and resid 84 through 94 removed outlier: 3.641A pdb=" N ILE H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 113 through 129 Processing helix chain 'H' and resid 130 through 145 removed outlier: 3.731A pdb=" N GLU H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 158 removed outlier: 4.026A pdb=" N PHE H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 451 through 479 removed outlier: 3.957A pdb=" N ALA H 458 " --> pdb=" O LEU H 454 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA H 459 " --> pdb=" O GLN H 455 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY H 461 " --> pdb=" O ALA H 457 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU H 462 " --> pdb=" O ALA H 458 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY H 472 " --> pdb=" O GLU H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 490 removed outlier: 3.608A pdb=" N HIS H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 513 Processing helix chain 'H' and resid 514 through 529 removed outlier: 3.509A pdb=" N GLU H 524 " --> pdb=" O ARG H 520 " (cutoff:3.500A) Processing helix chain 'H' and resid 535 through 546 removed outlier: 3.528A pdb=" N TYR H 539 " --> pdb=" O GLY H 535 " (cutoff:3.500A) Processing helix chain 'H' and resid 548 through 563 Processing helix chain 'H' and resid 566 through 580 removed outlier: 3.934A pdb=" N TRP H 570 " --> pdb=" O SER H 566 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE H 577 " --> pdb=" O ALA H 573 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 597 removed outlier: 3.562A pdb=" N LYS H 588 " --> pdb=" O ASP H 584 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE H 589 " --> pdb=" O ILE H 585 " (cutoff:3.500A) Processing helix chain 'H' and resid 600 through 615 removed outlier: 4.220A pdb=" N TYR H 604 " --> pdb=" O TYR H 600 " (cutoff:3.500A) Processing helix chain 'H' and resid 616 through 631 removed outlier: 3.749A pdb=" N ALA H 622 " --> pdb=" O ASP H 618 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS H 623 " --> pdb=" O LYS H 619 " (cutoff:3.500A) Processing helix chain 'H' and resid 634 through 648 removed outlier: 3.884A pdb=" N TRP H 638 " --> pdb=" O HIS H 634 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 665 Processing helix chain 'H' and resid 668 through 683 Processing helix chain 'H' and resid 684 through 699 Processing helix chain 'H' and resid 702 through 716 Processing helix chain 'H' and resid 718 through 733 removed outlier: 3.760A pdb=" N GLU H 728 " --> pdb=" O GLN H 724 " (cutoff:3.500A) Processing helix chain 'H' and resid 736 through 751 removed outlier: 3.708A pdb=" N TYR H 740 " --> pdb=" O GLU H 736 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS H 749 " --> pdb=" O LYS H 745 " (cutoff:3.500A) Processing helix chain 'H' and resid 752 through 767 Processing helix chain 'I' and resid 49 through 52 Processing helix chain 'I' and resid 132 through 137 removed outlier: 4.147A pdb=" N ASN I 136 " --> pdb=" O GLU I 132 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU I 137 " --> pdb=" O ASP I 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 132 through 137' Processing helix chain 'I' and resid 163 through 170 Processing helix chain 'I' and resid 190 through 192 No H-bonds generated for 'chain 'I' and resid 190 through 192' Processing helix chain 'I' and resid 238 through 244 Processing helix chain 'I' and resid 244 through 294 removed outlier: 3.690A pdb=" N ALA I 275 " --> pdb=" O CYS I 271 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP I 276 " --> pdb=" O MET I 272 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU I 278 " --> pdb=" O GLU I 274 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE I 279 " --> pdb=" O ALA I 275 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU I 280 " --> pdb=" O TRP I 276 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N MET I 281 " --> pdb=" O GLU I 277 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN I 282 " --> pdb=" O GLU I 278 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET I 283 " --> pdb=" O ILE I 279 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP I 284 " --> pdb=" O LEU I 280 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER I 285 " --> pdb=" O MET I 281 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG I 286 " --> pdb=" O GLN I 282 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU I 287 " --> pdb=" O MET I 283 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE I 290 " --> pdb=" O ARG I 286 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL I 291 " --> pdb=" O LEU I 287 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN I 292 " --> pdb=" O THR I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 310 Processing helix chain 'I' and resid 315 through 325 removed outlier: 3.529A pdb=" N GLN I 324 " --> pdb=" O LEU I 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 351 removed outlier: 3.506A pdb=" N ILE I 349 " --> pdb=" O GLN I 345 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER I 350 " --> pdb=" O LYS I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 372 removed outlier: 3.591A pdb=" N GLY I 368 " --> pdb=" O SER I 364 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N MET I 369 " --> pdb=" O GLU I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 377 Processing helix chain 'I' and resid 382 through 429 removed outlier: 3.536A pdb=" N ALA I 416 " --> pdb=" O LYS I 412 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG I 427 " --> pdb=" O VAL I 423 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET I 428 " --> pdb=" O ALA I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 441 through 456 Processing helix chain 'I' and resid 474 through 480 removed outlier: 4.251A pdb=" N TYR I 478 " --> pdb=" O ARG I 474 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU I 479 " --> pdb=" O VAL I 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 503 Processing helix chain 'I' and resid 521 through 548 removed outlier: 3.576A pdb=" N VAL I 525 " --> pdb=" O SER I 521 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS I 536 " --> pdb=" O ILE I 532 " (cutoff:3.500A) Proline residue: I 540 - end of helix removed outlier: 3.602A pdb=" N MET I 548 " --> pdb=" O ILE I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 672 through 674 No H-bonds generated for 'chain 'I' and resid 672 through 674' Processing helix chain 'I' and resid 679 through 683 Processing helix chain 'J' and resid 2 through 17 Processing helix chain 'J' and resid 18 through 34 Processing helix chain 'J' and resid 36 through 50 removed outlier: 3.554A pdb=" N TRP J 42 " --> pdb=" O GLN J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 63 removed outlier: 3.785A pdb=" N ARG J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 70 removed outlier: 3.642A pdb=" N LEU J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 84 removed outlier: 3.539A pdb=" N LEU J 75 " --> pdb=" O ALA J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 94 Processing helix chain 'J' and resid 124 through 143 Processing helix chain 'J' and resid 145 through 161 Processing helix chain 'J' and resid 163 through 173 removed outlier: 4.212A pdb=" N PHE J 167 " --> pdb=" O CYS J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 188 removed outlier: 3.536A pdb=" N GLU J 186 " --> pdb=" O LYS J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 208 removed outlier: 3.518A pdb=" N GLU J 199 " --> pdb=" O ASN J 195 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS J 208 " --> pdb=" O LEU J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 230 through 245 Processing helix chain 'J' and resid 246 through 261 removed outlier: 3.558A pdb=" N VAL J 256 " --> pdb=" O LYS J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 279 removed outlier: 4.529A pdb=" N VAL J 270 " --> pdb=" O SER J 266 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 295 Processing helix chain 'J' and resid 298 through 313 removed outlier: 3.934A pdb=" N TRP J 302 " --> pdb=" O ASN J 298 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY J 313 " --> pdb=" O TYR J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 330 Processing helix chain 'J' and resid 333 through 348 removed outlier: 3.662A pdb=" N TRP J 337 " --> pdb=" O TYR J 333 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE J 344 " --> pdb=" O TYR J 340 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 364 Processing helix chain 'J' and resid 368 through 381 Processing helix chain 'J' and resid 383 through 397 Processing helix chain 'J' and resid 401 through 416 Processing helix chain 'J' and resid 418 through 434 removed outlier: 3.582A pdb=" N ALA J 434 " --> pdb=" O GLU J 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 444 through 459 Processing helix chain 'J' and resid 460 through 475 Processing helix chain 'J' and resid 478 through 492 Processing helix chain 'J' and resid 494 through 509 Processing helix chain 'J' and resid 512 through 529 Processing helix chain 'K' and resid 2 through 17 Processing helix chain 'K' and resid 18 through 34 Processing helix chain 'K' and resid 36 through 50 removed outlier: 3.560A pdb=" N TRP K 42 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 62 Processing helix chain 'K' and resid 64 through 69 removed outlier: 3.656A pdb=" N LEU K 68 " --> pdb=" O LYS K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 84 Processing helix chain 'K' and resid 88 through 93 Processing helix chain 'K' and resid 130 through 143 Processing helix chain 'K' and resid 145 through 161 removed outlier: 3.508A pdb=" N LEU K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 172 removed outlier: 4.005A pdb=" N PHE K 167 " --> pdb=" O CYS K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 175 No H-bonds generated for 'chain 'K' and resid 173 through 175' Processing helix chain 'K' and resid 178 through 188 Processing helix chain 'K' and resid 194 through 211 removed outlier: 3.545A pdb=" N GLN K 198 " --> pdb=" O CYS K 194 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU K 199 " --> pdb=" O ASN K 195 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS K 208 " --> pdb=" O LEU K 204 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS K 211 " --> pdb=" O ASN K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 225 removed outlier: 3.557A pdb=" N GLU K 222 " --> pdb=" O THR K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 229 Processing helix chain 'K' and resid 230 through 245 Processing helix chain 'K' and resid 246 through 261 Processing helix chain 'K' and resid 266 through 279 removed outlier: 4.500A pdb=" N VAL K 270 " --> pdb=" O SER K 266 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 295 Processing helix chain 'K' and resid 298 through 313 removed outlier: 3.973A pdb=" N TRP K 302 " --> pdb=" O ASN K 298 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY K 313 " --> pdb=" O TYR K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 330 Processing helix chain 'K' and resid 334 through 348 removed outlier: 3.703A pdb=" N PHE K 344 " --> pdb=" O TYR K 340 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 364 Processing helix chain 'K' and resid 367 through 381 removed outlier: 4.760A pdb=" N MET K 371 " --> pdb=" O CYS K 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 398 removed outlier: 3.550A pdb=" N ILE K 397 " --> pdb=" O GLN K 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 401 through 416 Processing helix chain 'K' and resid 417 through 435 removed outlier: 3.507A pdb=" N ALA K 434 " --> pdb=" O GLU K 430 " (cutoff:3.500A) Processing helix chain 'K' and resid 440 through 459 removed outlier: 4.070A pdb=" N TRP K 444 " --> pdb=" O THR K 440 " (cutoff:3.500A) Proline residue: K 446 - end of helix Processing helix chain 'K' and resid 460 through 475 removed outlier: 3.608A pdb=" N LEU K 474 " --> pdb=" O GLN K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 492 Processing helix chain 'K' and resid 494 through 509 Processing helix chain 'K' and resid 512 through 527 Processing helix chain 'L' and resid 12 through 19 removed outlier: 3.590A pdb=" N LEU L 16 " --> pdb=" O ASP L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 Processing helix chain 'L' and resid 145 through 148 removed outlier: 3.715A pdb=" N GLY L 148 " --> pdb=" O HIS L 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 145 through 148' Processing helix chain 'L' and resid 174 through 179 removed outlier: 3.580A pdb=" N MET L 178 " --> pdb=" O THR L 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 16 removed outlier: 3.548A pdb=" N ILE M 15 " --> pdb=" O ILE M 11 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP M 16 " --> pdb=" O LEU M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 55 Processing helix chain 'N' and resid 15 through 29 removed outlier: 3.784A pdb=" N THR N 29 " --> pdb=" O ASN N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 63 Processing helix chain 'N' and resid 78 through 92 removed outlier: 3.634A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) Proline residue: N 89 - end of helix Processing helix chain 'N' and resid 93 through 99 Processing helix chain 'N' and resid 107 through 123 Processing helix chain 'N' and resid 126 through 139 removed outlier: 3.579A pdb=" N LEU N 132 " --> pdb=" O SER N 128 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS N 134 " --> pdb=" O GLU N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 162 removed outlier: 3.656A pdb=" N MET N 156 " --> pdb=" O GLU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 191 Processing helix chain 'N' and resid 203 through 213 Processing helix chain 'N' and resid 234 through 250 removed outlier: 3.804A pdb=" N LEU N 250 " --> pdb=" O VAL N 246 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 278 removed outlier: 3.975A pdb=" N ALA N 258 " --> pdb=" O GLU N 254 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU N 259 " --> pdb=" O ARG N 255 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA N 260 " --> pdb=" O VAL N 256 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR N 263 " --> pdb=" O GLU N 259 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG N 276 " --> pdb=" O ARG N 272 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG N 278 " --> pdb=" O GLU N 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 304 removed outlier: 3.982A pdb=" N LYS N 291 " --> pdb=" O ARG N 287 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE N 293 " --> pdb=" O PHE N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 322 through 349 removed outlier: 4.479A pdb=" N PHE N 345 " --> pdb=" O ILE N 341 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER N 346 " --> pdb=" O GLU N 342 " (cutoff:3.500A) Processing helix chain 'N' and resid 354 through 367 removed outlier: 3.623A pdb=" N ARG N 367 " --> pdb=" O TYR N 363 " (cutoff:3.500A) Processing helix chain 'N' and resid 370 through 386 Processing helix chain 'N' and resid 395 through 409 removed outlier: 4.145A pdb=" N LEU N 399 " --> pdb=" O ASP N 395 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 421 Processing helix chain 'N' and resid 421 through 432 removed outlier: 3.697A pdb=" N GLU N 432 " --> pdb=" O LEU N 428 " (cutoff:3.500A) Processing helix chain 'N' and resid 433 through 442 removed outlier: 4.092A pdb=" N GLN N 437 " --> pdb=" O ASP N 433 " (cutoff:3.500A) Processing helix chain 'N' and resid 451 through 458 removed outlier: 3.706A pdb=" N LYS N 458 " --> pdb=" O VAL N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 499 through 509 removed outlier: 3.668A pdb=" N TYR N 509 " --> pdb=" O LEU N 505 " (cutoff:3.500A) Processing helix chain 'N' and resid 512 through 530 removed outlier: 3.790A pdb=" N ASP N 525 " --> pdb=" O SER N 521 " (cutoff:3.500A) Processing helix chain 'N' and resid 536 through 549 Processing helix chain 'N' and resid 554 through 563 removed outlier: 3.773A pdb=" N MET N 560 " --> pdb=" O PHE N 556 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU N 561 " --> pdb=" O CYS N 557 " (cutoff:3.500A) Processing helix chain 'N' and resid 564 through 580 Processing helix chain 'N' and resid 612 through 630 removed outlier: 4.205A pdb=" N ALA N 617 " --> pdb=" O GLU N 613 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA N 618 " --> pdb=" O ASP N 614 " (cutoff:3.500A) Processing helix chain 'N' and resid 660 through 672 removed outlier: 3.918A pdb=" N ASP N 672 " --> pdb=" O LEU N 668 " (cutoff:3.500A) Processing helix chain 'N' and resid 677 through 686 Processing helix chain 'N' and resid 688 through 703 removed outlier: 3.656A pdb=" N VAL N 698 " --> pdb=" O ARG N 694 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 45 Processing helix chain 'O' and resid 53 through 70 removed outlier: 3.574A pdb=" N ARG O 58 " --> pdb=" O LEU O 54 " (cutoff:3.500A) Proline residue: O 66 - end of helix removed outlier: 3.505A pdb=" N GLN O 69 " --> pdb=" O LEU O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'O' and resid 86 through 103 removed outlier: 3.870A pdb=" N ALA O 90 " --> pdb=" O CYS O 86 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN O 91 " --> pdb=" O PRO O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 121 removed outlier: 3.666A pdb=" N MET O 108 " --> pdb=" O GLU O 104 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER O 120 " --> pdb=" O SER O 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 146 removed outlier: 3.510A pdb=" N LEU O 146 " --> pdb=" O ALA O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 169 removed outlier: 3.513A pdb=" N GLY O 165 " --> pdb=" O TYR O 161 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR O 169 " --> pdb=" O GLY O 165 " (cutoff:3.500A) Processing helix chain 'O' and resid 208 through 226 removed outlier: 3.637A pdb=" N GLU O 213 " --> pdb=" O GLN O 209 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE O 214 " --> pdb=" O LYS O 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 247 removed outlier: 3.667A pdb=" N PHE O 246 " --> pdb=" O ASN O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 251 through 264 removed outlier: 3.814A pdb=" N TYR O 255 " --> pdb=" O ALA O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 281 removed outlier: 3.665A pdb=" N SER O 270 " --> pdb=" O ASP O 266 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR O 271 " --> pdb=" O VAL O 267 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS O 276 " --> pdb=" O HIS O 272 " (cutoff:3.500A) Processing helix chain 'O' and resid 298 through 314 removed outlier: 4.119A pdb=" N TYR O 302 " --> pdb=" O ARG O 298 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA O 304 " --> pdb=" O LEU O 300 " (cutoff:3.500A) Processing helix chain 'O' and resid 316 through 334 removed outlier: 3.700A pdb=" N GLU O 326 " --> pdb=" O LEU O 322 " (cutoff:3.500A) Processing helix chain 'O' and resid 336 through 351 removed outlier: 3.609A pdb=" N LEU O 340 " --> pdb=" O ASP O 336 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS O 342 " --> pdb=" O VAL O 338 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP O 346 " --> pdb=" O HIS O 342 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL O 349 " --> pdb=" O SER O 345 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 370 removed outlier: 3.555A pdb=" N LYS O 366 " --> pdb=" O GLU O 362 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS O 370 " --> pdb=" O LYS O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 373 through 388 Processing helix chain 'O' and resid 394 through 413 removed outlier: 3.627A pdb=" N LEU O 408 " --> pdb=" O ASP O 404 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 432 removed outlier: 3.939A pdb=" N ILE O 418 " --> pdb=" O LEU O 414 " (cutoff:3.500A) Processing helix chain 'O' and resid 434 through 447 Processing helix chain 'O' and resid 462 through 480 removed outlier: 3.849A pdb=" N PHE O 466 " --> pdb=" O ASN O 462 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA O 467 " --> pdb=" O THR O 463 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS O 477 " --> pdb=" O LEU O 473 " (cutoff:3.500A) Processing helix chain 'O' and resid 482 through 497 removed outlier: 3.528A pdb=" N VAL O 489 " --> pdb=" O ALA O 485 " (cutoff:3.500A) Processing helix chain 'O' and resid 503 through 523 Processing helix chain 'O' and resid 524 through 539 removed outlier: 3.739A pdb=" N GLY O 534 " --> pdb=" O SER O 530 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU O 538 " --> pdb=" O GLY O 534 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 554 Processing helix chain 'O' and resid 556 through 574 Processing helix chain 'O' and resid 576 through 592 Processing helix chain 'O' and resid 596 through 599 Processing helix chain 'O' and resid 600 through 615 Processing helix chain 'O' and resid 616 through 634 removed outlier: 4.010A pdb=" N GLU O 622 " --> pdb=" O TYR O 618 " (cutoff:3.500A) Processing helix chain 'O' and resid 636 through 654 removed outlier: 4.240A pdb=" N MET O 646 " --> pdb=" O SER O 642 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA O 647 " --> pdb=" O LEU O 643 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU O 649 " --> pdb=" O HIS O 645 " (cutoff:3.500A) Proline residue: O 650 - end of helix removed outlier: 4.086A pdb=" N ASP O 654 " --> pdb=" O PRO O 650 " (cutoff:3.500A) Processing helix chain 'O' and resid 657 through 676 Processing helix chain 'O' and resid 682 through 705 removed outlier: 3.560A pdb=" N ALA O 689 " --> pdb=" O GLU O 685 " (cutoff:3.500A) Processing helix chain 'O' and resid 709 through 725 Processing helix chain 'O' and resid 726 through 741 removed outlier: 3.865A pdb=" N ARG O 730 " --> pdb=" O LYS O 726 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN O 731 " --> pdb=" O THR O 727 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARG O 732 " --> pdb=" O GLN O 728 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 47 Processing helix chain 'P' and resid 48 through 62 Processing helix chain 'P' and resid 77 through 97 removed outlier: 4.912A pdb=" N ASP P 85 " --> pdb=" O ALA P 81 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ALA P 86 " --> pdb=" O GLN P 82 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS P 97 " --> pdb=" O TYR P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 106 Processing helix chain 'P' and resid 107 through 109 No H-bonds generated for 'chain 'P' and resid 107 through 109' Processing helix chain 'P' and resid 111 through 134 Processing helix chain 'P' and resid 148 through 165 removed outlier: 3.578A pdb=" N ARG P 152 " --> pdb=" O ASN P 148 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU P 154 " --> pdb=" O ALA P 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 182 removed outlier: 3.554A pdb=" N TYR P 173 " --> pdb=" O GLY P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 199 removed outlier: 3.677A pdb=" N ASP P 190 " --> pdb=" O LYS P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 213 removed outlier: 3.684A pdb=" N TRP P 206 " --> pdb=" O HIS P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 215 through 222 Processing helix chain 'P' and resid 228 through 241 removed outlier: 3.810A pdb=" N PHE P 232 " --> pdb=" O TRP P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 257 removed outlier: 3.718A pdb=" N LEU P 254 " --> pdb=" O LYS P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 262 through 276 removed outlier: 3.827A pdb=" N VAL P 266 " --> pdb=" O SER P 262 " (cutoff:3.500A) Processing helix chain 'P' and resid 278 through 293 removed outlier: 3.806A pdb=" N ILE P 285 " --> pdb=" O LYS P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 299 through 310 Processing helix chain 'P' and resid 312 through 327 Processing helix chain 'P' and resid 330 through 344 Processing helix chain 'P' and resid 346 through 360 Processing helix chain 'P' and resid 365 through 378 removed outlier: 3.843A pdb=" N THR P 369 " --> pdb=" O LEU P 365 " (cutoff:3.500A) Processing helix chain 'P' and resid 380 through 395 Processing helix chain 'P' and resid 398 through 412 Processing helix chain 'P' and resid 414 through 427 removed outlier: 4.168A pdb=" N CYS P 418 " --> pdb=" O MET P 414 " (cutoff:3.500A) Processing helix chain 'P' and resid 432 through 447 removed outlier: 3.887A pdb=" N LEU P 436 " --> pdb=" O ASP P 432 " (cutoff:3.500A) Processing helix chain 'P' and resid 448 through 463 Processing helix chain 'P' and resid 468 through 480 removed outlier: 3.560A pdb=" N LYS P 472 " --> pdb=" O MET P 468 " (cutoff:3.500A) Processing helix chain 'P' and resid 483 through 500 Processing helix chain 'P' and resid 511 through 523 Processing helix chain 'P' and resid 525 through 538 Processing helix chain 'R' and resid 84 through 97 removed outlier: 3.598A pdb=" N VAL R 90 " --> pdb=" O ALA R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 121 Processing helix chain 'R' and resid 124 through 128 Processing helix chain 'W' and resid 12 through 25 removed outlier: 3.775A pdb=" N GLU W 18 " --> pdb=" O ASP W 14 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE W 19 " --> pdb=" O ASP W 15 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE W 22 " --> pdb=" O GLU W 18 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP W 25 " --> pdb=" O ASN W 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 48 Processing helix chain 'X' and resid 49 through 67 Processing helix chain 'X' and resid 72 through 90 Processing helix chain 'X' and resid 92 through 110 Processing helix chain 'X' and resid 134 through 150 Processing helix chain 'X' and resid 151 through 162 removed outlier: 3.780A pdb=" N ALA X 155 " --> pdb=" O GLN X 151 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE X 162 " --> pdb=" O ILE X 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 168 through 183 Processing helix chain 'X' and resid 184 through 199 Processing helix chain 'X' and resid 202 through 213 Processing helix chain 'X' and resid 214 through 229 removed outlier: 3.602A pdb=" N MET X 224 " --> pdb=" O ALA X 220 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN X 228 " --> pdb=" O MET X 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 235 through 249 removed outlier: 3.518A pdb=" N GLY X 249 " --> pdb=" O PHE X 245 " (cutoff:3.500A) Processing helix chain 'X' and resid 250 through 264 removed outlier: 3.588A pdb=" N SER X 256 " --> pdb=" O SER X 252 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 285 Processing helix chain 'X' and resid 286 through 301 removed outlier: 3.690A pdb=" N VAL X 291 " --> pdb=" O ASN X 287 " (cutoff:3.500A) Processing helix chain 'X' and resid 304 through 318 removed outlier: 4.154A pdb=" N ASP X 309 " --> pdb=" O ILE X 305 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL X 310 " --> pdb=" O LYS X 306 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR X 313 " --> pdb=" O ASP X 309 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA X 316 " --> pdb=" O GLY X 312 " (cutoff:3.500A) Processing helix chain 'X' and resid 320 through 335 removed outlier: 3.693A pdb=" N VAL X 324 " --> pdb=" O ARG X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 338 through 353 removed outlier: 4.152A pdb=" N TRP X 342 " --> pdb=" O HIS X 338 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE X 350 " --> pdb=" O GLY X 346 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR X 351 " --> pdb=" O CYS X 347 " (cutoff:3.500A) Processing helix chain 'X' and resid 354 through 369 removed outlier: 3.545A pdb=" N ALA X 358 " --> pdb=" O ARG X 354 " (cutoff:3.500A) Processing helix chain 'X' and resid 372 through 386 removed outlier: 4.167A pdb=" N LEU X 376 " --> pdb=" O SER X 372 " (cutoff:3.500A) Processing helix chain 'X' and resid 388 through 403 removed outlier: 3.625A pdb=" N ILE X 394 " --> pdb=" O GLN X 390 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS X 395 " --> pdb=" O GLU X 391 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE X 396 " --> pdb=" O ALA X 392 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG X 401 " --> pdb=" O ARG X 397 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU X 402 " --> pdb=" O GLU X 398 " (cutoff:3.500A) Processing helix chain 'X' and resid 406 through 421 removed outlier: 3.552A pdb=" N LEU X 413 " --> pdb=" O CYS X 409 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 438 Processing helix chain 'X' and resid 441 through 454 removed outlier: 3.641A pdb=" N THR X 445 " --> pdb=" O ALA X 441 " (cutoff:3.500A) Processing helix chain 'X' and resid 457 through 472 removed outlier: 3.549A pdb=" N THR X 463 " --> pdb=" O GLU X 459 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU X 464 " --> pdb=" O LYS X 460 " (cutoff:3.500A) Processing helix chain 'X' and resid 475 through 490 removed outlier: 3.547A pdb=" N LEU X 485 " --> pdb=" O LYS X 481 " (cutoff:3.500A) Processing helix chain 'X' and resid 492 through 506 removed outlier: 3.610A pdb=" N ALA X 497 " --> pdb=" O GLU X 493 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN X 501 " --> pdb=" O ALA X 497 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN X 505 " --> pdb=" O ASN X 501 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN X 506 " --> pdb=" O ALA X 502 " (cutoff:3.500A) Processing helix chain 'X' and resid 509 through 523 removed outlier: 4.099A pdb=" N ARG X 513 " --> pdb=" O CYS X 509 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA X 521 " --> pdb=" O ASP X 517 " (cutoff:3.500A) Processing helix chain 'X' and resid 524 through 539 Processing helix chain 'Y' and resid 36 through 48 Processing helix chain 'Y' and resid 49 through 67 Processing helix chain 'Y' and resid 72 through 91 Processing helix chain 'Y' and resid 92 through 110 Processing helix chain 'Y' and resid 134 through 150 Processing helix chain 'Y' and resid 151 through 162 removed outlier: 3.782A pdb=" N ALA Y 155 " --> pdb=" O GLN Y 151 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE Y 162 " --> pdb=" O ILE Y 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 168 through 183 Processing helix chain 'Y' and resid 184 through 199 Processing helix chain 'Y' and resid 202 through 213 Processing helix chain 'Y' and resid 214 through 229 removed outlier: 3.603A pdb=" N MET Y 224 " --> pdb=" O ALA Y 220 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN Y 228 " --> pdb=" O MET Y 224 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 249 removed outlier: 3.519A pdb=" N GLY Y 249 " --> pdb=" O PHE Y 245 " (cutoff:3.500A) Processing helix chain 'Y' and resid 250 through 264 removed outlier: 3.586A pdb=" N SER Y 256 " --> pdb=" O SER Y 252 " (cutoff:3.500A) Processing helix chain 'Y' and resid 270 through 285 Processing helix chain 'Y' and resid 286 through 301 removed outlier: 3.707A pdb=" N VAL Y 291 " --> pdb=" O ASN Y 287 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Y 292 " --> pdb=" O LYS Y 288 " (cutoff:3.500A) Processing helix chain 'Y' and resid 304 through 319 removed outlier: 4.180A pdb=" N ASP Y 309 " --> pdb=" O ILE Y 305 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL Y 310 " --> pdb=" O LYS Y 306 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR Y 313 " --> pdb=" O ASP Y 309 " (cutoff:3.500A) Processing helix chain 'Y' and resid 320 through 335 removed outlier: 3.693A pdb=" N VAL Y 324 " --> pdb=" O ARG Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 338 through 353 removed outlier: 4.153A pdb=" N TRP Y 342 " --> pdb=" O HIS Y 338 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE Y 350 " --> pdb=" O GLY Y 346 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR Y 351 " --> pdb=" O CYS Y 347 " (cutoff:3.500A) Processing helix chain 'Y' and resid 354 through 369 removed outlier: 3.546A pdb=" N ALA Y 358 " --> pdb=" O ARG Y 354 " (cutoff:3.500A) Processing helix chain 'Y' and resid 372 through 387 removed outlier: 4.140A pdb=" N LEU Y 376 " --> pdb=" O SER Y 372 " (cutoff:3.500A) Processing helix chain 'Y' and resid 388 through 403 removed outlier: 3.648A pdb=" N ILE Y 394 " --> pdb=" O GLN Y 390 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N HIS Y 395 " --> pdb=" O GLU Y 391 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE Y 396 " --> pdb=" O ALA Y 392 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG Y 401 " --> pdb=" O ARG Y 397 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU Y 402 " --> pdb=" O GLU Y 398 " (cutoff:3.500A) Processing helix chain 'Y' and resid 406 through 421 removed outlier: 3.637A pdb=" N LEU Y 413 " --> pdb=" O CYS Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 422 through 438 Processing helix chain 'Y' and resid 441 through 454 removed outlier: 3.645A pdb=" N THR Y 445 " --> pdb=" O ALA Y 441 " (cutoff:3.500A) Processing helix chain 'Y' and resid 457 through 472 removed outlier: 3.550A pdb=" N THR Y 463 " --> pdb=" O GLU Y 459 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU Y 464 " --> pdb=" O LYS Y 460 " (cutoff:3.500A) Processing helix chain 'Y' and resid 475 through 490 removed outlier: 3.545A pdb=" N LEU Y 485 " --> pdb=" O LYS Y 481 " (cutoff:3.500A) Processing helix chain 'Y' and resid 492 through 506 removed outlier: 3.610A pdb=" N ALA Y 497 " --> pdb=" O GLU Y 493 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN Y 501 " --> pdb=" O ALA Y 497 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN Y 505 " --> pdb=" O ASN Y 501 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN Y 506 " --> pdb=" O ALA Y 502 " (cutoff:3.500A) Processing helix chain 'Y' and resid 509 through 523 removed outlier: 4.101A pdb=" N ARG Y 513 " --> pdb=" O CYS Y 509 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA Y 521 " --> pdb=" O ASP Y 517 " (cutoff:3.500A) Processing helix chain 'Y' and resid 524 through 539 Processing helix chain 'Y' and resid 542 through 552 removed outlier: 4.126A pdb=" N GLY Y 548 " --> pdb=" O LYS Y 544 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET Y 549 " --> pdb=" O SER Y 545 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET Y 552 " --> pdb=" O GLY Y 548 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 18 through 19 removed outlier: 3.814A pdb=" N GLN A 18 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 73 through 78 removed outlier: 6.432A pdb=" N VAL A 100 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA A 116 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP A 102 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 127 through 132 Processing sheet with id=AD, first strand: chain 'A' and resid 177 through 180 removed outlier: 6.688A pdb=" N GLU A 190 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'A' and resid 237 through 238 removed outlier: 3.636A pdb=" N GLN A 237 " --> pdb=" O CYS A 225 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 245 through 250 removed outlier: 5.965A pdb=" N ILE A 246 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR A 259 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A 250 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE A 255 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'A' and resid 432 through 434 Processing sheet with id=AH, first strand: chain 'A' and resid 458 through 459 Processing sheet with id=AI, first strand: chain 'A' and resid 488 through 492 removed outlier: 3.642A pdb=" N ASN A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU A 497 " --> pdb=" O LYS A 508 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LYS A 508 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 499 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing sheet with id=AJ, first strand: chain 'A' and resid 1108 through 1111 Processing sheet with id=AK, first strand: chain 'A' and resid 1572 through 1574 removed outlier: 3.517A pdb=" N GLU A1615 " --> pdb=" O SER A1573 " (cutoff:3.500A) Processing sheet with id=AL, first strand: chain 'A' and resid 1620 through 1622 Processing sheet with id=AM, first strand: chain 'A' and resid 1648 through 1649 removed outlier: 6.649A pdb=" N GLU A1635 " --> pdb=" O ILE A1666 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE A1666 " --> pdb=" O GLU A1635 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR A1637 " --> pdb=" O LYS A1664 " (cutoff:3.500A) Processing sheet with id=NA, first strand: chain 'N' and resid 590 through 593 removed outlier: 3.668A pdb=" N GLY N 590 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE B 5 " --> pdb=" O ASP N 647 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASP N 647 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS B 7 " --> pdb=" O THR N 645 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR N 645 " --> pdb=" O CYS B 7 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU N 643 " --> pdb=" O ASN B 9 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU N 655 " --> pdb=" O VAL N 648 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 46 through 48 Processing sheet with id=IA, first strand: chain 'I' and resid 23 through 28 removed outlier: 6.968A pdb=" N VAL I 44 " --> pdb=" O SER I 57 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER I 57 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU I 46 " --> pdb=" O VAL I 55 " (cutoff:3.500A) Processing sheet with id=IB, first strand: chain 'I' and resid 68 through 73 removed outlier: 4.127A pdb=" N CYS I 70 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS I 93 " --> pdb=" O LEU I 80 " (cutoff:3.500A) Processing sheet with id=IC, first strand: chain 'I' and resid 112 through 117 Processing sheet with id=ID, first strand: chain 'I' and resid 184 through 189 removed outlier: 6.498A pdb=" N ILE I 185 " --> pdb=" O ARG I 197 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG I 197 " --> pdb=" O ILE I 185 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU I 187 " --> pdb=" O ILE I 195 " (cutoff:3.500A) Processing sheet with id=IE, first strand: chain 'I' and resid 204 through 210 removed outlier: 5.763A pdb=" N CYS I 205 " --> pdb=" O GLU I 222 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU I 222 " --> pdb=" O CYS I 205 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA I 207 " --> pdb=" O VAL I 220 " (cutoff:3.500A) Processing sheet with id=IF, first strand: chain 'I' and resid 229 through 230 Processing sheet with id=IG, first strand: chain 'I' and resid 574 through 578 removed outlier: 11.922A pdb=" N TYR I 596 " --> pdb=" O PHE I 620 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N PHE I 620 " --> pdb=" O TYR I 596 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET I 598 " --> pdb=" O ILE I 618 " (cutoff:3.500A) Processing sheet with id=IH, first strand: chain 'I' and resid 574 through 578 removed outlier: 11.922A pdb=" N TYR I 596 " --> pdb=" O PHE I 620 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N PHE I 620 " --> pdb=" O TYR I 596 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET I 598 " --> pdb=" O ILE I 618 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE I 707 " --> pdb=" O GLY I 621 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE I 623 " --> pdb=" O PHE I 707 " (cutoff:3.500A) Processing sheet with id=II, first strand: chain 'I' and resid 631 through 632 Processing sheet with id=IJ, first strand: chain 'I' and resid 636 through 645 removed outlier: 5.617A pdb=" N CYS I 638 " --> pdb=" O LYS I 654 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS I 654 " --> pdb=" O CYS I 638 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR I 648 " --> pdb=" O TYR I 644 " (cutoff:3.500A) Processing sheet with id=IK, first strand: chain 'I' and resid 719 through 724 Processing sheet with id=LA, first strand: chain 'L' and resid 22 through 24 removed outlier: 4.199A pdb=" N GLN L 155 " --> pdb=" O TYR L 80 " (cutoff:3.500A) Processing sheet with id=LB, first strand: chain 'L' and resid 30 through 33 removed outlier: 12.208A pdb=" N ILE L 66 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 11.182A pdb=" N ALA L 140 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 12.272A pdb=" N PHE L 68 " --> pdb=" O GLN L 138 " (cutoff:3.500A) removed outlier: 11.707A pdb=" N GLN L 138 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 11.126A pdb=" N ARG L 70 " --> pdb=" O MET L 136 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N MET L 136 " --> pdb=" O ARG L 70 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR L 72 " --> pdb=" O THR L 134 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR L 132 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE L 94 " --> pdb=" O GLN L 110 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLN L 110 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL L 96 " --> pdb=" O ILE L 108 " (cutoff:3.500A) Processing sheet with id=LC, first strand: chain 'L' and resid 54 through 55 Processing sheet with id=RA, first strand: chain 'R' and resid 175 through 177 removed outlier: 3.961A pdb=" N THR R 466 " --> pdb=" O ALA R 462 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA R 459 " --> pdb=" O LEU R 449 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU R 449 " --> pdb=" O ALA R 459 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA R 461 " --> pdb=" O LEU R 447 " (cutoff:3.500A) Processing sheet with id=RB, first strand: chain 'R' and resid 190 through 192 removed outlier: 6.833A pdb=" N VAL R 206 " --> pdb=" O LEU R 219 " (cutoff:3.500A) Processing sheet with id=RC, first strand: chain 'R' and resid 229 through 234 removed outlier: 6.236A pdb=" N VAL R 250 " --> pdb=" O ASN R 263 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASN R 263 " --> pdb=" O VAL R 250 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU R 252 " --> pdb=" O LEU R 261 " (cutoff:3.500A) Processing sheet with id=RD, first strand: chain 'R' and resid 271 through 277 removed outlier: 3.501A pdb=" N SER R 273 " --> pdb=" O GLY R 284 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N HIS R 289 " --> pdb=" O SER R 285 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE R 290 " --> pdb=" O THR R 304 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR R 304 " --> pdb=" O ILE R 290 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N HIS R 292 " --> pdb=" O VAL R 302 " (cutoff:3.500A) Processing sheet with id=RE, first strand: chain 'R' and resid 312 through 317 Processing sheet with id=RF, first strand: chain 'R' and resid 360 through 363 removed outlier: 3.780A pdb=" N ALA R 360 " --> pdb=" O GLY R 374 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE R 382 " --> pdb=" O ALA R 395 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA R 395 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE R 384 " --> pdb=" O LEU R 393 " (cutoff:3.500A) Processing sheet with id=RG, first strand: chain 'R' and resid 402 through 408 removed outlier: 4.062A pdb=" N SER R 404 " --> pdb=" O GLY R 417 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU R 425 " --> pdb=" O GLU R 438 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU R 438 " --> pdb=" O LEU R 425 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE R 427 " --> pdb=" O VAL R 436 " (cutoff:3.500A) 4018 hydrogen bonds defined for protein. 11916 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.26 Time building geometry restraints manager: 13.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.52: 45617 1.52 - 1.88: 21241 1.88 - 2.25: 1 2.25 - 2.61: 0 2.61 - 2.97: 5 Bond restraints: 66864 Sorted by residual: bond pdb=" C PRO N 166 " pdb=" N ARG N 167 " ideal model delta sigma weight residual 1.334 2.974 -1.640 1.38e-02 5.25e+03 1.41e+04 bond pdb=" C BCYS R 388 " pdb=" N SER R 389 " ideal model delta sigma weight residual 1.335 2.943 -1.608 1.42e-02 4.96e+03 1.28e+04 bond pdb=" C LEU A1228 " pdb=" N SER A1229 " ideal model delta sigma weight residual 1.332 2.887 -1.555 1.40e-02 5.10e+03 1.23e+04 bond pdb=" C PHE N 549 " pdb=" N GLY N 550 " ideal model delta sigma weight residual 1.331 2.951 -1.620 1.46e-02 4.69e+03 1.23e+04 bond pdb=" C ASP N 563 " pdb=" N MET N 564 " ideal model delta sigma weight residual 1.334 2.816 -1.482 1.49e-02 4.50e+03 9.90e+03 ... (remaining 66859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.27: 90081 7.27 - 14.53: 477 14.53 - 21.80: 14 21.80 - 29.07: 3 29.07 - 36.33: 1 Bond angle restraints: 90576 Sorted by residual: angle pdb=" O PHE N 549 " pdb=" C PHE N 549 " pdb=" N GLY N 550 " ideal model delta sigma weight residual 122.32 85.99 36.33 1.15e+00 7.56e-01 9.98e+02 angle pdb=" CA PHE N 549 " pdb=" C PHE N 549 " pdb=" N GLY N 550 " ideal model delta sigma weight residual 117.07 94.44 22.63 1.21e+00 6.83e-01 3.50e+02 angle pdb=" C ASP N 563 " pdb=" N MET N 564 " pdb=" CA MET N 564 " ideal model delta sigma weight residual 121.14 97.51 23.63 1.75e+00 3.27e-01 1.82e+02 angle pdb=" N PRO I 489 " pdb=" CA PRO I 489 " pdb=" C PRO I 489 " ideal model delta sigma weight residual 110.70 125.08 -14.38 1.22e+00 6.72e-01 1.39e+02 angle pdb=" C PRO N 166 " pdb=" N ARG N 167 " pdb=" CA ARG N 167 " ideal model delta sigma weight residual 121.18 99.63 21.55 1.98e+00 2.55e-01 1.18e+02 ... (remaining 90571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 33639 18.00 - 35.99: 4625 35.99 - 53.98: 1570 53.98 - 71.98: 349 71.98 - 89.97: 67 Dihedral angle restraints: 40250 sinusoidal: 15699 harmonic: 24551 Sorted by residual: dihedral pdb=" N ASN P 361 " pdb=" C ASN P 361 " pdb=" CA ASN P 361 " pdb=" CB ASN P 361 " ideal model delta harmonic sigma weight residual 122.80 151.55 -28.75 0 2.50e+00 1.60e-01 1.32e+02 dihedral pdb=" C ASN P 361 " pdb=" N ASN P 361 " pdb=" CA ASN P 361 " pdb=" CB ASN P 361 " ideal model delta harmonic sigma weight residual -122.60 -151.30 28.70 0 2.50e+00 1.60e-01 1.32e+02 dihedral pdb=" C ASN C 361 " pdb=" N ASN C 361 " pdb=" CA ASN C 361 " pdb=" CB ASN C 361 " ideal model delta harmonic sigma weight residual -122.60 -150.21 27.61 0 2.50e+00 1.60e-01 1.22e+02 ... (remaining 40247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.245: 9503 0.245 - 0.489: 640 0.489 - 0.734: 36 0.734 - 0.978: 5 0.978 - 1.223: 4 Chirality restraints: 10188 Sorted by residual: chirality pdb=" CA ASN P 361 " pdb=" N ASN P 361 " pdb=" C ASN P 361 " pdb=" CB ASN P 361 " both_signs ideal model delta sigma weight residual False 2.51 1.29 1.22 2.00e-01 2.50e+01 3.74e+01 chirality pdb=" CA ASN C 361 " pdb=" N ASN C 361 " pdb=" C ASN C 361 " pdb=" CB ASN C 361 " both_signs ideal model delta sigma weight residual False 2.51 1.34 1.17 2.00e-01 2.50e+01 3.41e+01 chirality pdb=" CA ASP N 395 " pdb=" N ASP N 395 " pdb=" C ASP N 395 " pdb=" CB ASP N 395 " both_signs ideal model delta sigma weight residual False 2.51 1.45 1.06 2.00e-01 2.50e+01 2.81e+01 ... (remaining 10185 not shown) Planarity restraints: 11506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE N 549 " 0.180 2.00e-02 2.50e+03 2.68e-01 7.16e+02 pdb=" C PHE N 549 " -0.440 2.00e-02 2.50e+03 pdb=" O PHE N 549 " 0.245 2.00e-02 2.50e+03 pdb=" N GLY N 550 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BCYS R 388 " -0.114 2.00e-02 2.50e+03 1.77e-01 3.14e+02 pdb=" C BCYS R 388 " 0.301 2.00e-02 2.50e+03 pdb=" O BCYS R 388 " -0.142 2.00e-02 2.50e+03 pdb=" N SER R 389 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP N 563 " -0.098 2.00e-02 2.50e+03 1.68e-01 2.81e+02 pdb=" C ASP N 563 " 0.284 2.00e-02 2.50e+03 pdb=" O ASP N 563 " -0.141 2.00e-02 2.50e+03 pdb=" N MET N 564 " -0.045 2.00e-02 2.50e+03 ... (remaining 11503 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 39 2.28 - 2.94: 25942 2.94 - 3.59: 99983 3.59 - 4.25: 154476 4.25 - 4.90: 256794 Nonbonded interactions: 537234 Sorted by model distance: nonbonded pdb=" CE1 TYR C 115 " pdb=" NZ LYS C 161 " model vdw 1.629 3.420 nonbonded pdb=" ND2 ASN O 42 " pdb=" OE1 GLU O 43 " model vdw 1.722 3.120 nonbonded pdb=" O THR A1225 " pdb=" N SER A1229 " model vdw 1.957 3.120 nonbonded pdb=" O ILE C 285 " pdb=" OE1 GLU C 288 " model vdw 1.995 3.040 nonbonded pdb=" O GLY A1332 " pdb=" CD1 ILE A1358 " model vdw 2.007 3.460 ... (remaining 537229 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 26 through 134 or resid 147 through 160 or (resid 161 and \ (name N or name CA or name C or name O or name CB )) or resid 162 through 496 or \ (resid 497 and (name N or name CA or name C or name O or name CB or name CG1 or \ name CG2)) or resid 498 through 500 or resid 511 through 538)) selection = chain 'P' } ncs_group { reference = (chain 'F' and resid 5 through 767) selection = (chain 'H' and (resid 5 through 455 or (resid 456 through 459 and (name N or nam \ e CA or name C or name O or name CB )) or resid 460 through 767)) } ncs_group { reference = chain 'G' selection = chain 'W' } ncs_group { reference = (chain 'J' and (resid 2 through 93 or resid 127 through 213 or (resid 214 and (n \ ame N or name CA or name C or name O or name CB )) or resid 215 through 527)) selection = (chain 'K' and (resid 2 through 221 or (resid 222 and (name N or name CA or name \ C or name O or name CB )) or resid 223 through 346 or (resid 347 and (name N or \ name CA or name C or name O or name CB )) or resid 348 through 523 or (resid 52 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 525 through \ 527)) } ncs_group { reference = (chain 'X' and (resid 36 through 141 or (resid 142 through 143 and (name N or na \ me CA or name C or name O or name CB )) or resid 144 through 540)) selection = (chain 'Y' and resid 36 through 540) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.750 Check model and map are aligned: 0.360 Set scattering table: 0.450 Process input model: 117.470 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 1.640 66864 Z= 1.135 Angle : 1.883 36.334 90576 Z= 1.210 Chirality : 0.131 1.223 10188 Planarity : 0.009 0.268 11506 Dihedral : 19.172 89.974 24330 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 2.24 % Allowed : 6.26 % Favored : 91.50 % Rotamer: Outliers : 13.63 % Allowed : 14.73 % Favored : 71.64 % Cbeta Deviations : 2.27 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 0.47 % Twisted Proline : 0.99 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.08), residues: 8171 helix: -0.98 (0.06), residues: 5181 sheet: -0.96 (0.21), residues: 529 loop : -2.72 (0.11), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.005 TRP K 302 HIS 0.039 0.004 HIS J 271 PHE 0.099 0.006 PHE P 116 TYR 0.066 0.006 TYR I 585 ARG 0.027 0.002 ARG K 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2934 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 938 poor density : 1996 time to evaluate : 5.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.6214 (tt) REVERT: A 40 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7549 (ptp90) REVERT: A 114 TYR cc_start: 0.8938 (t80) cc_final: 0.8524 (t80) REVERT: A 132 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7890 (tp) REVERT: A 161 MET cc_start: 0.9320 (mmt) cc_final: 0.9058 (mmt) REVERT: A 165 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8423 (tm-30) REVERT: A 167 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8015 (mtpt) REVERT: A 220 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8986 (mp) REVERT: A 242 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.6487 (m-70) REVERT: A 257 MET cc_start: 0.7036 (tpt) cc_final: 0.6833 (mmm) REVERT: A 439 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7285 (tp40) REVERT: A 617 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8747 (mt) REVERT: A 792 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.6650 (mt0) REVERT: A 795 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.6938 (ttp80) REVERT: A 796 ASP cc_start: 0.5051 (OUTLIER) cc_final: 0.4829 (t0) REVERT: A 875 LEU cc_start: 0.7118 (mt) cc_final: 0.6819 (tp) REVERT: A 879 LEU cc_start: 0.7353 (mt) cc_final: 0.6941 (mt) REVERT: A 930 LEU cc_start: 0.7710 (tp) cc_final: 0.7326 (tp) REVERT: A 955 ILE cc_start: 0.8770 (mt) cc_final: 0.8543 (mp) REVERT: A 1047 VAL cc_start: 0.3930 (OUTLIER) cc_final: 0.3495 (p) REVERT: A 1110 ARG cc_start: 0.8023 (mtt180) cc_final: 0.7778 (mmm-85) REVERT: A 1118 VAL cc_start: 0.5946 (OUTLIER) cc_final: 0.5572 (m) REVERT: A 1161 ASN cc_start: 0.3798 (m110) cc_final: 0.3545 (m110) REVERT: A 1170 ASN cc_start: 0.5701 (OUTLIER) cc_final: 0.5166 (t0) REVERT: A 1177 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.7989 (tpt) REVERT: A 1191 LEU cc_start: 0.6284 (OUTLIER) cc_final: 0.5844 (tt) REVERT: A 1210 LEU cc_start: 0.8513 (mt) cc_final: 0.8174 (mt) REVERT: A 1216 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7612 (mmmt) REVERT: A 1241 THR cc_start: 0.7616 (OUTLIER) cc_final: 0.7393 (p) REVERT: A 1268 HIS cc_start: 0.6436 (t-90) cc_final: 0.5990 (t-170) REVERT: A 1279 ARG cc_start: 0.5723 (OUTLIER) cc_final: 0.4937 (ttm-80) REVERT: A 1304 MET cc_start: 0.8314 (mtt) cc_final: 0.8080 (mtt) REVERT: A 1316 MET cc_start: 0.7029 (mmt) cc_final: 0.6089 (ttp) REVERT: A 1319 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6249 (tp) REVERT: A 1326 TYR cc_start: 0.5714 (t80) cc_final: 0.5389 (t80) REVERT: A 1329 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8383 (ppp) REVERT: A 1359 ASN cc_start: 0.5557 (OUTLIER) cc_final: 0.5158 (p0) REVERT: A 1380 ASN cc_start: 0.7220 (m-40) cc_final: 0.6996 (t0) REVERT: A 1411 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7462 (ttp80) REVERT: A 1474 PHE cc_start: 0.8623 (m-80) cc_final: 0.8252 (m-80) REVERT: A 1482 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8392 (mp) REVERT: A 1527 MET cc_start: 0.8664 (ptp) cc_final: 0.8310 (ppp) REVERT: A 1539 CYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7407 (m) REVERT: A 1581 ILE cc_start: 0.8873 (mt) cc_final: 0.8521 (mm) REVERT: A 1609 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7805 (mt) REVERT: A 1610 TYR cc_start: 0.8541 (p90) cc_final: 0.8206 (p90) REVERT: A 1611 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8664 (p) REVERT: A 1619 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7796 (tp) REVERT: A 1652 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6652 (mpp) REVERT: A 1688 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8546 (tptt) REVERT: A 1731 ARG cc_start: 0.6122 (OUTLIER) cc_final: 0.5849 (ptp-170) REVERT: A 1749 SER cc_start: 0.9622 (OUTLIER) cc_final: 0.9193 (m) REVERT: A 1774 VAL cc_start: 0.8056 (t) cc_final: 0.7580 (t) REVERT: A 1780 THR cc_start: 0.6773 (t) cc_final: 0.6465 (t) REVERT: A 1781 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7423 (mp10) REVERT: A 1782 GLU cc_start: 0.6295 (mp0) cc_final: 0.4957 (tm-30) REVERT: A 1798 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8561 (mmm-85) REVERT: A 1809 SER cc_start: 0.9351 (t) cc_final: 0.8962 (p) REVERT: A 1810 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8518 (mp0) REVERT: A 1891 TYR cc_start: 0.8506 (t80) cc_final: 0.7812 (t80) REVERT: B 1 MET cc_start: 0.3705 (mmm) cc_final: 0.3319 (ptp) REVERT: B 84 GLU cc_start: -0.0516 (OUTLIER) cc_final: -0.1572 (mp0) REVERT: C 93 TYR cc_start: 0.9027 (m-80) cc_final: 0.8742 (m-80) REVERT: C 143 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7709 (mmtp) REVERT: C 172 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8852 (mp) REVERT: C 182 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7821 (mm) REVERT: C 215 ASP cc_start: 0.7823 (t70) cc_final: 0.7622 (m-30) REVERT: C 291 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7460 (mtpt) REVERT: C 298 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8789 (mt-10) REVERT: C 300 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7936 (mmp) REVERT: C 303 PHE cc_start: 0.7395 (t80) cc_final: 0.7193 (t80) REVERT: C 315 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8399 (mp0) REVERT: C 389 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.6849 (tpt90) REVERT: C 435 MET cc_start: 0.9226 (mmm) cc_final: 0.8861 (mmm) REVERT: C 436 LEU cc_start: 0.8823 (mt) cc_final: 0.8433 (mt) REVERT: C 449 LEU cc_start: 0.8649 (mt) cc_final: 0.8403 (mp) REVERT: C 455 CYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8793 (t) REVERT: C 465 VAL cc_start: 0.6627 (OUTLIER) cc_final: 0.5900 (m) REVERT: C 466 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.5667 (mm-30) REVERT: C 490 TYR cc_start: 0.7115 (m-80) cc_final: 0.6772 (m-80) REVERT: C 557 ARG cc_start: 0.2176 (OUTLIER) cc_final: 0.1434 (mtp85) REVERT: D 7 SER cc_start: 0.8458 (p) cc_final: 0.8204 (m) REVERT: D 14 GLU cc_start: 0.5986 (mm-30) cc_final: 0.5661 (tp30) REVERT: D 19 ASN cc_start: 0.6926 (t0) cc_final: 0.6533 (p0) REVERT: D 28 THR cc_start: 0.4958 (p) cc_final: 0.4157 (t) REVERT: D 32 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8342 (mm-40) REVERT: E 79 MET cc_start: 0.6921 (mmp) cc_final: 0.6688 (mmt) REVERT: E 92 ASP cc_start: 0.8597 (t0) cc_final: 0.8223 (t0) REVERT: F 49 TYR cc_start: 0.7337 (t80) cc_final: 0.6968 (t80) REVERT: F 104 ASP cc_start: 0.9141 (OUTLIER) cc_final: 0.8857 (p0) REVERT: F 127 LYS cc_start: 0.8617 (tttt) cc_final: 0.8134 (mtpt) REVERT: F 148 LEU cc_start: 0.7333 (mt) cc_final: 0.6983 (mp) REVERT: F 463 MET cc_start: 0.7894 (ttm) cc_final: 0.7391 (ttp) REVERT: F 468 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7923 (pt0) REVERT: F 469 MET cc_start: 0.8528 (ttm) cc_final: 0.8082 (mtt) REVERT: F 474 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7370 (tp) REVERT: F 477 CYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7538 (t) REVERT: F 519 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8461 (tm-30) REVERT: F 583 HIS cc_start: 0.6332 (m90) cc_final: 0.5964 (m-70) REVERT: F 616 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.6222 (mt-10) REVERT: F 625 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.7050 (tpt170) REVERT: F 646 TYR cc_start: 0.7281 (t80) cc_final: 0.6990 (t80) REVERT: F 705 CYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7824 (p) REVERT: G 4 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7741 (ttp-110) REVERT: H 61 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9057 (mt) REVERT: H 109 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8177 (mt-10) REVERT: H 125 TYR cc_start: 0.9202 (m-80) cc_final: 0.8931 (m-80) REVERT: H 491 LEU cc_start: 0.8956 (mp) cc_final: 0.8716 (mt) REVERT: H 502 LEU cc_start: 0.9153 (mt) cc_final: 0.8919 (mp) REVERT: H 549 ASP cc_start: 0.6895 (p0) cc_final: 0.6312 (t0) REVERT: H 578 SER cc_start: 0.6290 (t) cc_final: 0.5883 (p) REVERT: H 643 MET cc_start: 0.8512 (mtp) cc_final: 0.7814 (tpp) REVERT: H 702 ASN cc_start: 0.9268 (OUTLIER) cc_final: 0.7983 (t0) REVERT: H 745 LYS cc_start: 0.7497 (mttt) cc_final: 0.7045 (mtpp) REVERT: H 746 VAL cc_start: 0.8951 (t) cc_final: 0.8714 (t) REVERT: H 764 MET cc_start: 0.7617 (mmm) cc_final: 0.7414 (mmt) REVERT: I 52 PHE cc_start: 0.8630 (t80) cc_final: 0.8142 (t80) REVERT: I 80 LEU cc_start: 0.7598 (tp) cc_final: 0.7395 (tp) REVERT: I 93 CYS cc_start: 0.6125 (t) cc_final: 0.5304 (m) REVERT: I 158 GLU cc_start: 0.7333 (tp30) cc_final: 0.6938 (mm-30) REVERT: I 164 ILE cc_start: 0.8552 (mm) cc_final: 0.8283 (pt) REVERT: I 322 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6798 (tpt) REVERT: I 340 SER cc_start: 0.7473 (OUTLIER) cc_final: 0.7232 (p) REVERT: I 399 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8838 (tppt) REVERT: I 404 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8803 (tp) REVERT: I 440 MET cc_start: 0.5097 (mmm) cc_final: 0.4766 (tpp) REVERT: I 552 ILE cc_start: 0.6444 (mp) cc_final: 0.5446 (mm) REVERT: I 570 PHE cc_start: 0.7231 (m-10) cc_final: 0.6849 (m-10) REVERT: I 603 ARG cc_start: 0.8932 (mtp-110) cc_final: 0.8529 (mtp180) REVERT: I 647 GLU cc_start: 0.9367 (mt-10) cc_final: 0.9091 (tp30) REVERT: I 708 GLU cc_start: 0.9145 (pt0) cc_final: 0.8924 (tp30) REVERT: J 15 ASP cc_start: 0.9068 (OUTLIER) cc_final: 0.8818 (m-30) REVERT: J 43 LEU cc_start: 0.9437 (tp) cc_final: 0.9226 (mp) REVERT: J 48 TYR cc_start: 0.8656 (t80) cc_final: 0.7926 (t80) REVERT: J 58 HIS cc_start: 0.8357 (t70) cc_final: 0.8021 (t70) REVERT: J 88 GLN cc_start: 0.9330 (mt0) cc_final: 0.8813 (mp10) REVERT: J 133 CYS cc_start: 0.7704 (m) cc_final: 0.7363 (t) REVERT: J 192 LYS cc_start: 0.8467 (mttt) cc_final: 0.8245 (mmmt) REVERT: J 231 LEU cc_start: 0.7878 (mp) cc_final: 0.7535 (mm) REVERT: J 261 ASP cc_start: 0.8368 (t0) cc_final: 0.8020 (t0) REVERT: J 293 ASP cc_start: 0.8271 (m-30) cc_final: 0.7761 (p0) REVERT: J 315 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7540 (tptt) REVERT: J 363 LEU cc_start: 0.8482 (tt) cc_final: 0.8209 (tt) REVERT: J 374 ILE cc_start: 0.6488 (mt) cc_final: 0.6090 (mt) REVERT: J 395 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7820 (mm) REVERT: J 478 ASN cc_start: 0.8205 (t0) cc_final: 0.7667 (t0) REVERT: J 511 ASP cc_start: 0.8978 (t70) cc_final: 0.8687 (p0) REVERT: K 54 HIS cc_start: 0.8691 (m-70) cc_final: 0.8491 (m-70) REVERT: K 64 LYS cc_start: 0.9041 (mttt) cc_final: 0.8826 (mmmt) REVERT: K 87 GLN cc_start: 0.8954 (tt0) cc_final: 0.8632 (tm-30) REVERT: K 254 THR cc_start: 0.6365 (OUTLIER) cc_final: 0.6084 (t) REVERT: K 331 LYS cc_start: 0.7438 (mttm) cc_final: 0.6966 (tppt) REVERT: K 364 MET cc_start: 0.7680 (mtp) cc_final: 0.7312 (ptp) REVERT: K 431 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8846 (mtpt) REVERT: K 440 THR cc_start: 0.7426 (p) cc_final: 0.6865 (p) REVERT: K 454 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8238 (p) REVERT: K 458 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7862 (mt) REVERT: K 482 TYR cc_start: 0.6594 (m-80) cc_final: 0.5952 (m-80) REVERT: L 12 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7413 (t0) REVERT: L 28 GLN cc_start: 0.6493 (mt0) cc_final: 0.5628 (mm-40) REVERT: L 37 LYS cc_start: 0.7260 (mtpt) cc_final: 0.6997 (mtmt) REVERT: L 47 ASP cc_start: 0.6175 (m-30) cc_final: 0.5281 (m-30) REVERT: L 63 LEU cc_start: 0.8790 (mt) cc_final: 0.8497 (mt) REVERT: L 89 TYR cc_start: 0.7150 (m-80) cc_final: 0.6488 (m-80) REVERT: L 93 LYS cc_start: 0.7590 (tttt) cc_final: 0.7363 (mtpp) REVERT: L 119 TRP cc_start: 0.6654 (m100) cc_final: 0.4757 (m100) REVERT: L 133 ARG cc_start: 0.7562 (ttm170) cc_final: 0.6936 (mtp85) REVERT: L 136 MET cc_start: 0.9121 (ttt) cc_final: 0.8909 (ttm) REVERT: L 141 VAL cc_start: 0.7916 (OUTLIER) cc_final: 0.7173 (p) REVERT: L 157 LYS cc_start: 0.7078 (mttt) cc_final: 0.6648 (mttp) REVERT: L 162 VAL cc_start: 0.7945 (OUTLIER) cc_final: 0.7483 (m) REVERT: L 163 GLU cc_start: 0.7717 (tt0) cc_final: 0.7233 (pm20) REVERT: L 178 MET cc_start: 0.9017 (mtt) cc_final: 0.8784 (mtp) REVERT: L 180 TYR cc_start: 0.9334 (m-80) cc_final: 0.8786 (m-80) REVERT: M 10 ARG cc_start: 0.8660 (tmm-80) cc_final: 0.8234 (ttp-110) REVERT: M 26 TYR cc_start: 0.7119 (m-80) cc_final: 0.6637 (m-80) REVERT: M 51 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7299 (tppt) REVERT: M 52 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7680 (mp0) REVERT: N 156 MET cc_start: 0.8621 (mmm) cc_final: 0.8323 (ttm) REVERT: N 171 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8524 (mt-10) REVERT: N 172 MET cc_start: 0.8797 (mmm) cc_final: 0.8480 (mmm) REVERT: N 206 ARG cc_start: 0.7445 (mtm110) cc_final: 0.6869 (mmm160) REVERT: N 213 TYR cc_start: 0.8982 (t80) cc_final: 0.8581 (p90) REVERT: N 271 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8458 (pp20) REVERT: N 274 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8507 (tm-30) REVERT: N 278 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8058 (mtm-85) REVERT: N 280 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.4766 (pt0) REVERT: N 283 ARG cc_start: 0.6527 (ttt180) cc_final: 0.4317 (ptt-90) REVERT: N 299 TRP cc_start: 0.6137 (OUTLIER) cc_final: 0.5878 (t-100) REVERT: N 300 LEU cc_start: 0.8509 (mt) cc_final: 0.8162 (mt) REVERT: N 323 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8020 (ttt180) REVERT: N 341 ILE cc_start: 0.8316 (mt) cc_final: 0.7997 (mt) REVERT: N 346 SER cc_start: 0.8111 (t) cc_final: 0.7861 (p) REVERT: N 372 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7559 (pm20) REVERT: N 373 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8696 (pt0) REVERT: N 387 LEU cc_start: 0.8232 (mt) cc_final: 0.8012 (mp) REVERT: N 421 CYS cc_start: 0.6124 (m) cc_final: 0.5431 (p) REVERT: N 422 GLU cc_start: 0.8011 (tt0) cc_final: 0.7748 (mt-10) REVERT: N 425 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7012 (ttm110) REVERT: N 514 LEU cc_start: 0.6533 (mm) cc_final: 0.6273 (tp) REVERT: N 515 PHE cc_start: 0.8420 (m-80) cc_final: 0.7333 (m-10) REVERT: N 529 HIS cc_start: 0.5988 (t70) cc_final: 0.5488 (t70) REVERT: N 537 ARG cc_start: 0.6917 (ptp-170) cc_final: 0.6262 (mmp80) REVERT: N 540 ARG cc_start: 0.8230 (mmm-85) cc_final: 0.8008 (mmt-90) REVERT: N 546 LYS cc_start: 0.7847 (tttt) cc_final: 0.7500 (tmtt) REVERT: N 560 MET cc_start: 0.5818 (OUTLIER) cc_final: 0.5407 (mmm) REVERT: N 561 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6694 (mm) REVERT: N 564 MET cc_start: 0.5246 (mmp) cc_final: 0.4910 (mmp) REVERT: N 594 VAL cc_start: 0.6508 (OUTLIER) cc_final: 0.6205 (p) REVERT: N 609 LEU cc_start: 0.0841 (OUTLIER) cc_final: -0.0773 (mt) REVERT: N 660 THR cc_start: 0.5068 (m) cc_final: 0.4837 (p) REVERT: N 670 PHE cc_start: 0.0353 (OUTLIER) cc_final: -0.0266 (m-80) REVERT: N 699 TRP cc_start: 0.2723 (OUTLIER) cc_final: 0.2210 (m100) REVERT: N 705 LEU cc_start: 0.1047 (OUTLIER) cc_final: 0.0161 (pp) REVERT: N 728 VAL cc_start: -0.3169 (OUTLIER) cc_final: -0.4371 (t) REVERT: O 38 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8700 (tt) REVERT: O 104 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8791 (tp30) REVERT: O 110 GLN cc_start: 0.8697 (tt0) cc_final: 0.8496 (tp-100) REVERT: O 115 LEU cc_start: 0.7430 (tp) cc_final: 0.7169 (tp) REVERT: O 132 VAL cc_start: 0.7791 (OUTLIER) cc_final: 0.7476 (p) REVERT: O 237 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: O 283 LEU cc_start: 0.1216 (OUTLIER) cc_final: 0.0682 (tp) REVERT: O 298 ARG cc_start: 0.2601 (mtp85) cc_final: 0.1874 (mmt90) REVERT: O 345 SER cc_start: 0.7933 (OUTLIER) cc_final: 0.7697 (m) REVERT: O 371 PHE cc_start: 0.7275 (m-80) cc_final: 0.7018 (m-80) REVERT: O 396 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.8059 (p0) REVERT: O 397 LYS cc_start: 0.7283 (mttt) cc_final: 0.7006 (mmmt) REVERT: O 465 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8540 (t) REVERT: O 501 SER cc_start: 0.7665 (OUTLIER) cc_final: 0.7046 (p) REVERT: O 508 MET cc_start: 0.9041 (mtt) cc_final: 0.8698 (mtp) REVERT: O 550 VAL cc_start: 0.9149 (p) cc_final: 0.8854 (t) REVERT: O 562 LYS cc_start: 0.8699 (mttt) cc_final: 0.8382 (mtmm) REVERT: O 617 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8233 (tp-100) REVERT: O 664 MET cc_start: 0.8370 (mmm) cc_final: 0.7986 (mmt) REVERT: O 680 GLN cc_start: 0.5451 (OUTLIER) cc_final: 0.4986 (pm20) REVERT: O 685 GLU cc_start: 0.8180 (tt0) cc_final: 0.7917 (tm-30) REVERT: O 753 ASN cc_start: 0.7527 (m-40) cc_final: 0.7069 (p0) REVERT: P 71 GLN cc_start: 0.8294 (pt0) cc_final: 0.7812 (pm20) REVERT: P 128 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8495 (ttpt) REVERT: P 154 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8938 (mp) REVERT: P 165 ARG cc_start: 0.9059 (mtp-110) cc_final: 0.8508 (mmm160) REVERT: P 167 LEU cc_start: 0.7327 (tp) cc_final: 0.6806 (tp) REVERT: P 211 ASN cc_start: 0.8419 (m-40) cc_final: 0.8090 (m-40) REVERT: P 221 PHE cc_start: 0.9180 (m-80) cc_final: 0.8937 (m-10) REVERT: P 243 LEU cc_start: 0.8338 (mt) cc_final: 0.8111 (tp) REVERT: P 321 HIS cc_start: 0.8398 (OUTLIER) cc_final: 0.7921 (p-80) REVERT: P 335 CYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9192 (p) REVERT: P 354 PHE cc_start: 0.8620 (m-80) cc_final: 0.7867 (m-80) REVERT: P 374 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8942 (mm-30) REVERT: P 431 ASN cc_start: 0.8442 (m-40) cc_final: 0.8127 (p0) REVERT: P 468 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6739 (mmm) REVERT: P 480 LEU cc_start: 0.8491 (mp) cc_final: 0.8231 (mt) REVERT: R 110 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8173 (tptt) REVERT: R 132 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7691 (ttm-80) REVERT: R 174 ARG cc_start: 0.7284 (mtm-85) cc_final: 0.6694 (mtp85) REVERT: R 198 LEU cc_start: 0.7168 (mt) cc_final: 0.6888 (tp) REVERT: R 200 VAL cc_start: 0.5594 (t) cc_final: 0.4937 (p) REVERT: R 222 MET cc_start: 0.2382 (mtp) cc_final: 0.1278 (ttt) REVERT: R 317 TRP cc_start: 0.3081 (m100) cc_final: 0.2701 (m100) REVERT: R 355 GLN cc_start: 0.6983 (mm110) cc_final: 0.6359 (pt0) REVERT: S 831 LEU cc_start: 0.3895 (OUTLIER) cc_final: 0.2348 (mt) REVERT: X 40 HIS cc_start: 0.8417 (m90) cc_final: 0.8137 (m170) REVERT: X 62 THR cc_start: 0.7650 (p) cc_final: 0.7052 (p) REVERT: X 75 GLN cc_start: 0.9342 (mt0) cc_final: 0.9065 (mt0) REVERT: X 79 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9265 (mt) REVERT: X 92 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8542 (mp0) REVERT: X 102 MET cc_start: 0.9219 (mtm) cc_final: 0.8991 (tpt) REVERT: X 255 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8724 (pt) REVERT: X 269 ASP cc_start: 0.7605 (m-30) cc_final: 0.7370 (p0) REVERT: X 306 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7485 (tptm) REVERT: X 309 ASP cc_start: 0.6905 (t0) cc_final: 0.6608 (p0) REVERT: X 340 GLU cc_start: 0.7970 (mp0) cc_final: 0.7472 (mm-30) REVERT: X 360 TYR cc_start: 0.6855 (m-80) cc_final: 0.6357 (m-80) REVERT: X 367 GLN cc_start: 0.9011 (tt0) cc_final: 0.8788 (mt0) REVERT: X 376 LEU cc_start: 0.8180 (tp) cc_final: 0.7798 (tp) REVERT: X 388 ARG cc_start: 0.8771 (mmm160) cc_final: 0.8542 (mmm160) REVERT: X 450 VAL cc_start: 0.7195 (OUTLIER) cc_final: 0.6958 (p) REVERT: X 475 TYR cc_start: 0.2910 (t80) cc_final: 0.2703 (t80) REVERT: X 484 GLU cc_start: 0.8308 (tt0) cc_final: 0.8008 (tm-30) REVERT: X 529 MET cc_start: 0.5404 (mmt) cc_final: 0.5187 (tpt) REVERT: Y 69 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8523 (tp30) REVERT: Y 77 TYR cc_start: 0.8049 (t80) cc_final: 0.7793 (t80) REVERT: Y 99 LYS cc_start: 0.8669 (mmtt) cc_final: 0.8337 (tppt) REVERT: Y 145 CYS cc_start: 0.8506 (m) cc_final: 0.7161 (m) REVERT: Y 173 MET cc_start: 0.8198 (ttp) cc_final: 0.7776 (tpp) REVERT: Y 201 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7526 (mp) REVERT: Y 230 VAL cc_start: 0.5677 (OUTLIER) cc_final: 0.5030 (t) REVERT: Y 247 HIS cc_start: 0.6963 (m-70) cc_final: 0.6669 (m90) REVERT: Y 267 LEU cc_start: 0.7381 (tp) cc_final: 0.6267 (tp) REVERT: Y 269 ASP cc_start: 0.8437 (m-30) cc_final: 0.8140 (p0) REVERT: Y 288 LYS cc_start: 0.9267 (mttt) cc_final: 0.9067 (ptmt) REVERT: Y 350 PHE cc_start: 0.6072 (m-80) cc_final: 0.5858 (m-80) REVERT: Y 371 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8617 (m-40) REVERT: Y 415 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8441 (mm-30) REVERT: Y 428 VAL cc_start: 0.9283 (t) cc_final: 0.9076 (p) REVERT: Y 445 THR cc_start: 0.8888 (p) cc_final: 0.8449 (t) REVERT: Y 446 LEU cc_start: 0.9027 (tt) cc_final: 0.8390 (mm) REVERT: Y 457 THR cc_start: 0.7680 (OUTLIER) cc_final: 0.7270 (p) REVERT: Y 477 LYS cc_start: 0.8802 (mttt) cc_final: 0.8585 (ttpp) REVERT: Y 512 HIS cc_start: 0.5283 (m-70) cc_final: 0.4851 (m-70) REVERT: Y 529 MET cc_start: 0.7857 (mmt) cc_final: 0.7484 (mmt) REVERT: Y 549 MET cc_start: 0.8054 (mmt) cc_final: 0.7754 (mmp) outliers start: 938 outliers final: 218 residues processed: 2629 average time/residue: 0.6327 time to fit residues: 2757.7780 Evaluate side-chains 1478 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 332 poor density : 1146 time to evaluate : 6.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 411 HIS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 795 ARG Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1170 ASN Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1216 LYS Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1241 THR Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1279 ARG Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1329 MET Chi-restraints excluded: chain A residue 1359 ASN Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1411 ARG Chi-restraints excluded: chain A residue 1426 VAL Chi-restraints excluded: chain A residue 1433 ILE Chi-restraints excluded: chain A residue 1482 LEU Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1539 CYS Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1573 SER Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1611 VAL Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1638 TYR Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1666 ILE Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1688 LYS Chi-restraints excluded: chain A residue 1731 ARG Chi-restraints excluded: chain A residue 1749 SER Chi-restraints excluded: chain A residue 1755 CYS Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1781 GLN Chi-restraints excluded: chain A residue 1798 ARG Chi-restraints excluded: chain A residue 1810 GLU Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1893 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 203 TRP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 429 ARG Chi-restraints excluded: chain C residue 455 CYS Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 518 GLN Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 477 CYS Chi-restraints excluded: chain F residue 520 ARG Chi-restraints excluded: chain F residue 527 ARG Chi-restraints excluded: chain F residue 530 ASN Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 576 CYS Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 625 ARG Chi-restraints excluded: chain F residue 705 CYS Chi-restraints excluded: chain G residue 4 ARG Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 521 ILE Chi-restraints excluded: chain H residue 530 ASN Chi-restraints excluded: chain H residue 702 ASN Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 322 MET Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 340 SER Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 399 LYS Chi-restraints excluded: chain I residue 401 ASN Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 505 SER Chi-restraints excluded: chain I residue 652 VAL Chi-restraints excluded: chain I residue 736 SER Chi-restraints excluded: chain J residue 15 ASP Chi-restraints excluded: chain J residue 163 CYS Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 267 CYS Chi-restraints excluded: chain J residue 315 LYS Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 506 LEU Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 63 ARG Chi-restraints excluded: chain K residue 78 ARG Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 267 CYS Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 376 LEU Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 458 LEU Chi-restraints excluded: chain K residue 510 ARG Chi-restraints excluded: chain K residue 515 SER Chi-restraints excluded: chain K residue 523 ILE Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain M residue 19 TRP Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 202 GLU Chi-restraints excluded: chain N residue 269 THR Chi-restraints excluded: chain N residue 271 GLU Chi-restraints excluded: chain N residue 274 GLU Chi-restraints excluded: chain N residue 278 ARG Chi-restraints excluded: chain N residue 280 GLU Chi-restraints excluded: chain N residue 299 TRP Chi-restraints excluded: chain N residue 323 ARG Chi-restraints excluded: chain N residue 364 CYS Chi-restraints excluded: chain N residue 373 GLN Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 388 HIS Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain N residue 425 ARG Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 560 MET Chi-restraints excluded: chain N residue 561 LEU Chi-restraints excluded: chain N residue 571 ASN Chi-restraints excluded: chain N residue 594 VAL Chi-restraints excluded: chain N residue 609 LEU Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain N residue 728 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 98 LYS Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 104 GLU Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 223 LEU Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 237 GLN Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 264 VAL Chi-restraints excluded: chain O residue 265 GLN Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 280 ARG Chi-restraints excluded: chain O residue 283 LEU Chi-restraints excluded: chain O residue 345 SER Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 358 TYR Chi-restraints excluded: chain O residue 364 SER Chi-restraints excluded: chain O residue 383 SER Chi-restraints excluded: chain O residue 396 ASN Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 429 TRP Chi-restraints excluded: chain O residue 465 SER Chi-restraints excluded: chain O residue 501 SER Chi-restraints excluded: chain O residue 510 CYS Chi-restraints excluded: chain O residue 531 LEU Chi-restraints excluded: chain O residue 533 THR Chi-restraints excluded: chain O residue 563 LEU Chi-restraints excluded: chain O residue 577 THR Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 616 LEU Chi-restraints excluded: chain O residue 617 GLN Chi-restraints excluded: chain O residue 619 LEU Chi-restraints excluded: chain O residue 623 THR Chi-restraints excluded: chain O residue 625 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 657 ILE Chi-restraints excluded: chain O residue 680 GLN Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 751 LEU Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 128 LYS Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 321 HIS Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 361 ASN Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 455 CYS Chi-restraints excluded: chain P residue 468 MET Chi-restraints excluded: chain R residue 110 LYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 499 ARG Chi-restraints excluded: chain S residue 831 LEU Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 255 ILE Chi-restraints excluded: chain X residue 306 LYS Chi-restraints excluded: chain X residue 310 VAL Chi-restraints excluded: chain X residue 401 ARG Chi-restraints excluded: chain X residue 450 VAL Chi-restraints excluded: chain X residue 487 SER Chi-restraints excluded: chain Y residue 201 LEU Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 303 TYR Chi-restraints excluded: chain Y residue 371 ASN Chi-restraints excluded: chain Y residue 407 LEU Chi-restraints excluded: chain Y residue 414 ILE Chi-restraints excluded: chain Y residue 423 ILE Chi-restraints excluded: chain Y residue 456 VAL Chi-restraints excluded: chain Y residue 457 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 695 optimal weight: 1.9990 chunk 624 optimal weight: 2.9990 chunk 346 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 421 optimal weight: 1.9990 chunk 333 optimal weight: 8.9990 chunk 645 optimal weight: 0.9990 chunk 249 optimal weight: 4.9990 chunk 392 optimal weight: 0.8980 chunk 480 optimal weight: 0.9990 chunk 748 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 GLN A 266 HIS ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 GLN A 643 ASN A 658 ASN A 666 ASN ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 ASN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 ASN A1165 HIS ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1351 GLN A1489 HIS A1558 HIS ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1595 HIS ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1813 GLN B 50 GLN C 236 HIS C 249 GLN C 373 HIS C 386 GLN C 518 GLN D 37 HIS D 49 ASN F 583 HIS F 599 ASN F 626 ASN ** F 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 754 HIS H 14 GLN H 517 GLN ** H 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 599 ASN H 648 GLN ** H 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 323 ASN I 351 HIS I 471 ASN I 535 GLN J 45 GLN J 58 HIS J 207 ASN J 228 GLN ** J 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 316 ASN J 342 HIS J 350 HIS J 362 GLN ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 GLN K 17 GLN K 20 GLN K 52 GLN K 198 GLN ** K 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 282 ASN ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 HIS L 152 HIS N 86 ASN N 266 HIS ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS ** N 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 571 ASN N 663 GLN N 702 GLN N 726 ASN O 62 GLN O 69 GLN O 138 HIS ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 242 ASN O 247 ASN ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 370 HIS ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN ** O 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 492 HIS O 521 ASN O 617 GLN O 717 GLN O 722 HIS O 754 HIS ** P 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 287 ASN P 305 ASN P 321 HIS P 347 HIS ** P 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN R 99 ASN R 369 ASN R 410 HIS X 50 HIS X 151 GLN X 298 GLN ** Y 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 298 GLN Y 371 ASN Y 395 HIS Y 471 GLN Y 490 GLN Y 531 GLN Total number of N/Q/H flips: 87 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 66864 Z= 0.274 Angle : 0.905 19.071 90576 Z= 0.464 Chirality : 0.048 0.273 10188 Planarity : 0.006 0.129 11506 Dihedral : 10.729 88.203 9725 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.92 % Allowed : 4.72 % Favored : 94.36 % Rotamer: Outliers : 7.71 % Allowed : 21.02 % Favored : 71.27 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.44 % Twisted Proline : 0.66 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.09), residues: 8183 helix: 0.51 (0.07), residues: 5344 sheet: -0.70 (0.21), residues: 529 loop : -2.27 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1386 HIS 0.017 0.002 HIS N 388 PHE 0.034 0.002 PHE J 247 TYR 0.045 0.002 TYR P 490 ARG 0.013 0.001 ARG N 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1775 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 530 poor density : 1245 time to evaluate : 5.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 HIS cc_start: 0.7941 (m-70) cc_final: 0.7662 (m-70) REVERT: A 114 TYR cc_start: 0.8830 (t80) cc_final: 0.8513 (t80) REVERT: A 159 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8259 (mt) REVERT: A 165 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8371 (tm-30) REVERT: A 167 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.7932 (mtpt) REVERT: A 170 ILE cc_start: 0.8763 (mt) cc_final: 0.8147 (tp) REVERT: A 185 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7392 (m-80) REVERT: A 242 HIS cc_start: 0.7227 (OUTLIER) cc_final: 0.6683 (m170) REVERT: A 439 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7175 (tp40) REVERT: A 617 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8518 (mt) REVERT: A 758 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.6799 (t-170) REVERT: A 779 MET cc_start: 0.9383 (mmt) cc_final: 0.8876 (tpp) REVERT: A 792 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6500 (pt0) REVERT: A 1036 ASP cc_start: 0.8280 (t0) cc_final: 0.7988 (t0) REVERT: A 1067 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7934 (tt0) REVERT: A 1078 MET cc_start: 0.6130 (mpp) cc_final: 0.5771 (mpp) REVERT: A 1118 VAL cc_start: 0.5027 (OUTLIER) cc_final: 0.4603 (p) REVERT: A 1187 LYS cc_start: 0.7107 (mtmm) cc_final: 0.6765 (tttp) REVERT: A 1216 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7412 (mmmt) REVERT: A 1220 MET cc_start: 0.5436 (mtm) cc_final: 0.5068 (mtt) REVERT: A 1229 SER cc_start: 0.6101 (m) cc_final: 0.5864 (m) REVERT: A 1230 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8222 (mm) REVERT: A 1268 HIS cc_start: 0.6483 (t-90) cc_final: 0.6070 (t-170) REVERT: A 1326 TYR cc_start: 0.5334 (t80) cc_final: 0.5009 (t80) REVERT: A 1329 MET cc_start: 0.8812 (ttm) cc_final: 0.8444 (tmm) REVERT: A 1482 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8389 (mp) REVERT: A 1527 MET cc_start: 0.8673 (ptp) cc_final: 0.8412 (ppp) REVERT: A 1572 TYR cc_start: 0.8324 (m-80) cc_final: 0.8097 (m-80) REVERT: A 1639 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6851 (pttm) REVERT: A 1652 MET cc_start: 0.6519 (OUTLIER) cc_final: 0.5782 (mpp) REVERT: A 1656 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7358 (mp) REVERT: A 1688 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8427 (tptt) REVERT: A 1733 PHE cc_start: 0.0816 (t80) cc_final: -0.1146 (t80) REVERT: A 1741 PHE cc_start: 0.8277 (m-80) cc_final: 0.8042 (m-80) REVERT: A 1774 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7925 (t) REVERT: A 1777 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8541 (tm-30) REVERT: A 1780 THR cc_start: 0.7184 (t) cc_final: 0.6982 (p) REVERT: A 1782 GLU cc_start: 0.6399 (mp0) cc_final: 0.5521 (tm-30) REVERT: A 1804 GLU cc_start: 0.8464 (pt0) cc_final: 0.7875 (tp30) REVERT: A 1807 GLU cc_start: 0.8687 (tt0) cc_final: 0.8138 (tp30) REVERT: A 1810 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8905 (pm20) REVERT: A 1891 TYR cc_start: 0.8607 (t80) cc_final: 0.8115 (t80) REVERT: C 119 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8925 (mmt) REVERT: C 182 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7299 (mt) REVERT: C 233 PHE cc_start: 0.9016 (t80) cc_final: 0.8781 (t80) REVERT: C 239 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8287 (t) REVERT: C 246 GLU cc_start: 0.8597 (tp30) cc_final: 0.7817 (pt0) REVERT: C 298 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8769 (mt-10) REVERT: C 315 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8699 (mp0) REVERT: C 333 THR cc_start: 0.8442 (t) cc_final: 0.8187 (t) REVERT: C 389 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6531 (tpt90) REVERT: C 398 ASP cc_start: 0.8334 (t0) cc_final: 0.8112 (t0) REVERT: C 557 ARG cc_start: 0.2374 (OUTLIER) cc_final: 0.1650 (ttt180) REVERT: D 19 ASN cc_start: 0.6774 (t0) cc_final: 0.6408 (p0) REVERT: D 26 GLU cc_start: 0.7055 (pt0) cc_final: 0.6725 (pt0) REVERT: D 28 THR cc_start: 0.5009 (p) cc_final: 0.4575 (t) REVERT: D 32 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8386 (mm-40) REVERT: D 47 LYS cc_start: 0.8444 (tmtt) cc_final: 0.7870 (tptt) REVERT: E 61 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.6553 (t80) REVERT: E 74 GLN cc_start: 0.7665 (mp10) cc_final: 0.7386 (mp10) REVERT: E 93 GLU cc_start: 0.9205 (tt0) cc_final: 0.8979 (mt-10) REVERT: F 48 TYR cc_start: 0.8476 (m-80) cc_final: 0.8081 (m-80) REVERT: F 49 TYR cc_start: 0.7631 (t80) cc_final: 0.7131 (t80) REVERT: F 469 MET cc_start: 0.8689 (ttm) cc_final: 0.8316 (mtt) REVERT: F 477 CYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7655 (t) REVERT: F 497 ASN cc_start: 0.8004 (m-40) cc_final: 0.7778 (p0) REVERT: F 519 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8550 (tm-30) REVERT: F 591 GLN cc_start: 0.9277 (mt0) cc_final: 0.9066 (mt0) REVERT: F 646 TYR cc_start: 0.7429 (t80) cc_final: 0.6968 (t80) REVERT: G 4 ARG cc_start: 0.8472 (mtt-85) cc_final: 0.8116 (ttm110) REVERT: G 10 GLU cc_start: 0.8075 (pm20) cc_final: 0.7821 (pm20) REVERT: G 15 ASP cc_start: 0.5713 (m-30) cc_final: 0.5390 (m-30) REVERT: G 16 ILE cc_start: 0.8234 (mm) cc_final: 0.7827 (mm) REVERT: H 61 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9117 (mt) REVERT: H 73 TYR cc_start: 0.8108 (t80) cc_final: 0.7843 (t80) REVERT: H 84 LYS cc_start: 0.8049 (mttt) cc_final: 0.7651 (ptpp) REVERT: H 109 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8054 (mt-10) REVERT: H 153 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7388 (mt-10) REVERT: H 502 LEU cc_start: 0.8907 (mt) cc_final: 0.8667 (mt) REVERT: H 525 VAL cc_start: 0.7390 (t) cc_final: 0.7148 (t) REVERT: H 549 ASP cc_start: 0.6475 (p0) cc_final: 0.6162 (t0) REVERT: H 578 SER cc_start: 0.5888 (t) cc_final: 0.5519 (p) REVERT: H 591 GLN cc_start: 0.8200 (mt0) cc_final: 0.7819 (mp10) REVERT: H 602 TYR cc_start: 0.7796 (t80) cc_final: 0.7591 (t80) REVERT: H 634 HIS cc_start: 0.8920 (t-90) cc_final: 0.8640 (t70) REVERT: H 643 MET cc_start: 0.8511 (mtp) cc_final: 0.8219 (mmm) REVERT: H 655 GLU cc_start: 0.8448 (tp30) cc_final: 0.7898 (tp30) REVERT: H 764 MET cc_start: 0.7702 (mmm) cc_final: 0.7477 (mmt) REVERT: I 93 CYS cc_start: 0.6861 (t) cc_final: 0.6524 (m) REVERT: I 99 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7918 (tm-30) REVERT: I 158 GLU cc_start: 0.7372 (tp30) cc_final: 0.7014 (mm-30) REVERT: I 308 LEU cc_start: 0.8041 (tt) cc_final: 0.7812 (tp) REVERT: I 371 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8623 (m) REVERT: I 404 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8844 (tp) REVERT: I 425 MET cc_start: 0.7947 (mmp) cc_final: 0.7710 (mmm) REVERT: I 471 ASN cc_start: 0.6857 (OUTLIER) cc_final: 0.6217 (p0) REVERT: I 570 PHE cc_start: 0.7507 (m-10) cc_final: 0.6957 (m-10) REVERT: I 603 ARG cc_start: 0.8868 (mtp-110) cc_final: 0.8578 (ttt180) REVERT: I 749 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8041 (p0) REVERT: J 20 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8808 (mp10) REVERT: J 25 TRP cc_start: 0.8156 (m100) cc_final: 0.7918 (m100) REVERT: J 48 TYR cc_start: 0.8399 (t80) cc_final: 0.8070 (t80) REVERT: J 128 ILE cc_start: 0.8655 (mt) cc_final: 0.8447 (tp) REVERT: J 133 CYS cc_start: 0.8075 (m) cc_final: 0.7433 (t) REVERT: J 192 LYS cc_start: 0.8459 (mttt) cc_final: 0.8169 (mmmt) REVERT: J 208 LYS cc_start: 0.5390 (pttt) cc_final: 0.5045 (pttt) REVERT: J 227 LEU cc_start: 0.4734 (tp) cc_final: 0.2725 (tp) REVERT: J 261 ASP cc_start: 0.7978 (t0) cc_final: 0.7759 (t0) REVERT: J 274 THR cc_start: 0.8907 (t) cc_final: 0.8662 (m) REVERT: J 315 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7893 (tppt) REVERT: J 322 TYR cc_start: 0.8590 (m-80) cc_final: 0.8302 (m-80) REVERT: J 349 GLU cc_start: 0.8498 (mp0) cc_final: 0.8134 (tp30) REVERT: J 395 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7826 (mm) REVERT: J 405 MET cc_start: 0.7272 (mpp) cc_final: 0.7066 (mtt) REVERT: J 475 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8518 (mp) REVERT: J 478 ASN cc_start: 0.8061 (t0) cc_final: 0.7592 (m110) REVERT: J 511 ASP cc_start: 0.8894 (t70) cc_final: 0.8625 (p0) REVERT: K 64 LYS cc_start: 0.8979 (mttt) cc_final: 0.8764 (mmmt) REVERT: K 331 LYS cc_start: 0.7123 (mttm) cc_final: 0.6779 (tppt) REVERT: K 388 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8937 (pt0) REVERT: K 414 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7947 (tp-100) REVERT: K 431 LYS cc_start: 0.9143 (mmtt) cc_final: 0.8871 (mtpt) REVERT: K 512 ASP cc_start: 0.6585 (t70) cc_final: 0.6281 (t0) REVERT: K 525 MET cc_start: 0.8369 (tpp) cc_final: 0.7974 (mtp) REVERT: L 12 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7682 (t0) REVERT: L 37 LYS cc_start: 0.7628 (mtpt) cc_final: 0.7332 (mtmt) REVERT: L 93 LYS cc_start: 0.7560 (tttt) cc_final: 0.7322 (mtpp) REVERT: L 119 TRP cc_start: 0.6865 (m100) cc_final: 0.5117 (m100) REVERT: L 157 LYS cc_start: 0.7049 (mttt) cc_final: 0.6836 (mttt) REVERT: L 162 VAL cc_start: 0.7731 (p) cc_final: 0.7186 (m) REVERT: L 163 GLU cc_start: 0.7784 (tt0) cc_final: 0.7220 (pm20) REVERT: L 180 TYR cc_start: 0.9241 (m-80) cc_final: 0.8916 (m-80) REVERT: M 10 ARG cc_start: 0.8366 (tmm-80) cc_final: 0.8122 (ttp80) REVERT: M 51 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.6797 (tppt) REVERT: N 172 MET cc_start: 0.8833 (mmm) cc_final: 0.8541 (mmm) REVERT: N 185 MET cc_start: 0.8313 (mmp) cc_final: 0.7984 (mmm) REVERT: N 213 TYR cc_start: 0.9015 (t80) cc_final: 0.8558 (p90) REVERT: N 274 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8727 (tm-30) REVERT: N 299 TRP cc_start: 0.6701 (OUTLIER) cc_final: 0.6126 (t-100) REVERT: N 373 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8899 (mp10) REVERT: N 515 PHE cc_start: 0.8415 (m-80) cc_final: 0.7287 (m-10) REVERT: N 537 ARG cc_start: 0.6479 (ptp-170) cc_final: 0.6233 (tpt90) REVERT: N 543 GLU cc_start: 0.8486 (pt0) cc_final: 0.8261 (mm-30) REVERT: N 546 LYS cc_start: 0.8085 (tttt) cc_final: 0.7763 (tmtt) REVERT: N 594 VAL cc_start: 0.6334 (OUTLIER) cc_final: 0.5819 (p) REVERT: N 639 HIS cc_start: 0.3733 (t70) cc_final: 0.3501 (t-90) REVERT: N 670 PHE cc_start: 0.0567 (OUTLIER) cc_final: 0.0111 (m-80) REVERT: N 699 TRP cc_start: 0.3216 (OUTLIER) cc_final: 0.2575 (m100) REVERT: N 705 LEU cc_start: 0.1113 (OUTLIER) cc_final: 0.0122 (pp) REVERT: O 110 GLN cc_start: 0.8659 (tt0) cc_final: 0.8286 (tp-100) REVERT: O 150 GLN cc_start: 0.8588 (mt0) cc_final: 0.8217 (mm110) REVERT: O 237 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: O 371 PHE cc_start: 0.7036 (m-80) cc_final: 0.6835 (m-80) REVERT: O 436 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8356 (t) REVERT: O 539 ASN cc_start: 0.8615 (t0) cc_final: 0.8360 (t0) REVERT: O 654 ASP cc_start: 0.7388 (p0) cc_final: 0.6969 (p0) REVERT: O 657 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8149 (tp) REVERT: O 664 MET cc_start: 0.8270 (mmm) cc_final: 0.7991 (mmt) REVERT: O 670 CYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9031 (t) REVERT: O 731 ASN cc_start: 0.2800 (OUTLIER) cc_final: 0.2167 (m110) REVERT: P 93 TYR cc_start: 0.8744 (m-80) cc_final: 0.8502 (m-80) REVERT: P 128 LYS cc_start: 0.8923 (mmtp) cc_final: 0.8614 (ttpt) REVERT: P 165 ARG cc_start: 0.8798 (mtp-110) cc_final: 0.8267 (mmm160) REVERT: P 210 CYS cc_start: 0.8038 (m) cc_final: 0.7826 (m) REVERT: P 211 ASN cc_start: 0.8059 (m-40) cc_final: 0.7354 (m110) REVERT: P 240 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7297 (mt-10) REVERT: P 354 PHE cc_start: 0.8539 (m-80) cc_final: 0.7917 (m-80) REVERT: P 431 ASN cc_start: 0.8593 (m-40) cc_final: 0.8282 (p0) REVERT: P 435 MET cc_start: 0.7458 (mmp) cc_final: 0.6299 (ttm) REVERT: P 445 LYS cc_start: 0.8700 (mtpt) cc_final: 0.8426 (mmmm) REVERT: R 132 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7302 (mtm-85) REVERT: R 174 ARG cc_start: 0.7309 (mtm-85) cc_final: 0.6956 (mtp85) REVERT: R 222 MET cc_start: 0.1836 (mtp) cc_final: 0.1356 (ttt) REVERT: R 351 PHE cc_start: 0.2544 (m-80) cc_final: 0.2238 (m-80) REVERT: R 355 GLN cc_start: 0.7167 (mm110) cc_final: 0.6543 (pt0) REVERT: W 15 ASP cc_start: 0.8272 (m-30) cc_final: 0.8039 (m-30) REVERT: W 23 ARG cc_start: 0.5087 (mtm-85) cc_final: 0.4553 (mtm-85) REVERT: X 102 MET cc_start: 0.9240 (mtm) cc_final: 0.8871 (tpt) REVERT: X 255 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8764 (pt) REVERT: X 269 ASP cc_start: 0.7741 (m-30) cc_final: 0.7532 (p0) REVERT: X 306 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7514 (tptp) REVERT: X 340 GLU cc_start: 0.7893 (mp0) cc_final: 0.7471 (mm-30) REVERT: X 342 TRP cc_start: 0.8174 (m100) cc_final: 0.7968 (m-90) REVERT: X 347 CYS cc_start: 0.9215 (m) cc_final: 0.8998 (p) REVERT: X 367 GLN cc_start: 0.9377 (tt0) cc_final: 0.8994 (mt0) REVERT: X 388 ARG cc_start: 0.8783 (mmm160) cc_final: 0.8512 (mmm160) REVERT: X 417 TYR cc_start: 0.8764 (m-80) cc_final: 0.8505 (m-80) REVERT: X 475 TYR cc_start: 0.3764 (t80) cc_final: 0.3480 (t80) REVERT: Y 69 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8455 (tp30) REVERT: Y 145 CYS cc_start: 0.7957 (m) cc_final: 0.7653 (m) REVERT: Y 173 MET cc_start: 0.7939 (ttp) cc_final: 0.7554 (tpp) REVERT: Y 210 LEU cc_start: 0.8751 (mt) cc_final: 0.8529 (mm) REVERT: Y 294 PHE cc_start: 0.8059 (t80) cc_final: 0.7841 (t80) REVERT: Y 301 ASP cc_start: 0.7891 (t0) cc_final: 0.7553 (t0) REVERT: Y 549 MET cc_start: 0.8056 (mmt) cc_final: 0.7817 (mmp) outliers start: 530 outliers final: 217 residues processed: 1643 average time/residue: 0.5968 time to fit residues: 1680.8241 Evaluate side-chains 1194 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 925 time to evaluate : 5.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1216 LYS Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1457 LEU Chi-restraints excluded: chain A residue 1482 LEU Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1611 VAL Chi-restraints excluded: chain A residue 1639 LYS Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1666 ILE Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1688 LYS Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1774 VAL Chi-restraints excluded: chain A residue 1781 GLN Chi-restraints excluded: chain A residue 1800 LEU Chi-restraints excluded: chain A residue 1810 GLU Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1814 ILE Chi-restraints excluded: chain A residue 1817 VAL Chi-restraints excluded: chain A residue 1821 PHE Chi-restraints excluded: chain A residue 1893 SER Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 203 TRP Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 429 ARG Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 467 LYS Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 477 CYS Chi-restraints excluded: chain F residue 530 ASN Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 628 ILE Chi-restraints excluded: chain F residue 721 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain H residue 47 CYS Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 546 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 257 HIS Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 471 ASN Chi-restraints excluded: chain I residue 609 GLN Chi-restraints excluded: chain I residue 652 VAL Chi-restraints excluded: chain I residue 686 THR Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 79 CYS Chi-restraints excluded: chain J residue 163 CYS Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 315 LYS Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 439 VAL Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 523 ILE Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 163 CYS Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain K residue 311 MET Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 359 THR Chi-restraints excluded: chain K residue 376 LEU Chi-restraints excluded: chain K residue 510 ARG Chi-restraints excluded: chain K residue 523 ILE Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 19 TRP Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 241 HIS Chi-restraints excluded: chain N residue 271 GLU Chi-restraints excluded: chain N residue 274 GLU Chi-restraints excluded: chain N residue 280 GLU Chi-restraints excluded: chain N residue 299 TRP Chi-restraints excluded: chain N residue 364 CYS Chi-restraints excluded: chain N residue 373 GLN Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 388 HIS Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 517 ASN Chi-restraints excluded: chain N residue 592 TYR Chi-restraints excluded: chain N residue 594 VAL Chi-restraints excluded: chain N residue 626 TYR Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 237 GLN Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 264 VAL Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 307 LEU Chi-restraints excluded: chain O residue 319 GLN Chi-restraints excluded: chain O residue 356 ASP Chi-restraints excluded: chain O residue 358 TYR Chi-restraints excluded: chain O residue 369 VAL Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 436 THR Chi-restraints excluded: chain O residue 473 LEU Chi-restraints excluded: chain O residue 527 LEU Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 533 THR Chi-restraints excluded: chain O residue 563 LEU Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 621 SER Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 657 ILE Chi-restraints excluded: chain O residue 670 CYS Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 731 ASN Chi-restraints excluded: chain O residue 754 HIS Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 219 LEU Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 302 THR Chi-restraints excluded: chain P residue 361 ASN Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 369 THR Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 192 TRP Chi-restraints excluded: chain R residue 326 SER Chi-restraints excluded: chain R residue 433 MET Chi-restraints excluded: chain R residue 450 THR Chi-restraints excluded: chain R residue 499 ARG Chi-restraints excluded: chain W residue 4 ARG Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 214 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 255 ILE Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain X residue 306 LYS Chi-restraints excluded: chain X residue 310 VAL Chi-restraints excluded: chain X residue 372 SER Chi-restraints excluded: chain X residue 401 ARG Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain Y residue 95 ASN Chi-restraints excluded: chain Y residue 212 LEU Chi-restraints excluded: chain Y residue 296 GLN Chi-restraints excluded: chain Y residue 310 VAL Chi-restraints excluded: chain Y residue 321 LEU Chi-restraints excluded: chain Y residue 324 VAL Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 394 ILE Chi-restraints excluded: chain Y residue 407 LEU Chi-restraints excluded: chain Y residue 464 LEU Chi-restraints excluded: chain Y residue 501 ASN Chi-restraints excluded: chain Y residue 503 LEU Chi-restraints excluded: chain Y residue 507 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 415 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 622 optimal weight: 6.9990 chunk 509 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 chunk 749 optimal weight: 1.9990 chunk 809 optimal weight: 9.9990 chunk 667 optimal weight: 2.9990 chunk 743 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 601 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 ASN A 125 GLN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 HIS ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 HIS C 347 HIS F 100 GLN F 517 GLN F 657 HIS ** F 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 545 HIS H 583 HIS H 599 ASN H 609 HIS ** H 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 HIS ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 GLN ** I 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** J 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 289 HIS J 449 ASN J 453 HIS ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 503 HIS K 54 HIS ** K 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 GLN ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN N 186 GLN N 245 GLN ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS ** N 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 702 GLN N 726 ASN O 159 GLN O 219 GLN ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 412 HIS O 424 GLN O 443 GLN ** O 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 680 GLN O 693 ASN O 754 HIS P 50 HIS P 236 HIS P 346 GLN ** P 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 426 HIS P 448 GLN P 485 GLN R 87 GLN R 323 HIS X 89 HIS X 338 HIS X 421 ASN ** Y 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 369 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 66864 Z= 0.293 Angle : 0.817 18.593 90576 Z= 0.418 Chirality : 0.045 0.274 10188 Planarity : 0.005 0.119 11506 Dihedral : 8.499 76.853 9323 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.09 % Favored : 94.19 % Rotamer: Outliers : 6.66 % Allowed : 22.66 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.45 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.09), residues: 8183 helix: 0.81 (0.07), residues: 5346 sheet: -0.67 (0.22), residues: 563 loop : -2.13 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 209 HIS 0.017 0.002 HIS N 388 PHE 0.024 0.002 PHE J 247 TYR 0.034 0.002 TYR P 490 ARG 0.026 0.001 ARG M 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1435 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 458 poor density : 977 time to evaluate : 5.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 HIS cc_start: 0.8423 (OUTLIER) cc_final: 0.8011 (t-90) REVERT: A 114 TYR cc_start: 0.8812 (t80) cc_final: 0.8529 (t80) REVERT: A 165 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8479 (tm-30) REVERT: A 167 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8046 (mtpt) REVERT: A 242 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.6899 (m170) REVERT: A 250 ASN cc_start: 0.7101 (OUTLIER) cc_final: 0.6623 (t0) REVERT: A 617 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8577 (mt) REVERT: A 637 MET cc_start: 0.8648 (tmm) cc_final: 0.8402 (tmm) REVERT: A 779 MET cc_start: 0.9268 (mmt) cc_final: 0.8838 (tpp) REVERT: A 1067 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7752 (tt0) REVERT: A 1078 MET cc_start: 0.6463 (mpp) cc_final: 0.6102 (mpp) REVERT: A 1125 ILE cc_start: 0.7314 (mt) cc_final: 0.6273 (mt) REVERT: A 1216 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7461 (mmmt) REVERT: A 1229 SER cc_start: 0.5601 (m) cc_final: 0.5248 (t) REVERT: A 1268 HIS cc_start: 0.6332 (t-90) cc_final: 0.5937 (t70) REVERT: A 1326 TYR cc_start: 0.5363 (t80) cc_final: 0.5067 (t80) REVERT: A 1329 MET cc_start: 0.8676 (ttm) cc_final: 0.8309 (tmm) REVERT: A 1464 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7730 (mp) REVERT: A 1482 LEU cc_start: 0.8750 (tt) cc_final: 0.8387 (mp) REVERT: A 1498 TYR cc_start: 0.6452 (OUTLIER) cc_final: 0.5757 (m-80) REVERT: A 1623 ASP cc_start: 0.8550 (t0) cc_final: 0.8172 (t70) REVERT: A 1639 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6552 (pttm) REVERT: A 1652 MET cc_start: 0.6510 (OUTLIER) cc_final: 0.5548 (mpp) REVERT: A 1688 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8475 (tptt) REVERT: A 1733 PHE cc_start: 0.1194 (t80) cc_final: -0.1227 (t80) REVERT: A 1734 LYS cc_start: 0.3280 (OUTLIER) cc_final: 0.2969 (mttm) REVERT: A 1748 LEU cc_start: 0.9385 (tt) cc_final: 0.9114 (mp) REVERT: A 1759 VAL cc_start: 0.6295 (OUTLIER) cc_final: 0.5816 (p) REVERT: A 1777 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8228 (tm-30) REVERT: A 1780 THR cc_start: 0.7108 (t) cc_final: 0.6867 (p) REVERT: A 1782 GLU cc_start: 0.5916 (mp0) cc_final: 0.5534 (tp30) REVERT: A 1804 GLU cc_start: 0.8470 (pt0) cc_final: 0.8248 (tp30) REVERT: A 1807 GLU cc_start: 0.8876 (tt0) cc_final: 0.8470 (tp30) REVERT: A 1810 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8902 (pm20) REVERT: A 1844 PHE cc_start: 0.8889 (t80) cc_final: 0.8644 (t80) REVERT: A 1858 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8699 (pt0) REVERT: A 1891 TYR cc_start: 0.8679 (t80) cc_final: 0.8086 (t80) REVERT: B 1 MET cc_start: 0.4200 (OUTLIER) cc_final: 0.3930 (tpp) REVERT: C 65 LEU cc_start: 0.5713 (OUTLIER) cc_final: 0.5501 (mm) REVERT: C 246 GLU cc_start: 0.8787 (tp30) cc_final: 0.7959 (pt0) REVERT: C 315 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8630 (mp0) REVERT: C 360 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8261 (mp) REVERT: C 557 ARG cc_start: 0.1679 (OUTLIER) cc_final: 0.1299 (ttt180) REVERT: D 47 LYS cc_start: 0.8472 (tmtt) cc_final: 0.7947 (tptt) REVERT: E 61 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.6676 (t80) REVERT: E 92 ASP cc_start: 0.8330 (t0) cc_final: 0.8127 (t0) REVERT: E 93 GLU cc_start: 0.9250 (tt0) cc_final: 0.9035 (mt-10) REVERT: F 49 TYR cc_start: 0.7748 (t80) cc_final: 0.7234 (t80) REVERT: F 148 LEU cc_start: 0.6517 (mt) cc_final: 0.6297 (mp) REVERT: F 469 MET cc_start: 0.8629 (ttm) cc_final: 0.8331 (mtt) REVERT: F 477 CYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7323 (t) REVERT: F 646 TYR cc_start: 0.7378 (t80) cc_final: 0.7041 (t80) REVERT: G 4 ARG cc_start: 0.8476 (mtt-85) cc_final: 0.8065 (ttm-80) REVERT: G 15 ASP cc_start: 0.5865 (m-30) cc_final: 0.5338 (t70) REVERT: G 16 ILE cc_start: 0.8111 (mm) cc_final: 0.7890 (mm) REVERT: H 61 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9135 (mt) REVERT: H 84 LYS cc_start: 0.7908 (mttt) cc_final: 0.7479 (ptpp) REVERT: H 502 LEU cc_start: 0.8904 (mt) cc_final: 0.8673 (mt) REVERT: H 564 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8345 (mtmm) REVERT: H 591 GLN cc_start: 0.8349 (mt0) cc_final: 0.7881 (mp10) REVERT: H 643 MET cc_start: 0.8530 (mtp) cc_final: 0.8064 (tpp) REVERT: H 655 GLU cc_start: 0.8460 (tp30) cc_final: 0.7915 (tp30) REVERT: H 764 MET cc_start: 0.7740 (mmm) cc_final: 0.7517 (mmt) REVERT: I 93 CYS cc_start: 0.6677 (t) cc_final: 0.6402 (m) REVERT: I 99 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8347 (tm-30) REVERT: I 158 GLU cc_start: 0.7092 (tp30) cc_final: 0.6799 (mm-30) REVERT: I 322 MET cc_start: 0.6774 (tpt) cc_final: 0.6139 (ptm) REVERT: I 386 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8537 (tt) REVERT: I 404 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8877 (tp) REVERT: I 570 PHE cc_start: 0.7769 (m-10) cc_final: 0.7267 (m-10) REVERT: I 603 ARG cc_start: 0.8847 (mtp-110) cc_final: 0.8542 (ttt180) REVERT: J 25 TRP cc_start: 0.8238 (m100) cc_final: 0.7968 (m100) REVERT: J 87 GLN cc_start: 0.7960 (tp-100) cc_final: 0.7710 (tp-100) REVERT: J 133 CYS cc_start: 0.8275 (m) cc_final: 0.7543 (t) REVERT: J 192 LYS cc_start: 0.8504 (mttt) cc_final: 0.8225 (mmmt) REVERT: J 261 ASP cc_start: 0.8199 (t0) cc_final: 0.7920 (t0) REVERT: J 270 VAL cc_start: 0.7185 (OUTLIER) cc_final: 0.6910 (p) REVERT: J 274 THR cc_start: 0.9032 (t) cc_final: 0.8811 (m) REVERT: J 311 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6669 (ptp) REVERT: J 349 GLU cc_start: 0.8312 (mp0) cc_final: 0.8039 (tp30) REVERT: J 395 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7991 (mm) REVERT: J 478 ASN cc_start: 0.7904 (t0) cc_final: 0.7493 (m-40) REVERT: K 64 LYS cc_start: 0.8946 (mttt) cc_final: 0.8685 (mmmt) REVERT: K 160 ASP cc_start: 0.6929 (t0) cc_final: 0.6701 (t0) REVERT: K 165 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8677 (mt-10) REVERT: K 331 LYS cc_start: 0.7176 (mttm) cc_final: 0.6734 (tppt) REVERT: K 364 MET cc_start: 0.8358 (mtt) cc_final: 0.7646 (mtm) REVERT: K 367 CYS cc_start: 0.8723 (t) cc_final: 0.8477 (t) REVERT: K 374 ILE cc_start: 0.8436 (mt) cc_final: 0.8129 (tp) REVERT: K 388 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8933 (pt0) REVERT: K 414 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7999 (tp-100) REVERT: K 431 LYS cc_start: 0.9129 (mmtt) cc_final: 0.8857 (mtpt) REVERT: K 482 TYR cc_start: 0.5641 (m-80) cc_final: 0.5041 (m-80) REVERT: K 525 MET cc_start: 0.8414 (tpp) cc_final: 0.7961 (mtp) REVERT: L 12 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7621 (t0) REVERT: L 119 TRP cc_start: 0.6867 (m100) cc_final: 0.4974 (m100) REVERT: L 156 ILE cc_start: 0.7722 (mp) cc_final: 0.7479 (mm) REVERT: L 162 VAL cc_start: 0.7689 (p) cc_final: 0.7105 (m) REVERT: L 163 GLU cc_start: 0.7946 (tt0) cc_final: 0.7435 (pm20) REVERT: L 179 MET cc_start: 0.8705 (tmm) cc_final: 0.8487 (tmm) REVERT: L 180 TYR cc_start: 0.9277 (m-80) cc_final: 0.8953 (m-80) REVERT: M 6 GLN cc_start: 0.7082 (mm-40) cc_final: 0.6786 (mm-40) REVERT: M 51 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6782 (ttpt) REVERT: N 172 MET cc_start: 0.8831 (mmm) cc_final: 0.8574 (mmm) REVERT: N 213 TYR cc_start: 0.8981 (t80) cc_final: 0.8479 (p90) REVERT: N 241 HIS cc_start: 0.9426 (OUTLIER) cc_final: 0.8777 (p-80) REVERT: N 271 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8464 (pp20) REVERT: N 274 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8757 (tm-30) REVERT: N 373 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8852 (mp10) REVERT: N 515 PHE cc_start: 0.8178 (m-80) cc_final: 0.7428 (m-10) REVERT: N 537 ARG cc_start: 0.5810 (ptp-170) cc_final: 0.5485 (tpt90) REVERT: N 543 GLU cc_start: 0.8635 (pt0) cc_final: 0.8294 (mm-30) REVERT: N 546 LYS cc_start: 0.8117 (tttt) cc_final: 0.7675 (tmtt) REVERT: N 660 THR cc_start: 0.4811 (m) cc_final: 0.4365 (p) REVERT: N 670 PHE cc_start: 0.0076 (OUTLIER) cc_final: -0.0634 (t80) REVERT: N 699 TRP cc_start: 0.2630 (OUTLIER) cc_final: 0.2145 (m100) REVERT: N 705 LEU cc_start: 0.0546 (OUTLIER) cc_final: -0.0074 (pp) REVERT: N 727 MET cc_start: -0.0774 (tpt) cc_final: -0.1282 (mmm) REVERT: O 110 GLN cc_start: 0.8549 (tt0) cc_final: 0.8154 (tp-100) REVERT: O 150 GLN cc_start: 0.8586 (mt0) cc_final: 0.8188 (mm110) REVERT: O 231 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8240 (mp) REVERT: O 237 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: O 508 MET cc_start: 0.9025 (mtm) cc_final: 0.8736 (mtp) REVERT: O 536 THR cc_start: 0.9357 (t) cc_final: 0.8978 (p) REVERT: O 680 GLN cc_start: 0.4624 (OUTLIER) cc_final: 0.4413 (pm20) REVERT: O 754 HIS cc_start: 0.6438 (OUTLIER) cc_final: 0.5909 (p-80) REVERT: P 128 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8615 (ttpt) REVERT: P 210 CYS cc_start: 0.7981 (m) cc_final: 0.7656 (m) REVERT: P 211 ASN cc_start: 0.8163 (m-40) cc_final: 0.7652 (m-40) REVERT: P 300 MET cc_start: 0.8409 (mmt) cc_final: 0.7941 (mmt) REVERT: P 346 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7558 (mt0) REVERT: P 354 PHE cc_start: 0.8554 (m-80) cc_final: 0.7932 (m-80) REVERT: P 431 ASN cc_start: 0.8737 (m-40) cc_final: 0.8438 (p0) REVERT: P 445 LYS cc_start: 0.8424 (mtpt) cc_final: 0.8168 (mmmm) REVERT: R 132 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7373 (mtm-85) REVERT: R 174 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7113 (mtp85) REVERT: R 220 LEU cc_start: 0.1107 (OUTLIER) cc_final: 0.0830 (pp) REVERT: R 222 MET cc_start: 0.1340 (mtp) cc_final: 0.0968 (ttt) REVERT: R 317 TRP cc_start: 0.3137 (m100) cc_final: 0.2641 (m100) REVERT: R 351 PHE cc_start: 0.2137 (m-80) cc_final: 0.1880 (m-80) REVERT: R 355 GLN cc_start: 0.7209 (mm110) cc_final: 0.6534 (pt0) REVERT: W 23 ARG cc_start: 0.5271 (mtm-85) cc_final: 0.4852 (mtm-85) REVERT: X 102 MET cc_start: 0.9286 (mtm) cc_final: 0.8861 (tpt) REVERT: X 269 ASP cc_start: 0.7731 (m-30) cc_final: 0.7499 (p0) REVERT: X 282 PHE cc_start: 0.8795 (t80) cc_final: 0.8590 (t80) REVERT: X 347 CYS cc_start: 0.9163 (m) cc_final: 0.8663 (t) REVERT: X 388 ARG cc_start: 0.8766 (mmm160) cc_final: 0.8497 (mmm160) REVERT: X 417 TYR cc_start: 0.8899 (m-80) cc_final: 0.8616 (m-80) REVERT: X 475 TYR cc_start: 0.3853 (t80) cc_final: 0.3593 (t80) REVERT: Y 69 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8464 (tp30) REVERT: Y 99 LYS cc_start: 0.8685 (mmtt) cc_final: 0.8449 (tppt) REVERT: Y 154 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8586 (t0) REVERT: Y 173 MET cc_start: 0.7862 (ttp) cc_final: 0.7540 (tpp) REVERT: Y 300 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7792 (mm) REVERT: Y 301 ASP cc_start: 0.7429 (t0) cc_final: 0.7126 (t0) outliers start: 458 outliers final: 236 residues processed: 1323 average time/residue: 0.6392 time to fit residues: 1475.1104 Evaluate side-chains 1110 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 828 time to evaluate : 5.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1216 LYS Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1397 ASP Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1457 LEU Chi-restraints excluded: chain A residue 1464 ILE Chi-restraints excluded: chain A residue 1498 TYR Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1639 LYS Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1666 ILE Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1688 LYS Chi-restraints excluded: chain A residue 1734 LYS Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1749 SER Chi-restraints excluded: chain A residue 1759 VAL Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1800 LEU Chi-restraints excluded: chain A residue 1810 GLU Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1814 ILE Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1850 CYS Chi-restraints excluded: chain A residue 1858 GLN Chi-restraints excluded: chain A residue 1877 LEU Chi-restraints excluded: chain A residue 1890 VAL Chi-restraints excluded: chain A residue 1893 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 429 ARG Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 477 CYS Chi-restraints excluded: chain F residue 530 ASN Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 565 ASN Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain F residue 628 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain H residue 47 CYS Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 564 LYS Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 617 LEU Chi-restraints excluded: chain H residue 685 SER Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 257 HIS Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain I residue 281 MET Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 386 ILE Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 529 MET Chi-restraints excluded: chain I residue 564 ASP Chi-restraints excluded: chain I residue 609 GLN Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain I residue 652 VAL Chi-restraints excluded: chain I residue 686 THR Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 311 MET Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 513 THR Chi-restraints excluded: chain J residue 523 ILE Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 311 MET Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 510 ARG Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 19 TRP Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 241 HIS Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 271 GLU Chi-restraints excluded: chain N residue 274 GLU Chi-restraints excluded: chain N residue 280 GLU Chi-restraints excluded: chain N residue 299 TRP Chi-restraints excluded: chain N residue 358 ILE Chi-restraints excluded: chain N residue 364 CYS Chi-restraints excluded: chain N residue 373 GLN Chi-restraints excluded: chain N residue 388 HIS Chi-restraints excluded: chain N residue 419 VAL Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 517 ASN Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 556 PHE Chi-restraints excluded: chain N residue 626 TYR Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 231 LEU Chi-restraints excluded: chain O residue 237 GLN Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 307 LEU Chi-restraints excluded: chain O residue 319 GLN Chi-restraints excluded: chain O residue 356 ASP Chi-restraints excluded: chain O residue 358 TYR Chi-restraints excluded: chain O residue 369 VAL Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain O residue 527 LEU Chi-restraints excluded: chain O residue 533 THR Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 618 TYR Chi-restraints excluded: chain O residue 632 LEU Chi-restraints excluded: chain O residue 634 LEU Chi-restraints excluded: chain O residue 667 VAL Chi-restraints excluded: chain O residue 680 GLN Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 754 HIS Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 302 THR Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 346 GLN Chi-restraints excluded: chain P residue 360 LEU Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain R residue 87 GLN Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 326 SER Chi-restraints excluded: chain R residue 433 MET Chi-restraints excluded: chain R residue 450 THR Chi-restraints excluded: chain R residue 499 ARG Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 227 ILE Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain X residue 310 VAL Chi-restraints excluded: chain X residue 372 SER Chi-restraints excluded: chain X residue 401 ARG Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 95 ASN Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 212 LEU Chi-restraints excluded: chain Y residue 214 VAL Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 296 GLN Chi-restraints excluded: chain Y residue 300 LEU Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 321 LEU Chi-restraints excluded: chain Y residue 324 VAL Chi-restraints excluded: chain Y residue 329 CYS Chi-restraints excluded: chain Y residue 373 VAL Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 407 LEU Chi-restraints excluded: chain Y residue 464 LEU Chi-restraints excluded: chain Y residue 476 ILE Chi-restraints excluded: chain Y residue 501 ASN Chi-restraints excluded: chain Y residue 519 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 740 optimal weight: 0.8980 chunk 563 optimal weight: 6.9990 chunk 389 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 357 optimal weight: 10.0000 chunk 503 optimal weight: 1.9990 chunk 752 optimal weight: 10.0000 chunk 796 optimal weight: 2.9990 chunk 393 optimal weight: 0.0570 chunk 713 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 ASN ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1266 HIS ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** F 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 634 HIS ** H 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 708 HIS ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 455 HIS ** J 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 271 HIS J 489 HIS J 503 HIS ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 HIS K 271 HIS L 65 ASN ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 754 HIS P 426 HIS P 427 GLN R 289 HIS ** Y 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 66864 Z= 0.249 Angle : 0.767 18.474 90576 Z= 0.390 Chirality : 0.043 0.282 10188 Planarity : 0.005 0.116 11506 Dihedral : 7.591 73.996 9232 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.66 % Allowed : 4.98 % Favored : 94.36 % Rotamer: Outliers : 5.92 % Allowed : 23.57 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.45 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.09), residues: 8183 helix: 0.94 (0.07), residues: 5355 sheet: -0.62 (0.22), residues: 559 loop : -2.07 (0.13), residues: 2269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 209 HIS 0.019 0.001 HIS X 247 PHE 0.023 0.002 PHE O 371 TYR 0.032 0.002 TYR P 490 ARG 0.011 0.001 ARG N 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1335 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 407 poor density : 928 time to evaluate : 5.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.8026 (t-90) REVERT: A 114 TYR cc_start: 0.8854 (t80) cc_final: 0.8586 (t80) REVERT: A 125 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8111 (mp10) REVERT: A 165 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8665 (tm-30) REVERT: A 167 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8082 (mtpt) REVERT: A 185 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.7835 (t80) REVERT: A 242 HIS cc_start: 0.7688 (OUTLIER) cc_final: 0.6865 (t70) REVERT: A 250 ASN cc_start: 0.6983 (t160) cc_final: 0.6529 (t0) REVERT: A 945 GLU cc_start: 0.8012 (tp30) cc_final: 0.7740 (mt-10) REVERT: A 1067 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7759 (tt0) REVERT: A 1120 LEU cc_start: 0.5122 (OUTLIER) cc_final: 0.4776 (mt) REVERT: A 1229 SER cc_start: 0.5508 (m) cc_final: 0.5215 (t) REVERT: A 1268 HIS cc_start: 0.6390 (t-90) cc_final: 0.5926 (t70) REVERT: A 1304 MET cc_start: 0.8044 (mtm) cc_final: 0.7811 (mtm) REVERT: A 1326 TYR cc_start: 0.5491 (t80) cc_final: 0.4950 (t80) REVERT: A 1329 MET cc_start: 0.8674 (ttm) cc_final: 0.8296 (tmm) REVERT: A 1350 TYR cc_start: 0.6799 (m-80) cc_final: 0.6533 (m-10) REVERT: A 1498 TYR cc_start: 0.6432 (OUTLIER) cc_final: 0.5792 (m-80) REVERT: A 1527 MET cc_start: 0.8854 (ptm) cc_final: 0.8139 (tmm) REVERT: A 1606 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6334 (tp) REVERT: A 1623 ASP cc_start: 0.8511 (t0) cc_final: 0.8117 (t70) REVERT: A 1652 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.5511 (mpp) REVERT: A 1688 LYS cc_start: 0.8728 (ttpt) cc_final: 0.8467 (tptt) REVERT: A 1744 ASP cc_start: 0.8169 (t0) cc_final: 0.7860 (t0) REVERT: A 1748 LEU cc_start: 0.9347 (tt) cc_final: 0.9108 (mp) REVERT: A 1759 VAL cc_start: 0.6076 (OUTLIER) cc_final: 0.5656 (p) REVERT: A 1777 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8121 (tm-30) REVERT: A 1782 GLU cc_start: 0.6341 (mp0) cc_final: 0.6077 (tp30) REVERT: A 1802 ARG cc_start: 0.9044 (ttm110) cc_final: 0.8773 (ttm110) REVERT: A 1807 GLU cc_start: 0.8746 (tt0) cc_final: 0.8350 (tp30) REVERT: A 1810 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8830 (pm20) REVERT: A 1891 TYR cc_start: 0.8574 (t80) cc_final: 0.7958 (t80) REVERT: C 119 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8931 (mmt) REVERT: C 246 GLU cc_start: 0.8789 (tp30) cc_final: 0.8582 (tp30) REVERT: C 333 THR cc_start: 0.8066 (t) cc_final: 0.7865 (t) REVERT: C 360 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8214 (mp) REVERT: C 388 TYR cc_start: 0.7911 (m-80) cc_final: 0.7555 (m-80) REVERT: C 441 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: C 466 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7490 (tm-30) REVERT: C 557 ARG cc_start: 0.1696 (OUTLIER) cc_final: 0.1288 (ttm110) REVERT: D 47 LYS cc_start: 0.8549 (tmtt) cc_final: 0.7960 (tptt) REVERT: E 61 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.7142 (t80) REVERT: E 85 LEU cc_start: 0.6731 (tp) cc_final: 0.6514 (tp) REVERT: E 92 ASP cc_start: 0.8300 (t0) cc_final: 0.8054 (t0) REVERT: E 93 GLU cc_start: 0.9269 (tt0) cc_final: 0.9052 (mt-10) REVERT: F 49 TYR cc_start: 0.7704 (t80) cc_final: 0.7327 (t80) REVERT: F 469 MET cc_start: 0.8635 (ttm) cc_final: 0.8373 (mtt) REVERT: F 477 CYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7368 (t) REVERT: F 646 TYR cc_start: 0.7490 (t80) cc_final: 0.7066 (t80) REVERT: G 4 ARG cc_start: 0.8396 (mtt-85) cc_final: 0.7961 (ttp-110) REVERT: G 15 ASP cc_start: 0.5914 (m-30) cc_final: 0.5381 (t70) REVERT: H 61 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9023 (mt) REVERT: H 84 LYS cc_start: 0.7894 (mttt) cc_final: 0.7458 (ptpp) REVERT: H 147 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: H 502 LEU cc_start: 0.8772 (mt) cc_final: 0.8549 (mt) REVERT: H 634 HIS cc_start: 0.8972 (t70) cc_final: 0.8577 (t70) REVERT: H 643 MET cc_start: 0.8639 (mtp) cc_final: 0.8166 (tpp) REVERT: H 764 MET cc_start: 0.7751 (mmm) cc_final: 0.7531 (mmt) REVERT: I 26 LEU cc_start: 0.8311 (pp) cc_final: 0.7978 (tt) REVERT: I 93 CYS cc_start: 0.7044 (t) cc_final: 0.6169 (m) REVERT: I 99 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8398 (tm-30) REVERT: I 117 GLU cc_start: 0.8909 (pm20) cc_final: 0.8523 (tt0) REVERT: I 158 GLU cc_start: 0.6860 (tp30) cc_final: 0.6576 (mm-30) REVERT: I 309 LEU cc_start: 0.4375 (OUTLIER) cc_final: 0.3875 (mp) REVERT: I 322 MET cc_start: 0.6829 (tpt) cc_final: 0.6277 (ptm) REVERT: I 404 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8877 (tp) REVERT: I 569 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.5531 (mp) REVERT: I 570 PHE cc_start: 0.7764 (m-10) cc_final: 0.7206 (m-10) REVERT: I 603 ARG cc_start: 0.8852 (mtp-110) cc_final: 0.8542 (ttt180) REVERT: J 25 TRP cc_start: 0.8175 (m100) cc_final: 0.7855 (m100) REVERT: J 39 ASP cc_start: 0.6262 (m-30) cc_final: 0.5363 (t0) REVERT: J 43 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9218 (mp) REVERT: J 133 CYS cc_start: 0.8441 (m) cc_final: 0.7760 (t) REVERT: J 192 LYS cc_start: 0.8491 (mttt) cc_final: 0.8207 (mmmt) REVERT: J 261 ASP cc_start: 0.8236 (t0) cc_final: 0.7952 (t0) REVERT: J 270 VAL cc_start: 0.7163 (OUTLIER) cc_final: 0.6881 (p) REVERT: J 274 THR cc_start: 0.9029 (t) cc_final: 0.8791 (m) REVERT: J 322 TYR cc_start: 0.8630 (m-80) cc_final: 0.8304 (m-80) REVERT: J 349 GLU cc_start: 0.8352 (mp0) cc_final: 0.8029 (tp30) REVERT: J 371 MET cc_start: 0.7842 (mmm) cc_final: 0.7377 (mmm) REVERT: J 395 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8023 (mm) REVERT: K 64 LYS cc_start: 0.8923 (mttt) cc_final: 0.8654 (mmmt) REVERT: K 160 ASP cc_start: 0.6955 (t0) cc_final: 0.6676 (t0) REVERT: K 327 THR cc_start: 0.6015 (t) cc_final: 0.5676 (p) REVERT: K 331 LYS cc_start: 0.7141 (mttm) cc_final: 0.6737 (tppt) REVERT: K 349 GLU cc_start: 0.5722 (mm-30) cc_final: 0.5345 (mm-30) REVERT: K 364 MET cc_start: 0.8171 (mtt) cc_final: 0.7181 (mtm) REVERT: K 367 CYS cc_start: 0.8882 (t) cc_final: 0.8184 (p) REVERT: K 388 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8973 (pt0) REVERT: K 482 TYR cc_start: 0.5986 (m-80) cc_final: 0.5408 (m-80) REVERT: K 525 MET cc_start: 0.8427 (tpp) cc_final: 0.8035 (mtp) REVERT: L 12 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7523 (t0) REVERT: L 45 LEU cc_start: 0.7937 (tt) cc_final: 0.7227 (mt) REVERT: L 119 TRP cc_start: 0.6703 (m100) cc_final: 0.5316 (m100) REVERT: L 136 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7929 (ptm) REVERT: L 153 MET cc_start: 0.5711 (tmm) cc_final: 0.5180 (tmm) REVERT: L 157 LYS cc_start: 0.6526 (mttp) cc_final: 0.6292 (mttp) REVERT: L 162 VAL cc_start: 0.7524 (p) cc_final: 0.6900 (m) REVERT: L 163 GLU cc_start: 0.7948 (tt0) cc_final: 0.7476 (pm20) REVERT: L 177 PHE cc_start: 0.8786 (t80) cc_final: 0.8465 (t80) REVERT: L 178 MET cc_start: 0.9059 (mtm) cc_final: 0.8695 (mpp) REVERT: L 179 MET cc_start: 0.8766 (tmm) cc_final: 0.8536 (tmm) REVERT: M 6 GLN cc_start: 0.6508 (mm-40) cc_final: 0.6183 (mm-40) REVERT: N 172 MET cc_start: 0.8845 (mmm) cc_final: 0.8618 (mmm) REVERT: N 213 TYR cc_start: 0.8980 (t80) cc_final: 0.8512 (p90) REVERT: N 271 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8448 (pp20) REVERT: N 280 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6145 (pm20) REVERT: N 299 TRP cc_start: 0.6560 (OUTLIER) cc_final: 0.5384 (t-100) REVERT: N 373 GLN cc_start: 0.9040 (mt0) cc_final: 0.8777 (mp10) REVERT: N 425 ARG cc_start: 0.7523 (mtt-85) cc_final: 0.7316 (ttm110) REVERT: N 515 PHE cc_start: 0.8389 (m-80) cc_final: 0.7639 (m-80) REVERT: N 537 ARG cc_start: 0.5656 (ptp-170) cc_final: 0.5415 (tpt90) REVERT: N 543 GLU cc_start: 0.8590 (pt0) cc_final: 0.8246 (mm-30) REVERT: N 546 LYS cc_start: 0.8044 (tttt) cc_final: 0.7639 (tmtt) REVERT: N 584 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5967 (tm-30) REVERT: N 639 HIS cc_start: 0.3233 (t-90) cc_final: 0.2978 (t70) REVERT: N 660 THR cc_start: 0.4671 (m) cc_final: 0.4346 (p) REVERT: N 670 PHE cc_start: 0.0108 (OUTLIER) cc_final: -0.0644 (t80) REVERT: N 699 TRP cc_start: 0.2727 (OUTLIER) cc_final: 0.2300 (m100) REVERT: N 705 LEU cc_start: 0.0501 (OUTLIER) cc_final: 0.0014 (pp) REVERT: N 727 MET cc_start: 0.0288 (tpt) cc_final: -0.0414 (mmm) REVERT: O 110 GLN cc_start: 0.8517 (tt0) cc_final: 0.8150 (mm-40) REVERT: O 150 GLN cc_start: 0.8682 (mt0) cc_final: 0.8312 (mm110) REVERT: O 419 ASP cc_start: 0.9166 (m-30) cc_final: 0.8895 (p0) REVERT: O 447 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.8196 (p) REVERT: O 508 MET cc_start: 0.9049 (mtm) cc_final: 0.8761 (mtp) REVERT: O 536 THR cc_start: 0.9387 (t) cc_final: 0.9084 (p) REVERT: O 708 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7629 (mm-30) REVERT: O 754 HIS cc_start: 0.6652 (OUTLIER) cc_final: 0.6052 (p-80) REVERT: P 117 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7293 (tt) REVERT: P 128 LYS cc_start: 0.8883 (mmtp) cc_final: 0.8602 (ttpt) REVERT: P 208 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7881 (mm-30) REVERT: P 300 MET cc_start: 0.8346 (mmt) cc_final: 0.7946 (mmt) REVERT: P 431 ASN cc_start: 0.8822 (m-40) cc_final: 0.8490 (p0) REVERT: P 435 MET cc_start: 0.7336 (mmp) cc_final: 0.6458 (mtm) REVERT: P 445 LYS cc_start: 0.8313 (mtpt) cc_final: 0.8052 (mmmm) REVERT: R 174 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7262 (mtp85) REVERT: R 220 LEU cc_start: 0.1007 (OUTLIER) cc_final: 0.0727 (pp) REVERT: R 222 MET cc_start: 0.1338 (mtp) cc_final: 0.1099 (ttt) REVERT: R 317 TRP cc_start: 0.3321 (m100) cc_final: 0.2803 (m100) REVERT: R 499 ARG cc_start: 0.6299 (OUTLIER) cc_final: 0.5305 (tmm160) REVERT: W 23 ARG cc_start: 0.5461 (mtm-85) cc_final: 0.5104 (ttm-80) REVERT: X 269 ASP cc_start: 0.7683 (m-30) cc_final: 0.7446 (p0) REVERT: X 282 PHE cc_start: 0.8631 (t80) cc_final: 0.8421 (t80) REVERT: X 347 CYS cc_start: 0.9084 (m) cc_final: 0.8529 (t) REVERT: X 388 ARG cc_start: 0.8824 (mmm160) cc_final: 0.8548 (mmm160) REVERT: X 475 TYR cc_start: 0.3948 (t80) cc_final: 0.3633 (t80) REVERT: Y 69 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8509 (tp30) REVERT: Y 80 LEU cc_start: 0.8764 (tp) cc_final: 0.8263 (tp) REVERT: Y 99 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8123 (mmmm) REVERT: Y 154 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8433 (t70) REVERT: Y 173 MET cc_start: 0.7843 (ttp) cc_final: 0.7519 (tpp) REVERT: Y 300 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7790 (mm) REVERT: Y 301 ASP cc_start: 0.7298 (t0) cc_final: 0.6977 (t0) REVERT: Y 308 MET cc_start: 0.8814 (mmp) cc_final: 0.8421 (mmm) outliers start: 407 outliers final: 213 residues processed: 1240 average time/residue: 0.6422 time to fit residues: 1384.6780 Evaluate side-chains 1067 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 812 time to evaluate : 5.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1397 ASP Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1498 TYR Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1581 ILE Chi-restraints excluded: chain A residue 1606 LEU Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1666 ILE Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1734 LYS Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1749 SER Chi-restraints excluded: chain A residue 1759 VAL Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1800 LEU Chi-restraints excluded: chain A residue 1810 GLU Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1817 VAL Chi-restraints excluded: chain A residue 1850 CYS Chi-restraints excluded: chain A residue 1893 SER Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 477 CYS Chi-restraints excluded: chain F residue 530 ASN Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 565 ASN Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain F residue 628 ILE Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 617 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 257 HIS Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 529 MET Chi-restraints excluded: chain I residue 564 ASP Chi-restraints excluded: chain I residue 569 LEU Chi-restraints excluded: chain I residue 609 GLN Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain I residue 652 VAL Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain J residue 485 ILE Chi-restraints excluded: chain J residue 513 THR Chi-restraints excluded: chain K residue 73 ARG Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 447 LEU Chi-restraints excluded: chain K residue 510 ARG Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain M residue 19 TRP Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 271 GLU Chi-restraints excluded: chain N residue 280 GLU Chi-restraints excluded: chain N residue 299 TRP Chi-restraints excluded: chain N residue 327 HIS Chi-restraints excluded: chain N residue 364 CYS Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 517 ASN Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 626 TYR Chi-restraints excluded: chain N residue 640 THR Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain N residue 705 LEU Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 307 LEU Chi-restraints excluded: chain O residue 319 GLN Chi-restraints excluded: chain O residue 356 ASP Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 436 THR Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain O residue 468 VAL Chi-restraints excluded: chain O residue 527 LEU Chi-restraints excluded: chain O residue 533 THR Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 618 TYR Chi-restraints excluded: chain O residue 621 SER Chi-restraints excluded: chain O residue 632 LEU Chi-restraints excluded: chain O residue 634 LEU Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 708 GLU Chi-restraints excluded: chain O residue 754 HIS Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 302 THR Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 360 LEU Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 369 THR Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 455 CYS Chi-restraints excluded: chain P residue 480 LEU Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 326 SER Chi-restraints excluded: chain R residue 433 MET Chi-restraints excluded: chain R residue 499 ARG Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain X residue 372 SER Chi-restraints excluded: chain X residue 401 ARG Chi-restraints excluded: chain X residue 445 THR Chi-restraints excluded: chain X residue 507 SER Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 92 GLU Chi-restraints excluded: chain Y residue 95 ASN Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 212 LEU Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 296 GLN Chi-restraints excluded: chain Y residue 300 LEU Chi-restraints excluded: chain Y residue 321 LEU Chi-restraints excluded: chain Y residue 324 VAL Chi-restraints excluded: chain Y residue 329 CYS Chi-restraints excluded: chain Y residue 373 VAL Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 407 LEU Chi-restraints excluded: chain Y residue 476 ILE Chi-restraints excluded: chain Y residue 507 SER Chi-restraints excluded: chain Y residue 519 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 663 optimal weight: 10.0000 chunk 452 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 593 optimal weight: 7.9990 chunk 328 optimal weight: 9.9990 chunk 679 optimal weight: 2.9990 chunk 550 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 406 optimal weight: 0.9990 chunk 714 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 HIS ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 HIS ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN C 292 GLN F 100 GLN ** F 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS ** H 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 716 ASN ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 503 HIS ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 HIS ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 319 GLN ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 754 HIS P 211 ASN P 426 HIS R 87 GLN X 66 ASN X 105 GLN X 367 GLN X 385 ASN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 66864 Z= 0.256 Angle : 0.756 18.351 90576 Z= 0.383 Chirality : 0.042 0.248 10188 Planarity : 0.005 0.116 11506 Dihedral : 7.067 74.948 9179 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.27 % Favored : 94.09 % Rotamer: Outliers : 5.55 % Allowed : 24.79 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.43 % Twisted Proline : 0.66 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.09), residues: 8183 helix: 1.02 (0.07), residues: 5343 sheet: -0.64 (0.21), residues: 564 loop : -2.04 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP X 342 HIS 0.028 0.001 HIS N 327 PHE 0.027 0.002 PHE X 518 TYR 0.027 0.002 TYR P 490 ARG 0.011 0.001 ARG N 548 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 381 poor density : 860 time to evaluate : 5.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8624 (tm-30) REVERT: A 167 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8097 (mtpt) REVERT: A 250 ASN cc_start: 0.7213 (OUTLIER) cc_final: 0.6804 (t0) REVERT: A 1019 MET cc_start: 0.7034 (mmm) cc_final: 0.6632 (mmp) REVERT: A 1067 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7650 (tt0) REVERT: A 1078 MET cc_start: 0.6365 (mmm) cc_final: 0.6132 (mpp) REVERT: A 1120 LEU cc_start: 0.5206 (OUTLIER) cc_final: 0.4755 (mt) REVERT: A 1268 HIS cc_start: 0.6389 (t-90) cc_final: 0.5980 (t-170) REVERT: A 1304 MET cc_start: 0.8032 (mtm) cc_final: 0.7814 (mtm) REVERT: A 1326 TYR cc_start: 0.5481 (t80) cc_final: 0.5211 (t80) REVERT: A 1329 MET cc_start: 0.8646 (ttm) cc_final: 0.8299 (tmm) REVERT: A 1498 TYR cc_start: 0.6507 (OUTLIER) cc_final: 0.5894 (m-80) REVERT: A 1527 MET cc_start: 0.8704 (ptm) cc_final: 0.7954 (tmm) REVERT: A 1606 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.5601 (tp) REVERT: A 1609 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8546 (mp) REVERT: A 1623 ASP cc_start: 0.8574 (t0) cc_final: 0.8223 (t70) REVERT: A 1652 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.5797 (mpp) REVERT: A 1688 LYS cc_start: 0.8807 (ttpt) cc_final: 0.8607 (tptt) REVERT: A 1731 ARG cc_start: 0.7043 (tmm160) cc_final: 0.6038 (ptp-170) REVERT: A 1733 PHE cc_start: 0.0242 (t80) cc_final: -0.1822 (t80) REVERT: A 1744 ASP cc_start: 0.8217 (t0) cc_final: 0.7926 (t0) REVERT: A 1759 VAL cc_start: 0.6151 (OUTLIER) cc_final: 0.5778 (p) REVERT: A 1777 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8259 (tm-30) REVERT: A 1782 GLU cc_start: 0.6761 (mp0) cc_final: 0.6144 (tp30) REVERT: A 1858 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8635 (pt0) REVERT: B 1 MET cc_start: 0.5171 (tpp) cc_final: 0.4841 (tpp) REVERT: C 119 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8965 (mmt) REVERT: C 245 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8475 (pp20) REVERT: C 360 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8171 (mp) REVERT: C 388 TYR cc_start: 0.7988 (m-80) cc_final: 0.7771 (m-80) REVERT: C 435 MET cc_start: 0.8649 (tpp) cc_final: 0.8263 (tpp) REVERT: C 441 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: C 557 ARG cc_start: 0.1478 (OUTLIER) cc_final: 0.1000 (ttm110) REVERT: D 47 LYS cc_start: 0.8564 (tmtt) cc_final: 0.7966 (tptt) REVERT: E 92 ASP cc_start: 0.8331 (t0) cc_final: 0.8076 (t0) REVERT: E 100 GLU cc_start: 0.8351 (mp0) cc_final: 0.8092 (mm-30) REVERT: F 49 TYR cc_start: 0.7853 (t80) cc_final: 0.7522 (t80) REVERT: F 100 GLN cc_start: 0.8133 (mt0) cc_final: 0.7831 (mt0) REVERT: F 469 MET cc_start: 0.8623 (ttm) cc_final: 0.8339 (mtt) REVERT: F 584 ASP cc_start: 0.7455 (m-30) cc_final: 0.7096 (p0) REVERT: F 646 TYR cc_start: 0.7473 (t80) cc_final: 0.7030 (t80) REVERT: H 84 LYS cc_start: 0.7984 (mttt) cc_final: 0.7533 (ptpp) REVERT: H 643 MET cc_start: 0.8587 (mtp) cc_final: 0.8149 (tpp) REVERT: H 764 MET cc_start: 0.7902 (mmm) cc_final: 0.7650 (mmt) REVERT: I 93 CYS cc_start: 0.6883 (t) cc_final: 0.6075 (m) REVERT: I 99 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8476 (tm-30) REVERT: I 117 GLU cc_start: 0.8914 (pm20) cc_final: 0.8530 (tt0) REVERT: I 158 GLU cc_start: 0.6840 (tp30) cc_final: 0.6616 (mm-30) REVERT: I 309 LEU cc_start: 0.4677 (OUTLIER) cc_final: 0.4174 (mp) REVERT: I 322 MET cc_start: 0.6852 (tpt) cc_final: 0.6314 (ptm) REVERT: I 404 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8909 (tp) REVERT: I 569 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.6094 (mp) REVERT: I 620 PHE cc_start: 0.6832 (m-80) cc_final: 0.6068 (t80) REVERT: J 39 ASP cc_start: 0.6229 (m-30) cc_final: 0.5336 (t0) REVERT: J 133 CYS cc_start: 0.8469 (m) cc_final: 0.7789 (t) REVERT: J 192 LYS cc_start: 0.8491 (mttt) cc_final: 0.8164 (mmmt) REVERT: J 261 ASP cc_start: 0.8420 (t0) cc_final: 0.8034 (t0) REVERT: J 270 VAL cc_start: 0.7241 (OUTLIER) cc_final: 0.6968 (p) REVERT: J 274 THR cc_start: 0.9078 (t) cc_final: 0.8849 (m) REVERT: J 311 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6633 (ptp) REVERT: J 349 GLU cc_start: 0.8265 (mp0) cc_final: 0.7915 (tp30) REVERT: J 371 MET cc_start: 0.7881 (mmm) cc_final: 0.7508 (mmm) REVERT: J 395 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7899 (mm) REVERT: K 13 TYR cc_start: 0.8851 (m-80) cc_final: 0.8603 (m-80) REVERT: K 64 LYS cc_start: 0.8920 (mttt) cc_final: 0.8656 (mmmt) REVERT: K 160 ASP cc_start: 0.7009 (t0) cc_final: 0.6768 (t0) REVERT: K 258 MET cc_start: 0.6011 (mmp) cc_final: 0.5702 (mmp) REVERT: K 327 THR cc_start: 0.6004 (t) cc_final: 0.5659 (p) REVERT: K 331 LYS cc_start: 0.6883 (mttm) cc_final: 0.6470 (tppt) REVERT: K 364 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7324 (mtm) REVERT: K 367 CYS cc_start: 0.8850 (t) cc_final: 0.8196 (p) REVERT: K 482 TYR cc_start: 0.6018 (m-80) cc_final: 0.5435 (m-80) REVERT: K 525 MET cc_start: 0.8341 (tpp) cc_final: 0.7941 (mtp) REVERT: L 12 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7685 (t0) REVERT: L 45 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7379 (mt) REVERT: L 136 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7914 (ptm) REVERT: L 150 ASP cc_start: 0.5982 (m-30) cc_final: 0.5613 (m-30) REVERT: L 163 GLU cc_start: 0.7899 (tt0) cc_final: 0.7451 (pm20) REVERT: L 177 PHE cc_start: 0.8829 (t80) cc_final: 0.8506 (t80) REVERT: L 178 MET cc_start: 0.9139 (mtm) cc_final: 0.8828 (mpp) REVERT: N 172 MET cc_start: 0.8849 (mmm) cc_final: 0.8629 (mmm) REVERT: N 213 TYR cc_start: 0.8971 (t80) cc_final: 0.8520 (p90) REVERT: N 271 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8461 (pp20) REVERT: N 280 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.5976 (pm20) REVERT: N 299 TRP cc_start: 0.6337 (OUTLIER) cc_final: 0.5033 (t-100) REVERT: N 373 GLN cc_start: 0.8981 (mt0) cc_final: 0.8766 (mp10) REVERT: N 422 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7390 (mm-30) REVERT: N 425 ARG cc_start: 0.7506 (mtt-85) cc_final: 0.7154 (ttm170) REVERT: N 515 PHE cc_start: 0.8387 (m-80) cc_final: 0.7575 (m-10) REVERT: N 543 GLU cc_start: 0.8532 (pt0) cc_final: 0.8178 (mm-30) REVERT: N 546 LYS cc_start: 0.8076 (tttt) cc_final: 0.7672 (tmtt) REVERT: N 584 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.6022 (tm-30) REVERT: N 639 HIS cc_start: 0.3009 (t-90) cc_final: 0.2779 (t70) REVERT: N 670 PHE cc_start: 0.0160 (OUTLIER) cc_final: -0.0571 (t80) REVERT: N 699 TRP cc_start: 0.2694 (OUTLIER) cc_final: 0.2340 (m100) REVERT: N 727 MET cc_start: 0.0328 (tpt) cc_final: -0.0377 (mmm) REVERT: O 150 GLN cc_start: 0.8703 (mt0) cc_final: 0.8359 (mm110) REVERT: O 397 LYS cc_start: 0.7205 (mttm) cc_final: 0.6924 (mmmt) REVERT: O 437 MET cc_start: 0.7446 (mmm) cc_final: 0.6925 (tpp) REVERT: O 447 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8101 (p) REVERT: O 502 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: O 508 MET cc_start: 0.9090 (mtm) cc_final: 0.8838 (mtp) REVERT: O 533 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8504 (m) REVERT: O 536 THR cc_start: 0.9391 (t) cc_final: 0.9087 (p) REVERT: O 708 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7534 (mm-30) REVERT: O 754 HIS cc_start: 0.6575 (OUTLIER) cc_final: 0.5704 (p-80) REVERT: P 117 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7349 (tt) REVERT: P 208 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7838 (mm-30) REVERT: P 300 MET cc_start: 0.8255 (mmt) cc_final: 0.7914 (mmt) REVERT: P 431 ASN cc_start: 0.8792 (m-40) cc_final: 0.8447 (p0) REVERT: P 445 LYS cc_start: 0.8306 (mtpt) cc_final: 0.8070 (mmmt) REVERT: R 174 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7299 (mtp85) REVERT: R 317 TRP cc_start: 0.3390 (m100) cc_final: 0.2945 (m100) REVERT: R 351 PHE cc_start: 0.2212 (m-80) cc_final: 0.1981 (m-80) REVERT: R 499 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5240 (tmm160) REVERT: W 23 ARG cc_start: 0.5463 (mtm-85) cc_final: 0.5180 (ttm-80) REVERT: X 269 ASP cc_start: 0.7692 (m-30) cc_final: 0.7464 (p0) REVERT: X 282 PHE cc_start: 0.8752 (t80) cc_final: 0.8463 (t80) REVERT: X 342 TRP cc_start: 0.8727 (m100) cc_final: 0.8494 (m-10) REVERT: X 388 ARG cc_start: 0.8586 (mmm160) cc_final: 0.8378 (mmm160) REVERT: X 475 TYR cc_start: 0.4092 (t80) cc_final: 0.3734 (t80) REVERT: Y 69 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8507 (tp30) REVERT: Y 99 LYS cc_start: 0.8624 (mmtt) cc_final: 0.8230 (mmmm) REVERT: Y 173 MET cc_start: 0.7886 (ttp) cc_final: 0.7613 (tpp) REVERT: Y 300 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7659 (mm) REVERT: Y 301 ASP cc_start: 0.7089 (t0) cc_final: 0.6768 (t0) REVERT: Y 308 MET cc_start: 0.8901 (mmp) cc_final: 0.8452 (mmm) outliers start: 381 outliers final: 241 residues processed: 1146 average time/residue: 0.6097 time to fit residues: 1217.3781 Evaluate side-chains 1071 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 792 time to evaluate : 5.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 785 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1316 MET Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1397 ASP Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1433 ILE Chi-restraints excluded: chain A residue 1498 TYR Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1581 ILE Chi-restraints excluded: chain A residue 1606 LEU Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1666 ILE Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1749 SER Chi-restraints excluded: chain A residue 1759 VAL Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1800 LEU Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1850 CYS Chi-restraints excluded: chain A residue 1858 GLN Chi-restraints excluded: chain A residue 1893 SER Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 530 ASN Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain F residue 628 ILE Chi-restraints excluded: chain F residue 757 LEU Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 617 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 257 HIS Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 529 MET Chi-restraints excluded: chain I residue 564 ASP Chi-restraints excluded: chain I residue 569 LEU Chi-restraints excluded: chain I residue 609 GLN Chi-restraints excluded: chain I residue 652 VAL Chi-restraints excluded: chain I residue 667 VAL Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 289 HIS Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 311 MET Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain J residue 485 ILE Chi-restraints excluded: chain J residue 513 THR Chi-restraints excluded: chain K residue 73 ARG Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 364 MET Chi-restraints excluded: chain K residue 506 LEU Chi-restraints excluded: chain K residue 510 ARG Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 4 GLU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 19 TRP Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 271 GLU Chi-restraints excluded: chain N residue 280 GLU Chi-restraints excluded: chain N residue 299 TRP Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 364 CYS Chi-restraints excluded: chain N residue 414 MET Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 501 ILE Chi-restraints excluded: chain N residue 517 ASN Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 626 TYR Chi-restraints excluded: chain N residue 640 THR Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 699 TRP Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 307 LEU Chi-restraints excluded: chain O residue 350 LEU Chi-restraints excluded: chain O residue 356 ASP Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 436 THR Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain O residue 468 VAL Chi-restraints excluded: chain O residue 502 GLN Chi-restraints excluded: chain O residue 527 LEU Chi-restraints excluded: chain O residue 533 THR Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 618 TYR Chi-restraints excluded: chain O residue 621 SER Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 708 GLU Chi-restraints excluded: chain O residue 754 HIS Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 302 THR Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 360 LEU Chi-restraints excluded: chain P residue 364 TYR Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 369 THR Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 455 CYS Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 326 SER Chi-restraints excluded: chain R residue 403 CYS Chi-restraints excluded: chain R residue 433 MET Chi-restraints excluded: chain R residue 450 THR Chi-restraints excluded: chain R residue 499 ARG Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 265 SER Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain X residue 296 GLN Chi-restraints excluded: chain X residue 310 VAL Chi-restraints excluded: chain X residue 372 SER Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 445 THR Chi-restraints excluded: chain X residue 507 SER Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 95 ASN Chi-restraints excluded: chain Y residue 212 LEU Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 233 LEU Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 296 GLN Chi-restraints excluded: chain Y residue 300 LEU Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 321 LEU Chi-restraints excluded: chain Y residue 324 VAL Chi-restraints excluded: chain Y residue 329 CYS Chi-restraints excluded: chain Y residue 373 VAL Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 407 LEU Chi-restraints excluded: chain Y residue 476 ILE Chi-restraints excluded: chain Y residue 507 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 267 optimal weight: 2.9990 chunk 717 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 467 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 797 optimal weight: 5.9990 chunk 661 optimal weight: 1.9990 chunk 369 optimal weight: 3.9990 chunk 66 optimal weight: 0.0270 chunk 263 optimal weight: 10.0000 chunk 418 optimal weight: 8.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1309 HIS ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN F 36 HIS F 626 ASN ** F 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 HIS J 264 HIS J 318 HIS J 503 HIS ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 HIS K 393 GLN ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 396 ASN ** O 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 505 GLN O 754 HIS P 346 GLN ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 GLN X 40 HIS X 367 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.5758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 66864 Z= 0.307 Angle : 0.775 18.220 90576 Z= 0.394 Chirality : 0.043 0.282 10188 Planarity : 0.005 0.118 11506 Dihedral : 6.869 77.379 9154 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.45 % Favored : 93.91 % Rotamer: Outliers : 5.85 % Allowed : 24.88 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.43 % Twisted Proline : 0.66 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.09), residues: 8183 helix: 0.98 (0.07), residues: 5349 sheet: -0.70 (0.21), residues: 560 loop : -2.06 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 203 HIS 0.019 0.002 HIS O 754 PHE 0.027 0.002 PHE C 303 TYR 0.036 0.002 TYR X 417 ARG 0.009 0.001 ARG F 520 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 402 poor density : 825 time to evaluate : 5.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.8135 (t-90) REVERT: A 165 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8510 (tm-30) REVERT: A 167 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8092 (mtpt) REVERT: A 185 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7255 (t80) REVERT: A 250 ASN cc_start: 0.6943 (OUTLIER) cc_final: 0.6461 (t0) REVERT: A 626 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7240 (mmmt) REVERT: A 637 MET cc_start: 0.8821 (tmm) cc_final: 0.8420 (tmm) REVERT: A 947 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6689 (tt) REVERT: A 1019 MET cc_start: 0.6388 (mmm) cc_final: 0.6080 (mmp) REVERT: A 1067 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7826 (tt0) REVERT: A 1268 HIS cc_start: 0.6300 (t-90) cc_final: 0.5982 (t-170) REVERT: A 1304 MET cc_start: 0.8077 (mtm) cc_final: 0.7832 (mtm) REVERT: A 1317 SER cc_start: 0.8165 (m) cc_final: 0.7818 (p) REVERT: A 1326 TYR cc_start: 0.5503 (t80) cc_final: 0.5214 (t80) REVERT: A 1329 MET cc_start: 0.8796 (ttm) cc_final: 0.8387 (tmm) REVERT: A 1455 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8391 (pm20) REVERT: A 1498 TYR cc_start: 0.6702 (OUTLIER) cc_final: 0.6152 (m-80) REVERT: A 1527 MET cc_start: 0.8711 (ptm) cc_final: 0.8164 (ppp) REVERT: A 1606 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6380 (mm) REVERT: A 1609 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8613 (mp) REVERT: A 1623 ASP cc_start: 0.8518 (t0) cc_final: 0.8159 (t70) REVERT: A 1652 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.5863 (mpp) REVERT: A 1688 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8598 (tptt) REVERT: A 1759 VAL cc_start: 0.6512 (OUTLIER) cc_final: 0.6288 (p) REVERT: A 1782 GLU cc_start: 0.6804 (mp0) cc_final: 0.6300 (tp30) REVERT: A 1858 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8646 (pt0) REVERT: B 1 MET cc_start: 0.5212 (tpp) cc_final: 0.4835 (tpp) REVERT: C 119 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8956 (mmt) REVERT: C 203 TRP cc_start: 0.8532 (m100) cc_final: 0.8081 (t60) REVERT: C 215 ASP cc_start: 0.7728 (t0) cc_final: 0.7493 (t0) REVERT: C 218 MET cc_start: 0.8399 (ptp) cc_final: 0.8197 (pmm) REVERT: C 245 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8493 (pp20) REVERT: C 303 PHE cc_start: 0.7186 (t80) cc_final: 0.6953 (t80) REVERT: C 360 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8140 (mp) REVERT: C 436 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8429 (mm) REVERT: C 441 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.7827 (pm20) REVERT: C 455 CYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8764 (t) REVERT: C 522 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.6336 (mttp) REVERT: C 557 ARG cc_start: 0.1112 (OUTLIER) cc_final: 0.0785 (ttt180) REVERT: D 47 LYS cc_start: 0.8567 (tmtt) cc_final: 0.7993 (tptt) REVERT: E 57 SER cc_start: 0.6572 (OUTLIER) cc_final: 0.6016 (p) REVERT: E 85 LEU cc_start: 0.6495 (tp) cc_final: 0.6198 (tt) REVERT: E 100 GLU cc_start: 0.8250 (mp0) cc_final: 0.7997 (mm-30) REVERT: F 469 MET cc_start: 0.8647 (ttm) cc_final: 0.8365 (mtt) REVERT: F 584 ASP cc_start: 0.7480 (m-30) cc_final: 0.7121 (p0) REVERT: F 646 TYR cc_start: 0.7544 (t80) cc_final: 0.7135 (t80) REVERT: H 584 ASP cc_start: 0.7024 (p0) cc_final: 0.6768 (t0) REVERT: H 764 MET cc_start: 0.7902 (mmm) cc_final: 0.7655 (mmt) REVERT: I 99 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8453 (tm-30) REVERT: I 117 GLU cc_start: 0.8935 (pm20) cc_final: 0.8559 (tt0) REVERT: I 309 LEU cc_start: 0.4845 (OUTLIER) cc_final: 0.4506 (mp) REVERT: I 322 MET cc_start: 0.6807 (tpt) cc_final: 0.6274 (ptm) REVERT: I 569 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.6052 (mp) REVERT: I 620 PHE cc_start: 0.6987 (m-80) cc_final: 0.6264 (t80) REVERT: J 133 CYS cc_start: 0.8475 (m) cc_final: 0.7822 (t) REVERT: J 192 LYS cc_start: 0.8541 (mttt) cc_final: 0.8272 (mmmt) REVERT: J 311 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7221 (ptp) REVERT: J 349 GLU cc_start: 0.8233 (mp0) cc_final: 0.7943 (tp30) REVERT: J 371 MET cc_start: 0.8032 (mmm) cc_final: 0.7646 (mmm) REVERT: J 395 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8004 (mm) REVERT: J 525 MET cc_start: 0.7782 (mmm) cc_final: 0.7358 (tpp) REVERT: K 13 TYR cc_start: 0.8884 (m-80) cc_final: 0.8640 (m-80) REVERT: K 64 LYS cc_start: 0.8862 (mttt) cc_final: 0.8603 (mmmt) REVERT: K 143 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8233 (mm) REVERT: K 160 ASP cc_start: 0.7146 (t0) cc_final: 0.6897 (t0) REVERT: K 258 MET cc_start: 0.6336 (mmp) cc_final: 0.6100 (mmp) REVERT: K 327 THR cc_start: 0.6300 (t) cc_final: 0.5895 (p) REVERT: K 331 LYS cc_start: 0.7052 (mttm) cc_final: 0.6642 (tppt) REVERT: K 349 GLU cc_start: 0.5754 (OUTLIER) cc_final: 0.5398 (mm-30) REVERT: K 364 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7071 (mtm) REVERT: K 367 CYS cc_start: 0.8805 (t) cc_final: 0.8193 (p) REVERT: K 430 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8789 (tp30) REVERT: K 482 TYR cc_start: 0.6095 (m-80) cc_final: 0.5720 (m-80) REVERT: L 12 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7648 (t0) REVERT: L 45 LEU cc_start: 0.8066 (tt) cc_final: 0.7335 (mt) REVERT: L 136 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.7845 (ptm) REVERT: L 150 ASP cc_start: 0.5875 (m-30) cc_final: 0.5504 (m-30) REVERT: L 153 MET cc_start: 0.6056 (tmm) cc_final: 0.5515 (tmm) REVERT: L 163 GLU cc_start: 0.7923 (tt0) cc_final: 0.7428 (pm20) REVERT: N 172 MET cc_start: 0.8824 (mmm) cc_final: 0.8567 (mmm) REVERT: N 213 TYR cc_start: 0.8934 (t80) cc_final: 0.8515 (p90) REVERT: N 271 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8519 (pp20) REVERT: N 299 TRP cc_start: 0.6279 (OUTLIER) cc_final: 0.4947 (t-100) REVERT: N 373 GLN cc_start: 0.8973 (mt0) cc_final: 0.8772 (mp10) REVERT: N 392 ASN cc_start: 0.8095 (t0) cc_final: 0.7578 (m-40) REVERT: N 515 PHE cc_start: 0.8353 (m-80) cc_final: 0.7525 (m-10) REVERT: N 543 GLU cc_start: 0.8484 (pt0) cc_final: 0.8134 (mm-30) REVERT: N 546 LYS cc_start: 0.8112 (tttt) cc_final: 0.7713 (tmtt) REVERT: N 584 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.6058 (tm-30) REVERT: N 670 PHE cc_start: -0.0057 (OUTLIER) cc_final: -0.0595 (t80) REVERT: O 150 GLN cc_start: 0.8801 (mt0) cc_final: 0.8472 (mm110) REVERT: O 256 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8086 (tm) REVERT: O 397 LYS cc_start: 0.7248 (mttm) cc_final: 0.6901 (mmmt) REVERT: O 437 MET cc_start: 0.7314 (mmm) cc_final: 0.6917 (tpp) REVERT: O 447 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8063 (p) REVERT: O 508 MET cc_start: 0.9090 (mtm) cc_final: 0.8857 (mtp) REVERT: O 531 LEU cc_start: 0.8838 (tp) cc_final: 0.8587 (tp) REVERT: O 536 THR cc_start: 0.9380 (t) cc_final: 0.9110 (p) REVERT: O 670 CYS cc_start: 0.9387 (t) cc_final: 0.9111 (t) REVERT: O 708 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7680 (mm-30) REVERT: O 754 HIS cc_start: 0.6604 (OUTLIER) cc_final: 0.5740 (p-80) REVERT: P 117 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7397 (tt) REVERT: P 378 MET cc_start: 0.8700 (mmm) cc_final: 0.8442 (mmm) REVERT: P 445 LYS cc_start: 0.8339 (mtpt) cc_final: 0.8117 (mmmt) REVERT: R 174 ARG cc_start: 0.7956 (mtm-85) cc_final: 0.7373 (mtp85) REVERT: R 317 TRP cc_start: 0.3209 (m100) cc_final: 0.2931 (m100) REVERT: R 499 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.5917 (tmm160) REVERT: X 269 ASP cc_start: 0.7680 (m-30) cc_final: 0.7446 (p0) REVERT: X 282 PHE cc_start: 0.8798 (t80) cc_final: 0.8446 (t80) REVERT: X 347 CYS cc_start: 0.9098 (m) cc_final: 0.8782 (p) REVERT: X 388 ARG cc_start: 0.8602 (mmm160) cc_final: 0.8367 (mmm160) REVERT: X 409 CYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8714 (p) REVERT: X 423 ILE cc_start: 0.7904 (pt) cc_final: 0.7680 (mt) REVERT: X 475 TYR cc_start: 0.4034 (t80) cc_final: 0.3681 (t80) REVERT: Y 69 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8509 (tp30) REVERT: Y 99 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8129 (mmmm) REVERT: Y 154 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8668 (t70) REVERT: Y 173 MET cc_start: 0.7893 (ttp) cc_final: 0.7612 (tpp) REVERT: Y 300 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7685 (mm) REVERT: Y 301 ASP cc_start: 0.7010 (t0) cc_final: 0.6634 (t0) REVERT: Y 308 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8364 (mmm) outliers start: 402 outliers final: 248 residues processed: 1130 average time/residue: 0.5929 time to fit residues: 1169.6174 Evaluate side-chains 1052 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 759 time to evaluate : 5.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 785 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1316 MET Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1397 ASP Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1433 ILE Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1496 MET Chi-restraints excluded: chain A residue 1498 TYR Chi-restraints excluded: chain A residue 1503 ASN Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1606 LEU Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1666 ILE Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1688 LYS Chi-restraints excluded: chain A residue 1759 VAL Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1800 LEU Chi-restraints excluded: chain A residue 1817 VAL Chi-restraints excluded: chain A residue 1850 CYS Chi-restraints excluded: chain A residue 1858 GLN Chi-restraints excluded: chain A residue 1893 SER Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 389 ARG Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 455 CYS Chi-restraints excluded: chain C residue 522 LYS Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 530 ASN Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 594 ILE Chi-restraints excluded: chain F residue 628 ILE Chi-restraints excluded: chain F residue 757 LEU Chi-restraints excluded: chain H residue 47 CYS Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 560 THR Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 612 VAL Chi-restraints excluded: chain H residue 617 LEU Chi-restraints excluded: chain H residue 738 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 257 HIS Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 441 THR Chi-restraints excluded: chain I residue 529 MET Chi-restraints excluded: chain I residue 564 ASP Chi-restraints excluded: chain I residue 569 LEU Chi-restraints excluded: chain I residue 609 GLN Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain I residue 667 VAL Chi-restraints excluded: chain I residue 688 THR Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 289 HIS Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 311 MET Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain J residue 485 ILE Chi-restraints excluded: chain J residue 513 THR Chi-restraints excluded: chain J residue 523 ILE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 349 GLU Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 364 MET Chi-restraints excluded: chain K residue 447 LEU Chi-restraints excluded: chain K residue 506 LEU Chi-restraints excluded: chain K residue 510 ARG Chi-restraints excluded: chain K residue 523 ILE Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 19 TRP Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 245 GLN Chi-restraints excluded: chain N residue 271 GLU Chi-restraints excluded: chain N residue 299 TRP Chi-restraints excluded: chain N residue 346 SER Chi-restraints excluded: chain N residue 364 CYS Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 501 ILE Chi-restraints excluded: chain N residue 517 ASN Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 626 TYR Chi-restraints excluded: chain N residue 640 THR Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 262 LEU Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 356 ASP Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 436 THR Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain O residue 468 VAL Chi-restraints excluded: chain O residue 527 LEU Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 585 LEU Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 618 TYR Chi-restraints excluded: chain O residue 621 SER Chi-restraints excluded: chain O residue 632 LEU Chi-restraints excluded: chain O residue 634 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 648 ILE Chi-restraints excluded: chain O residue 667 VAL Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 708 GLU Chi-restraints excluded: chain O residue 754 HIS Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 302 THR Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 360 LEU Chi-restraints excluded: chain P residue 364 TYR Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 369 THR Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 455 CYS Chi-restraints excluded: chain R residue 116 TRP Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 326 SER Chi-restraints excluded: chain R residue 403 CYS Chi-restraints excluded: chain R residue 433 MET Chi-restraints excluded: chain R residue 450 THR Chi-restraints excluded: chain R residue 499 ARG Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 199 CYS Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 265 SER Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain X residue 296 GLN Chi-restraints excluded: chain X residue 372 SER Chi-restraints excluded: chain X residue 402 LEU Chi-restraints excluded: chain X residue 409 CYS Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 95 ASN Chi-restraints excluded: chain Y residue 154 ASP Chi-restraints excluded: chain Y residue 212 LEU Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 233 LEU Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 296 GLN Chi-restraints excluded: chain Y residue 300 LEU Chi-restraints excluded: chain Y residue 308 MET Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 321 LEU Chi-restraints excluded: chain Y residue 324 VAL Chi-restraints excluded: chain Y residue 329 CYS Chi-restraints excluded: chain Y residue 350 PHE Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 407 LEU Chi-restraints excluded: chain Y residue 476 ILE Chi-restraints excluded: chain Y residue 507 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 768 optimal weight: 0.0060 chunk 89 optimal weight: 0.0270 chunk 454 optimal weight: 6.9990 chunk 582 optimal weight: 1.9990 chunk 451 optimal weight: 6.9990 chunk 671 optimal weight: 10.0000 chunk 445 optimal weight: 1.9990 chunk 794 optimal weight: 9.9990 chunk 497 optimal weight: 6.9990 chunk 484 optimal weight: 8.9990 chunk 366 optimal weight: 1.9990 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 GLN ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1537 GLN ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1591 HIS ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1646 GLN ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 754 HIS ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 353 GLN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 HIS ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN L 103 HIS ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 GLN ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 127 HIS ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 754 HIS ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN X 105 GLN X 367 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.5943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 66864 Z= 0.220 Angle : 0.749 18.174 90576 Z= 0.375 Chirality : 0.042 0.280 10188 Planarity : 0.005 0.119 11506 Dihedral : 6.570 76.383 9138 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.17 % Favored : 94.20 % Rotamer: Outliers : 4.88 % Allowed : 26.10 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.43 % Twisted Proline : 0.66 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.09), residues: 8183 helix: 1.09 (0.07), residues: 5343 sheet: -0.65 (0.21), residues: 558 loop : -2.02 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 116 HIS 0.016 0.001 HIS X 247 PHE 0.022 0.002 PHE F 152 TYR 0.034 0.002 TYR L 180 ARG 0.014 0.000 ARG J 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1197 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 862 time to evaluate : 5.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.8156 (t-90) REVERT: A 165 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8472 (tm-30) REVERT: A 167 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8002 (mtpt) REVERT: A 185 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.7224 (t80) REVERT: A 250 ASN cc_start: 0.7297 (OUTLIER) cc_final: 0.6868 (t0) REVERT: A 626 LYS cc_start: 0.7595 (mmmt) cc_final: 0.7242 (mmmt) REVERT: A 637 MET cc_start: 0.8871 (tmm) cc_final: 0.8409 (tmm) REVERT: A 947 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6684 (tt) REVERT: A 1067 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7851 (tt0) REVERT: A 1118 VAL cc_start: 0.4234 (OUTLIER) cc_final: 0.3949 (p) REVERT: A 1268 HIS cc_start: 0.6348 (t-90) cc_final: 0.6027 (t-170) REVERT: A 1300 LEU cc_start: 0.7136 (mt) cc_final: 0.6600 (mt) REVERT: A 1304 MET cc_start: 0.7989 (mtm) cc_final: 0.7746 (mtm) REVERT: A 1326 TYR cc_start: 0.5551 (t80) cc_final: 0.5056 (t80) REVERT: A 1329 MET cc_start: 0.8749 (ttm) cc_final: 0.8308 (tmm) REVERT: A 1498 TYR cc_start: 0.6593 (OUTLIER) cc_final: 0.6099 (m-80) REVERT: A 1527 MET cc_start: 0.8730 (ptm) cc_final: 0.8181 (ppp) REVERT: A 1606 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.5595 (tp) REVERT: A 1609 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8592 (mp) REVERT: A 1623 ASP cc_start: 0.8522 (t0) cc_final: 0.8153 (t70) REVERT: A 1652 MET cc_start: 0.7063 (tpt) cc_final: 0.5786 (mpp) REVERT: A 1688 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8575 (tptt) REVERT: A 1759 VAL cc_start: 0.6347 (OUTLIER) cc_final: 0.6145 (p) REVERT: A 1782 GLU cc_start: 0.6562 (mp0) cc_final: 0.6341 (tp30) REVERT: A 1850 CYS cc_start: 0.9540 (t) cc_final: 0.9235 (t) REVERT: A 1858 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8641 (pt0) REVERT: B 1 MET cc_start: 0.5363 (tpp) cc_final: 0.4961 (tpp) REVERT: C 119 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8971 (mmt) REVERT: C 245 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8492 (pp20) REVERT: C 303 PHE cc_start: 0.7343 (t80) cc_final: 0.6949 (t80) REVERT: C 360 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8093 (mp) REVERT: C 441 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7974 (pm20) REVERT: C 455 CYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8784 (t) REVERT: C 522 LYS cc_start: 0.6657 (OUTLIER) cc_final: 0.6344 (mttp) REVERT: D 47 LYS cc_start: 0.8528 (tmtt) cc_final: 0.7931 (tptt) REVERT: E 73 ASP cc_start: 0.8241 (m-30) cc_final: 0.8035 (p0) REVERT: E 100 GLU cc_start: 0.8261 (mp0) cc_final: 0.7994 (mm-30) REVERT: F 91 ILE cc_start: 0.9119 (mt) cc_final: 0.8854 (mt) REVERT: F 646 TYR cc_start: 0.7385 (t80) cc_final: 0.6927 (t80) REVERT: H 145 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.7260 (t0) REVERT: H 564 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8459 (mtmm) REVERT: H 584 ASP cc_start: 0.6888 (p0) cc_final: 0.6671 (t0) REVERT: H 764 MET cc_start: 0.7868 (mmm) cc_final: 0.7619 (mmt) REVERT: I 99 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8532 (tm-30) REVERT: I 170 ASP cc_start: 0.6232 (p0) cc_final: 0.6026 (p0) REVERT: I 276 TRP cc_start: 0.6682 (t60) cc_final: 0.6358 (t-100) REVERT: I 309 LEU cc_start: 0.4598 (OUTLIER) cc_final: 0.4163 (mp) REVERT: I 322 MET cc_start: 0.6782 (tpt) cc_final: 0.6251 (ptm) REVERT: I 569 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5934 (mp) REVERT: I 620 PHE cc_start: 0.6909 (m-80) cc_final: 0.6141 (t80) REVERT: J 133 CYS cc_start: 0.8244 (m) cc_final: 0.7729 (t) REVERT: J 192 LYS cc_start: 0.8522 (mttt) cc_final: 0.8230 (mmmt) REVERT: J 258 MET cc_start: 0.8004 (mmm) cc_final: 0.7731 (mmm) REVERT: J 311 MET cc_start: 0.7484 (mtp) cc_final: 0.7110 (ptp) REVERT: J 349 GLU cc_start: 0.8204 (mp0) cc_final: 0.7890 (tp30) REVERT: J 371 MET cc_start: 0.7889 (mmm) cc_final: 0.7456 (mmm) REVERT: J 395 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7979 (mm) REVERT: J 478 ASN cc_start: 0.7235 (m110) cc_final: 0.6888 (m110) REVERT: J 525 MET cc_start: 0.7944 (mmm) cc_final: 0.7510 (tpp) REVERT: K 13 TYR cc_start: 0.8862 (m-80) cc_final: 0.8622 (m-80) REVERT: K 64 LYS cc_start: 0.8869 (mttt) cc_final: 0.8592 (mmmt) REVERT: K 143 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8228 (mm) REVERT: K 160 ASP cc_start: 0.7030 (t0) cc_final: 0.6808 (t0) REVERT: K 258 MET cc_start: 0.6160 (mmp) cc_final: 0.5852 (mmp) REVERT: K 282 ASN cc_start: 0.7996 (m-40) cc_final: 0.7434 (p0) REVERT: K 327 THR cc_start: 0.6247 (t) cc_final: 0.5810 (p) REVERT: K 331 LYS cc_start: 0.6903 (mttm) cc_final: 0.6532 (tppt) REVERT: K 349 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5843 (mm-30) REVERT: K 364 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7190 (mtm) REVERT: K 367 CYS cc_start: 0.8746 (t) cc_final: 0.8122 (p) REVERT: K 430 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8794 (tp30) REVERT: K 482 TYR cc_start: 0.6108 (m-80) cc_final: 0.5712 (m-80) REVERT: L 12 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7664 (t0) REVERT: L 45 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7352 (mt) REVERT: L 101 ASN cc_start: 0.8572 (m-40) cc_final: 0.8371 (m110) REVERT: L 136 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7877 (ptm) REVERT: L 150 ASP cc_start: 0.5786 (m-30) cc_final: 0.5408 (m-30) REVERT: L 153 MET cc_start: 0.6139 (tmm) cc_final: 0.5586 (tmm) REVERT: L 163 GLU cc_start: 0.7927 (tt0) cc_final: 0.7465 (pm20) REVERT: L 178 MET cc_start: 0.8958 (mtm) cc_final: 0.8749 (mpp) REVERT: N 79 LEU cc_start: 0.8880 (pt) cc_final: 0.8539 (tp) REVERT: N 92 TRP cc_start: 0.6739 (OUTLIER) cc_final: 0.5704 (m-90) REVERT: N 172 MET cc_start: 0.8808 (mmm) cc_final: 0.8569 (mmm) REVERT: N 213 TYR cc_start: 0.8955 (t80) cc_final: 0.8558 (p90) REVERT: N 271 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8639 (pp20) REVERT: N 299 TRP cc_start: 0.6461 (OUTLIER) cc_final: 0.5169 (t-100) REVERT: N 373 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8765 (mp10) REVERT: N 515 PHE cc_start: 0.8339 (m-80) cc_final: 0.7520 (m-10) REVERT: N 543 GLU cc_start: 0.8483 (pt0) cc_final: 0.8131 (mm-30) REVERT: N 546 LYS cc_start: 0.8105 (tttt) cc_final: 0.7711 (tmtt) REVERT: N 584 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.6060 (tm-30) REVERT: N 670 PHE cc_start: -0.0470 (OUTLIER) cc_final: -0.1086 (t80) REVERT: N 727 MET cc_start: 0.0154 (tpt) cc_final: -0.0570 (mmm) REVERT: O 100 MET cc_start: 0.8739 (mtp) cc_final: 0.8443 (tpt) REVERT: O 150 GLN cc_start: 0.8799 (mt0) cc_final: 0.8466 (mm110) REVERT: O 256 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8080 (tm) REVERT: O 397 LYS cc_start: 0.7360 (mttm) cc_final: 0.6975 (mmmt) REVERT: O 437 MET cc_start: 0.7360 (mmm) cc_final: 0.6977 (tpp) REVERT: O 447 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8113 (p) REVERT: O 531 LEU cc_start: 0.8773 (tp) cc_final: 0.8510 (tp) REVERT: O 536 THR cc_start: 0.9362 (t) cc_final: 0.9089 (p) REVERT: O 579 MET cc_start: 0.8774 (mmm) cc_final: 0.8537 (mmm) REVERT: O 670 CYS cc_start: 0.9387 (t) cc_final: 0.9119 (t) REVERT: O 708 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7672 (mm-30) REVERT: O 754 HIS cc_start: 0.6443 (p-80) cc_final: 0.5541 (p-80) REVERT: P 297 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8293 (mp) REVERT: P 300 MET cc_start: 0.8221 (mmt) cc_final: 0.7866 (mmm) REVERT: P 378 MET cc_start: 0.8720 (mmm) cc_final: 0.8457 (mmm) REVERT: P 445 LYS cc_start: 0.8326 (mtpt) cc_final: 0.8114 (mmmt) REVERT: R 174 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7386 (mtp85) REVERT: R 222 MET cc_start: 0.3734 (ttt) cc_final: 0.3512 (ttt) REVERT: R 317 TRP cc_start: 0.3214 (m100) cc_final: 0.2979 (m100) REVERT: R 351 PHE cc_start: 0.2063 (m-80) cc_final: 0.1749 (m-80) REVERT: W 4 ARG cc_start: 0.7666 (tmm-80) cc_final: 0.7297 (ttp-110) REVERT: X 56 LEU cc_start: 0.9424 (tp) cc_final: 0.9040 (pp) REVERT: X 269 ASP cc_start: 0.7663 (m-30) cc_final: 0.7457 (p0) REVERT: X 347 CYS cc_start: 0.9018 (m) cc_final: 0.8735 (p) REVERT: X 388 ARG cc_start: 0.8626 (mmm160) cc_final: 0.8390 (mmm160) REVERT: X 409 CYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8705 (p) REVERT: X 423 ILE cc_start: 0.7951 (pt) cc_final: 0.7707 (mt) REVERT: X 475 TYR cc_start: 0.3981 (t80) cc_final: 0.3631 (t80) REVERT: Y 69 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8498 (tp30) REVERT: Y 99 LYS cc_start: 0.8506 (mmtt) cc_final: 0.8114 (mmmm) REVERT: Y 145 CYS cc_start: 0.7281 (m) cc_final: 0.6935 (t) REVERT: Y 173 MET cc_start: 0.7905 (ttp) cc_final: 0.7653 (tpp) REVERT: Y 222 MET cc_start: 0.9026 (tpt) cc_final: 0.8487 (mtt) REVERT: Y 300 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7623 (mm) REVERT: Y 301 ASP cc_start: 0.6933 (t0) cc_final: 0.6464 (t0) REVERT: Y 308 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8403 (mmm) outliers start: 335 outliers final: 229 residues processed: 1112 average time/residue: 0.5800 time to fit residues: 1125.9066 Evaluate side-chains 1045 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 774 time to evaluate : 5.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 785 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1316 MET Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1397 ASP Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1433 ILE Chi-restraints excluded: chain A residue 1498 TYR Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1606 LEU Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1666 ILE Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1688 LYS Chi-restraints excluded: chain A residue 1759 VAL Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1800 LEU Chi-restraints excluded: chain A residue 1814 ILE Chi-restraints excluded: chain A residue 1858 GLN Chi-restraints excluded: chain A residue 1893 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 429 ARG Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 455 CYS Chi-restraints excluded: chain C residue 522 LYS Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 530 ASN Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 628 ILE Chi-restraints excluded: chain F residue 721 SER Chi-restraints excluded: chain F residue 757 LEU Chi-restraints excluded: chain H residue 47 CYS Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 564 LYS Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 617 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 257 HIS Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 529 MET Chi-restraints excluded: chain I residue 564 ASP Chi-restraints excluded: chain I residue 569 LEU Chi-restraints excluded: chain I residue 609 GLN Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 289 HIS Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain J residue 485 ILE Chi-restraints excluded: chain J residue 513 THR Chi-restraints excluded: chain J residue 523 ILE Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 349 GLU Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 364 MET Chi-restraints excluded: chain K residue 510 ARG Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 19 TRP Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 53 GLN Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 245 GLN Chi-restraints excluded: chain N residue 271 GLU Chi-restraints excluded: chain N residue 299 TRP Chi-restraints excluded: chain N residue 364 CYS Chi-restraints excluded: chain N residue 373 GLN Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 501 ILE Chi-restraints excluded: chain N residue 517 ASN Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 556 PHE Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 626 TYR Chi-restraints excluded: chain N residue 640 THR Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 208 SER Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 350 LEU Chi-restraints excluded: chain O residue 356 ASP Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 436 THR Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain O residue 468 VAL Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 618 TYR Chi-restraints excluded: chain O residue 621 SER Chi-restraints excluded: chain O residue 632 LEU Chi-restraints excluded: chain O residue 634 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 708 GLU Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 297 ILE Chi-restraints excluded: chain P residue 302 THR Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 360 LEU Chi-restraints excluded: chain P residue 361 ASN Chi-restraints excluded: chain P residue 364 TYR Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 369 THR Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 455 CYS Chi-restraints excluded: chain R residue 87 GLN Chi-restraints excluded: chain R residue 116 TRP Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 326 SER Chi-restraints excluded: chain R residue 403 CYS Chi-restraints excluded: chain R residue 433 MET Chi-restraints excluded: chain R residue 450 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 16 ILE Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 199 CYS Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain X residue 402 LEU Chi-restraints excluded: chain X residue 409 CYS Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 445 THR Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 212 LEU Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 300 LEU Chi-restraints excluded: chain Y residue 308 MET Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 321 LEU Chi-restraints excluded: chain Y residue 324 VAL Chi-restraints excluded: chain Y residue 329 CYS Chi-restraints excluded: chain Y residue 350 PHE Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 476 ILE Chi-restraints excluded: chain Y residue 507 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 491 optimal weight: 1.9990 chunk 317 optimal weight: 3.9990 chunk 474 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 504 optimal weight: 7.9990 chunk 541 optimal weight: 0.0050 chunk 392 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 chunk 624 optimal weight: 3.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1591 HIS ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 257 HIS ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 HIS ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 367 GLN Y 232 ASN ** Y 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 505 ASN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 66864 Z= 0.205 Angle : 0.750 18.080 90576 Z= 0.373 Chirality : 0.042 0.349 10188 Planarity : 0.005 0.119 11506 Dihedral : 6.300 79.434 9120 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.12 % Favored : 94.30 % Rotamer: Outliers : 4.25 % Allowed : 27.04 % Favored : 68.70 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.43 % Twisted Proline : 0.66 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.09), residues: 8183 helix: 1.12 (0.07), residues: 5346 sheet: -0.60 (0.21), residues: 569 loop : -2.03 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP X 235 HIS 0.023 0.001 HIS L 103 PHE 0.040 0.002 PHE L 102 TYR 0.028 0.001 TYR X 417 ARG 0.008 0.000 ARG A1802 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 858 time to evaluate : 5.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.8126 (t-90) REVERT: A 37 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6227 (tt) REVERT: A 165 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8553 (tm-30) REVERT: A 167 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.7985 (mtpt) REVERT: A 250 ASN cc_start: 0.7276 (OUTLIER) cc_final: 0.6598 (t0) REVERT: A 1067 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7848 (tt0) REVERT: A 1118 VAL cc_start: 0.4218 (OUTLIER) cc_final: 0.3927 (p) REVERT: A 1268 HIS cc_start: 0.6369 (t-90) cc_final: 0.5972 (t-170) REVERT: A 1300 LEU cc_start: 0.7125 (mt) cc_final: 0.6790 (mt) REVERT: A 1304 MET cc_start: 0.7926 (mtm) cc_final: 0.7678 (mtm) REVERT: A 1317 SER cc_start: 0.7983 (m) cc_final: 0.7567 (p) REVERT: A 1329 MET cc_start: 0.8585 (ttm) cc_final: 0.8306 (tmm) REVERT: A 1498 TYR cc_start: 0.6662 (OUTLIER) cc_final: 0.6155 (m-80) REVERT: A 1527 MET cc_start: 0.8676 (ptm) cc_final: 0.7903 (ppp) REVERT: A 1606 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6259 (mm) REVERT: A 1609 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8592 (mp) REVERT: A 1623 ASP cc_start: 0.8517 (t0) cc_final: 0.8150 (t70) REVERT: A 1652 MET cc_start: 0.6928 (tpt) cc_final: 0.5802 (mpp) REVERT: A 1782 GLU cc_start: 0.6531 (mp0) cc_final: 0.6278 (tp30) REVERT: A 1850 CYS cc_start: 0.9531 (t) cc_final: 0.9233 (t) REVERT: A 1858 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8633 (pt0) REVERT: B 1 MET cc_start: 0.5379 (tpp) cc_final: 0.4981 (tpp) REVERT: C 218 MET cc_start: 0.8207 (ptp) cc_final: 0.7906 (pmm) REVERT: C 245 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8479 (pp20) REVERT: C 303 PHE cc_start: 0.7359 (t80) cc_final: 0.6935 (t80) REVERT: C 360 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8064 (mp) REVERT: C 436 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8400 (mm) REVERT: C 441 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8102 (pm20) REVERT: C 455 CYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8803 (t) REVERT: C 522 LYS cc_start: 0.6580 (OUTLIER) cc_final: 0.6261 (mttp) REVERT: C 557 ARG cc_start: 0.0650 (OUTLIER) cc_final: 0.0434 (ttm110) REVERT: D 47 LYS cc_start: 0.8517 (tmtt) cc_final: 0.7919 (tptt) REVERT: E 73 ASP cc_start: 0.8245 (m-30) cc_final: 0.8030 (p0) REVERT: E 100 GLU cc_start: 0.8266 (mp0) cc_final: 0.7977 (mm-30) REVERT: F 91 ILE cc_start: 0.9100 (mt) cc_final: 0.8818 (mt) REVERT: F 646 TYR cc_start: 0.7367 (t80) cc_final: 0.6903 (t80) REVERT: H 145 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7207 (t0) REVERT: H 564 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8485 (mtmm) REVERT: H 584 ASP cc_start: 0.6978 (p0) cc_final: 0.6759 (t0) REVERT: H 702 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.7923 (t0) REVERT: I 80 LEU cc_start: 0.7582 (mt) cc_final: 0.7223 (mm) REVERT: I 93 CYS cc_start: 0.7842 (t) cc_final: 0.7026 (p) REVERT: I 99 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8563 (tm-30) REVERT: I 309 LEU cc_start: 0.4579 (OUTLIER) cc_final: 0.4213 (mp) REVERT: I 322 MET cc_start: 0.7047 (tpt) cc_final: 0.6476 (ptm) REVERT: I 569 LEU cc_start: 0.6089 (OUTLIER) cc_final: 0.5862 (mp) REVERT: J 133 CYS cc_start: 0.8321 (m) cc_final: 0.7791 (t) REVERT: J 192 LYS cc_start: 0.8512 (mttt) cc_final: 0.8223 (mmmt) REVERT: J 258 MET cc_start: 0.7948 (mmm) cc_final: 0.7650 (mmm) REVERT: J 259 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8233 (tt0) REVERT: J 311 MET cc_start: 0.7478 (mtp) cc_final: 0.7049 (ptp) REVERT: J 322 TYR cc_start: 0.8629 (m-80) cc_final: 0.8334 (m-80) REVERT: J 349 GLU cc_start: 0.8141 (mp0) cc_final: 0.7713 (tt0) REVERT: J 395 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8090 (mm) REVERT: J 478 ASN cc_start: 0.7367 (m110) cc_final: 0.7021 (m110) REVERT: J 525 MET cc_start: 0.8039 (mmm) cc_final: 0.7623 (tpp) REVERT: K 13 TYR cc_start: 0.8864 (m-80) cc_final: 0.8614 (m-80) REVERT: K 64 LYS cc_start: 0.8815 (mttt) cc_final: 0.8508 (mmmt) REVERT: K 143 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8236 (mm) REVERT: K 258 MET cc_start: 0.6144 (mmp) cc_final: 0.5802 (mmp) REVERT: K 282 ASN cc_start: 0.7932 (m-40) cc_final: 0.7365 (p0) REVERT: K 327 THR cc_start: 0.6195 (OUTLIER) cc_final: 0.5882 (p) REVERT: K 331 LYS cc_start: 0.6881 (mttm) cc_final: 0.6495 (tppt) REVERT: K 364 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7263 (mtm) REVERT: K 367 CYS cc_start: 0.8711 (t) cc_final: 0.8092 (p) REVERT: K 430 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8810 (tp30) REVERT: K 482 TYR cc_start: 0.6099 (m-80) cc_final: 0.5731 (m-80) REVERT: K 512 ASP cc_start: 0.6415 (t70) cc_final: 0.6175 (t0) REVERT: L 12 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7462 (t0) REVERT: L 45 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7366 (mt) REVERT: L 109 ARG cc_start: 0.8286 (ttt90) cc_final: 0.7751 (ttm-80) REVERT: L 119 TRP cc_start: 0.6713 (m100) cc_final: 0.5287 (m100) REVERT: L 136 MET cc_start: 0.8508 (ttp) cc_final: 0.7872 (ptm) REVERT: L 150 ASP cc_start: 0.5666 (m-30) cc_final: 0.5326 (m-30) REVERT: L 153 MET cc_start: 0.6097 (tmm) cc_final: 0.5586 (tmm) REVERT: L 163 GLU cc_start: 0.7917 (tt0) cc_final: 0.7411 (pm20) REVERT: L 178 MET cc_start: 0.8958 (mtm) cc_final: 0.8708 (mpp) REVERT: N 74 TRP cc_start: 0.8067 (p-90) cc_final: 0.7383 (p-90) REVERT: N 79 LEU cc_start: 0.8819 (pt) cc_final: 0.8503 (tp) REVERT: N 92 TRP cc_start: 0.6743 (OUTLIER) cc_final: 0.5713 (m-90) REVERT: N 172 MET cc_start: 0.8751 (mmm) cc_final: 0.8513 (mmm) REVERT: N 213 TYR cc_start: 0.8927 (t80) cc_final: 0.8508 (p90) REVERT: N 271 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8551 (pp20) REVERT: N 287 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7357 (mmp80) REVERT: N 299 TRP cc_start: 0.6415 (OUTLIER) cc_final: 0.5139 (t-100) REVERT: N 366 GLU cc_start: 0.7899 (tp30) cc_final: 0.7444 (pt0) REVERT: N 373 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8764 (mp10) REVERT: N 392 ASN cc_start: 0.7320 (t0) cc_final: 0.6483 (m110) REVERT: N 422 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7603 (mm-30) REVERT: N 515 PHE cc_start: 0.8415 (m-80) cc_final: 0.7566 (m-10) REVERT: N 543 GLU cc_start: 0.8182 (pt0) cc_final: 0.7905 (mm-30) REVERT: N 546 LYS cc_start: 0.8270 (tttt) cc_final: 0.7911 (tmtt) REVERT: N 584 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.6063 (tm-30) REVERT: N 670 PHE cc_start: -0.0490 (OUTLIER) cc_final: -0.1101 (t80) REVERT: N 727 MET cc_start: 0.0178 (tpt) cc_final: -0.0544 (mmm) REVERT: O 100 MET cc_start: 0.8691 (mtp) cc_final: 0.8470 (tpt) REVERT: O 150 GLN cc_start: 0.8762 (mt0) cc_final: 0.8498 (mm110) REVERT: O 256 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8022 (tm) REVERT: O 397 LYS cc_start: 0.7347 (mttm) cc_final: 0.6979 (mmmt) REVERT: O 419 ASP cc_start: 0.9158 (m-30) cc_final: 0.8851 (p0) REVERT: O 447 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8107 (p) REVERT: O 531 LEU cc_start: 0.8727 (tp) cc_final: 0.8426 (tp) REVERT: O 579 MET cc_start: 0.8891 (mmm) cc_final: 0.8621 (mmm) REVERT: O 670 CYS cc_start: 0.9388 (t) cc_final: 0.9071 (t) REVERT: O 708 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7846 (mm-30) REVERT: O 754 HIS cc_start: 0.6561 (p-80) cc_final: 0.5488 (p-80) REVERT: P 297 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.8006 (mp) REVERT: P 300 MET cc_start: 0.8218 (mmt) cc_final: 0.7896 (mmm) REVERT: P 445 LYS cc_start: 0.8267 (mtpt) cc_final: 0.8020 (mmmm) REVERT: P 455 CYS cc_start: 0.6836 (m) cc_final: 0.5943 (t) REVERT: R 78 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7615 (tpt-90) REVERT: R 174 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.7402 (mtp85) REVERT: R 259 LYS cc_start: 0.4945 (tptt) cc_final: 0.4318 (ptmm) REVERT: R 317 TRP cc_start: 0.3197 (m100) cc_final: 0.2959 (m100) REVERT: R 351 PHE cc_start: 0.2400 (m-80) cc_final: 0.2097 (m-80) REVERT: W 4 ARG cc_start: 0.7697 (tmm-80) cc_final: 0.7354 (ttp-110) REVERT: X 269 ASP cc_start: 0.7627 (m-30) cc_final: 0.7415 (p0) REVERT: X 347 CYS cc_start: 0.9001 (m) cc_final: 0.8704 (p) REVERT: X 388 ARG cc_start: 0.8648 (mmm160) cc_final: 0.8392 (mmm160) REVERT: X 409 CYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8674 (p) REVERT: X 423 ILE cc_start: 0.7950 (pt) cc_final: 0.7710 (mt) REVERT: X 475 TYR cc_start: 0.3785 (t80) cc_final: 0.3477 (t80) REVERT: Y 69 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8433 (tp30) REVERT: Y 99 LYS cc_start: 0.8397 (mmtt) cc_final: 0.8028 (mmmm) REVERT: Y 173 MET cc_start: 0.7953 (ttp) cc_final: 0.7679 (tpp) REVERT: Y 222 MET cc_start: 0.8970 (tpt) cc_final: 0.8409 (mtt) REVERT: Y 292 LEU cc_start: 0.8502 (tt) cc_final: 0.8295 (mt) REVERT: Y 300 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7555 (mm) REVERT: Y 301 ASP cc_start: 0.6886 (t0) cc_final: 0.6548 (t0) REVERT: Y 308 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8439 (mmm) REVERT: Y 407 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.8005 (mp) outliers start: 292 outliers final: 200 residues processed: 1076 average time/residue: 0.6260 time to fit residues: 1175.8536 Evaluate side-chains 1027 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 784 time to evaluate : 5.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 785 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1316 MET Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1397 ASP Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1433 ILE Chi-restraints excluded: chain A residue 1498 TYR Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1606 LEU Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1800 LEU Chi-restraints excluded: chain A residue 1814 ILE Chi-restraints excluded: chain A residue 1858 GLN Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 429 ARG Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 455 CYS Chi-restraints excluded: chain C residue 522 LYS Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain H residue 47 CYS Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 564 LYS Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 617 LEU Chi-restraints excluded: chain H residue 644 ILE Chi-restraints excluded: chain H residue 702 ASN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 501 LEU Chi-restraints excluded: chain I residue 529 MET Chi-restraints excluded: chain I residue 569 LEU Chi-restraints excluded: chain I residue 609 GLN Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain J residue 485 ILE Chi-restraints excluded: chain J residue 513 THR Chi-restraints excluded: chain J residue 523 ILE Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 327 THR Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 364 MET Chi-restraints excluded: chain K residue 510 ARG Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 271 GLU Chi-restraints excluded: chain N residue 287 ARG Chi-restraints excluded: chain N residue 299 TRP Chi-restraints excluded: chain N residue 327 HIS Chi-restraints excluded: chain N residue 364 CYS Chi-restraints excluded: chain N residue 373 GLN Chi-restraints excluded: chain N residue 414 MET Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 501 ILE Chi-restraints excluded: chain N residue 517 ASN Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 626 TYR Chi-restraints excluded: chain N residue 640 THR Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 208 SER Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 217 SER Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 356 ASP Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 436 THR Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain O residue 468 VAL Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 621 SER Chi-restraints excluded: chain O residue 632 LEU Chi-restraints excluded: chain O residue 634 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 708 GLU Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 297 ILE Chi-restraints excluded: chain P residue 302 THR Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 360 LEU Chi-restraints excluded: chain P residue 361 ASN Chi-restraints excluded: chain P residue 364 TYR Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 116 TRP Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 326 SER Chi-restraints excluded: chain R residue 403 CYS Chi-restraints excluded: chain R residue 433 MET Chi-restraints excluded: chain R residue 450 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 199 CYS Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain X residue 402 LEU Chi-restraints excluded: chain X residue 409 CYS Chi-restraints excluded: chain X residue 445 THR Chi-restraints excluded: chain Y residue 212 LEU Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 300 LEU Chi-restraints excluded: chain Y residue 308 MET Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 324 VAL Chi-restraints excluded: chain Y residue 329 CYS Chi-restraints excluded: chain Y residue 350 PHE Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 407 LEU Chi-restraints excluded: chain Y residue 476 ILE Chi-restraints excluded: chain Y residue 507 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 722 optimal weight: 6.9990 chunk 760 optimal weight: 0.7980 chunk 694 optimal weight: 10.0000 chunk 740 optimal weight: 3.9990 chunk 445 optimal weight: 6.9990 chunk 322 optimal weight: 4.9990 chunk 581 optimal weight: 0.7980 chunk 227 optimal weight: 0.0070 chunk 668 optimal weight: 0.9990 chunk 699 optimal weight: 3.9990 chunk 737 optimal weight: 7.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 GLN ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 ASN A1351 GLN ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1558 HIS ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 145 ASN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 HIS ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 HIS ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 242 GLN ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS N 702 GLN ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 503 HIS ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN X 105 GLN ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 ASN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 296 GLN Y 505 ASN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 66864 Z= 0.221 Angle : 0.763 17.955 90576 Z= 0.379 Chirality : 0.042 0.329 10188 Planarity : 0.005 0.121 11506 Dihedral : 6.140 82.749 9102 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.97 % Favored : 94.46 % Rotamer: Outliers : 4.12 % Allowed : 27.23 % Favored : 68.65 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.43 % Twisted Proline : 0.66 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.09), residues: 8183 helix: 1.13 (0.07), residues: 5348 sheet: -0.56 (0.22), residues: 561 loop : -2.03 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP X 235 HIS 0.047 0.001 HIS N 327 PHE 0.039 0.002 PHE P 233 TYR 0.026 0.001 TYR X 417 ARG 0.010 0.000 ARG H 625 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 812 time to evaluate : 5.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6338 (tt) REVERT: A 165 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8553 (tm-30) REVERT: A 167 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.7997 (mtpt) REVERT: A 250 ASN cc_start: 0.7253 (OUTLIER) cc_final: 0.6638 (t0) REVERT: A 626 LYS cc_start: 0.7652 (mmmt) cc_final: 0.7338 (mmmt) REVERT: A 637 MET cc_start: 0.8739 (tmm) cc_final: 0.8380 (tmm) REVERT: A 667 MET cc_start: 0.8863 (tpp) cc_final: 0.8554 (mmm) REVERT: A 1067 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7945 (tt0) REVERT: A 1118 VAL cc_start: 0.4210 (OUTLIER) cc_final: 0.3949 (p) REVERT: A 1268 HIS cc_start: 0.6377 (t-90) cc_final: 0.6056 (t-170) REVERT: A 1317 SER cc_start: 0.7985 (m) cc_final: 0.7621 (p) REVERT: A 1329 MET cc_start: 0.8697 (ttm) cc_final: 0.8282 (tmm) REVERT: A 1527 MET cc_start: 0.8744 (ptm) cc_final: 0.8325 (ppp) REVERT: A 1606 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6235 (mm) REVERT: A 1609 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8590 (mp) REVERT: A 1623 ASP cc_start: 0.8495 (t0) cc_final: 0.8121 (t70) REVERT: A 1652 MET cc_start: 0.6967 (tpt) cc_final: 0.5827 (mpp) REVERT: A 1782 GLU cc_start: 0.6578 (mp0) cc_final: 0.5969 (mm-30) REVERT: A 1805 MET cc_start: 0.1317 (OUTLIER) cc_final: 0.1094 (mtt) REVERT: A 1850 CYS cc_start: 0.9540 (OUTLIER) cc_final: 0.9242 (t) REVERT: B 1 MET cc_start: 0.5389 (tpp) cc_final: 0.4982 (tpp) REVERT: C 245 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8494 (pp20) REVERT: C 303 PHE cc_start: 0.7353 (t80) cc_final: 0.7118 (t80) REVERT: C 360 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8045 (mp) REVERT: C 436 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8385 (mm) REVERT: C 441 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: C 455 CYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8834 (t) REVERT: C 466 GLU cc_start: 0.7943 (tm-30) cc_final: 0.6545 (mm-30) REVERT: C 522 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.6253 (mttp) REVERT: D 47 LYS cc_start: 0.8498 (tmtt) cc_final: 0.7911 (tptt) REVERT: E 73 ASP cc_start: 0.8125 (m-30) cc_final: 0.7908 (p0) REVERT: E 100 GLU cc_start: 0.8258 (mp0) cc_final: 0.7937 (mm-30) REVERT: F 584 ASP cc_start: 0.7759 (m-30) cc_final: 0.7328 (p0) REVERT: F 646 TYR cc_start: 0.7377 (t80) cc_final: 0.6908 (t80) REVERT: H 145 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.7132 (t0) REVERT: H 702 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.7733 (t0) REVERT: H 758 MET cc_start: 0.6868 (tpt) cc_final: 0.6595 (tpt) REVERT: I 80 LEU cc_start: 0.7500 (mt) cc_final: 0.7111 (mm) REVERT: I 93 CYS cc_start: 0.7674 (t) cc_final: 0.6947 (p) REVERT: I 99 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8567 (tm-30) REVERT: I 117 GLU cc_start: 0.8981 (pm20) cc_final: 0.8604 (tt0) REVERT: I 263 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7832 (mp10) REVERT: I 309 LEU cc_start: 0.4586 (OUTLIER) cc_final: 0.4293 (mp) REVERT: I 322 MET cc_start: 0.7053 (tpt) cc_final: 0.6529 (mtm) REVERT: I 569 LEU cc_start: 0.5881 (OUTLIER) cc_final: 0.5624 (mp) REVERT: I 601 LEU cc_start: 0.8820 (tp) cc_final: 0.8563 (pp) REVERT: I 620 PHE cc_start: 0.6287 (m-80) cc_final: 0.5578 (t80) REVERT: J 133 CYS cc_start: 0.8413 (m) cc_final: 0.7874 (t) REVERT: J 192 LYS cc_start: 0.8522 (mttt) cc_final: 0.8231 (mmmt) REVERT: J 258 MET cc_start: 0.7982 (mmm) cc_final: 0.7698 (mmm) REVERT: J 259 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8228 (tt0) REVERT: J 311 MET cc_start: 0.7473 (mtp) cc_final: 0.7034 (ptp) REVERT: J 354 MET cc_start: 0.9094 (mtt) cc_final: 0.8878 (mmm) REVERT: J 371 MET cc_start: 0.7790 (mmm) cc_final: 0.7314 (mmm) REVERT: J 395 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8098 (mm) REVERT: J 478 ASN cc_start: 0.7213 (m110) cc_final: 0.6852 (m110) REVERT: J 525 MET cc_start: 0.8049 (mmm) cc_final: 0.7630 (tpp) REVERT: K 13 TYR cc_start: 0.8866 (m-80) cc_final: 0.8608 (m-80) REVERT: K 64 LYS cc_start: 0.8822 (mttt) cc_final: 0.8535 (mmmt) REVERT: K 143 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8224 (mm) REVERT: K 258 MET cc_start: 0.6351 (mmp) cc_final: 0.5991 (mmp) REVERT: K 282 ASN cc_start: 0.7937 (m-40) cc_final: 0.7362 (p0) REVERT: K 327 THR cc_start: 0.6185 (OUTLIER) cc_final: 0.5783 (p) REVERT: K 331 LYS cc_start: 0.6986 (mttm) cc_final: 0.6597 (tppt) REVERT: K 349 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.5702 (mm-30) REVERT: K 354 MET cc_start: 0.8757 (mmm) cc_final: 0.8467 (ptt) REVERT: K 364 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7243 (mtm) REVERT: K 367 CYS cc_start: 0.8674 (t) cc_final: 0.8137 (p) REVERT: K 430 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8852 (tp30) REVERT: K 482 TYR cc_start: 0.6055 (m-80) cc_final: 0.5580 (m-80) REVERT: L 12 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7492 (t0) REVERT: L 45 LEU cc_start: 0.8124 (tt) cc_final: 0.7396 (mt) REVERT: L 109 ARG cc_start: 0.8210 (ttt90) cc_final: 0.7753 (mtp-110) REVERT: L 136 MET cc_start: 0.8604 (ttp) cc_final: 0.7974 (ptm) REVERT: L 150 ASP cc_start: 0.5776 (m-30) cc_final: 0.5265 (m-30) REVERT: L 153 MET cc_start: 0.6063 (tmm) cc_final: 0.5524 (tmm) REVERT: L 163 GLU cc_start: 0.7916 (tt0) cc_final: 0.7417 (pm20) REVERT: L 178 MET cc_start: 0.8955 (mtm) cc_final: 0.8708 (mpp) REVERT: M 21 GLU cc_start: 0.8812 (pm20) cc_final: 0.8591 (pm20) REVERT: N 79 LEU cc_start: 0.8825 (pt) cc_final: 0.8539 (tp) REVERT: N 92 TRP cc_start: 0.6801 (OUTLIER) cc_final: 0.5757 (m-90) REVERT: N 172 MET cc_start: 0.8767 (mmm) cc_final: 0.8537 (mmm) REVERT: N 287 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7356 (mmp80) REVERT: N 299 TRP cc_start: 0.6431 (OUTLIER) cc_final: 0.5031 (t-100) REVERT: N 366 GLU cc_start: 0.7803 (tp30) cc_final: 0.7370 (pt0) REVERT: N 392 ASN cc_start: 0.7416 (t0) cc_final: 0.6627 (m-40) REVERT: N 422 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7661 (mm-30) REVERT: N 515 PHE cc_start: 0.8405 (m-80) cc_final: 0.7578 (m-10) REVERT: N 543 GLU cc_start: 0.8151 (pt0) cc_final: 0.7846 (mm-30) REVERT: N 546 LYS cc_start: 0.8190 (tttt) cc_final: 0.7846 (tmtt) REVERT: N 584 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.6067 (tm-30) REVERT: N 670 PHE cc_start: -0.0596 (OUTLIER) cc_final: -0.1257 (t80) REVERT: N 727 MET cc_start: 0.0245 (tpt) cc_final: -0.0513 (mmm) REVERT: O 100 MET cc_start: 0.8689 (mtp) cc_final: 0.8470 (tpt) REVERT: O 150 GLN cc_start: 0.8756 (mt0) cc_final: 0.8510 (mm110) REVERT: O 256 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8001 (tm) REVERT: O 397 LYS cc_start: 0.7244 (mttm) cc_final: 0.6897 (mmmt) REVERT: O 419 ASP cc_start: 0.9164 (m-30) cc_final: 0.8859 (p0) REVERT: O 447 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8070 (p) REVERT: O 531 LEU cc_start: 0.8755 (tp) cc_final: 0.8474 (tp) REVERT: O 579 MET cc_start: 0.8770 (mmm) cc_final: 0.8500 (mmm) REVERT: O 603 MET cc_start: 0.7641 (mmm) cc_final: 0.7261 (mtt) REVERT: O 670 CYS cc_start: 0.9384 (t) cc_final: 0.9115 (t) REVERT: O 708 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7842 (mm-30) REVERT: O 754 HIS cc_start: 0.6527 (p-80) cc_final: 0.5453 (p-80) REVERT: P 297 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7878 (mp) REVERT: P 300 MET cc_start: 0.8182 (mmt) cc_final: 0.7823 (mmm) REVERT: R 78 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7323 (tpt-90) REVERT: R 174 ARG cc_start: 0.8036 (mtm-85) cc_final: 0.7421 (mtp85) REVERT: R 222 MET cc_start: 0.4328 (ttt) cc_final: 0.4021 (ttt) REVERT: R 259 LYS cc_start: 0.4951 (tptt) cc_final: 0.4347 (ptmm) REVERT: R 277 ASN cc_start: 0.1677 (t0) cc_final: 0.1113 (p0) REVERT: R 317 TRP cc_start: 0.3218 (m100) cc_final: 0.2442 (m100) REVERT: R 351 PHE cc_start: 0.2132 (m-80) cc_final: 0.1840 (m-80) REVERT: R 355 GLN cc_start: 0.7549 (mm110) cc_final: 0.7245 (mp10) REVERT: X 269 ASP cc_start: 0.7741 (m-30) cc_final: 0.7516 (p0) REVERT: X 347 CYS cc_start: 0.8977 (m) cc_final: 0.8698 (p) REVERT: X 388 ARG cc_start: 0.8527 (mmm160) cc_final: 0.8306 (mmm160) REVERT: X 409 CYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8660 (p) REVERT: X 423 ILE cc_start: 0.7981 (pt) cc_final: 0.7755 (mt) REVERT: X 475 TYR cc_start: 0.3771 (t80) cc_final: 0.3481 (t80) REVERT: Y 69 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8475 (tp30) REVERT: Y 99 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8005 (mmmm) REVERT: Y 149 LEU cc_start: 0.8381 (mt) cc_final: 0.8163 (mp) REVERT: Y 173 MET cc_start: 0.7996 (ttp) cc_final: 0.7761 (tpp) REVERT: Y 222 MET cc_start: 0.8984 (tpt) cc_final: 0.8412 (mtt) REVERT: Y 292 LEU cc_start: 0.8480 (tt) cc_final: 0.8269 (mt) REVERT: Y 294 PHE cc_start: 0.7738 (t80) cc_final: 0.7483 (t80) REVERT: Y 300 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7560 (mm) REVERT: Y 373 VAL cc_start: 0.8087 (OUTLIER) cc_final: 0.7819 (p) outliers start: 283 outliers final: 201 residues processed: 1024 average time/residue: 0.5841 time to fit residues: 1039.5727 Evaluate side-chains 1000 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 761 time to evaluate : 5.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 663 CYS Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 785 SER Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1019 MET Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1316 MET Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1397 ASP Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1433 ILE Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1606 LEU Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1800 LEU Chi-restraints excluded: chain A residue 1805 MET Chi-restraints excluded: chain A residue 1814 ILE Chi-restraints excluded: chain A residue 1850 CYS Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 115 TYR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 203 TRP Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 429 ARG Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 455 CYS Chi-restraints excluded: chain C residue 522 LYS Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 721 SER Chi-restraints excluded: chain H residue 47 CYS Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 617 LEU Chi-restraints excluded: chain H residue 644 ILE Chi-restraints excluded: chain H residue 702 ASN Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 263 GLN Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 359 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 501 LEU Chi-restraints excluded: chain I residue 529 MET Chi-restraints excluded: chain I residue 569 LEU Chi-restraints excluded: chain I residue 609 GLN Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 289 HIS Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain J residue 485 ILE Chi-restraints excluded: chain J residue 513 THR Chi-restraints excluded: chain J residue 523 ILE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 327 THR Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 349 GLU Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 364 MET Chi-restraints excluded: chain K residue 510 ARG Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 287 ARG Chi-restraints excluded: chain N residue 299 TRP Chi-restraints excluded: chain N residue 327 HIS Chi-restraints excluded: chain N residue 364 CYS Chi-restraints excluded: chain N residue 394 CYS Chi-restraints excluded: chain N residue 414 MET Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 501 ILE Chi-restraints excluded: chain N residue 517 ASN Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 626 TYR Chi-restraints excluded: chain N residue 640 THR Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 208 SER Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 217 SER Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 350 LEU Chi-restraints excluded: chain O residue 356 ASP Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 436 THR Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 621 SER Chi-restraints excluded: chain O residue 632 LEU Chi-restraints excluded: chain O residue 634 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 708 GLU Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 297 ILE Chi-restraints excluded: chain P residue 302 THR Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 360 LEU Chi-restraints excluded: chain P residue 364 TYR Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 455 CYS Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 87 GLN Chi-restraints excluded: chain R residue 116 TRP Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 326 SER Chi-restraints excluded: chain R residue 403 CYS Chi-restraints excluded: chain R residue 433 MET Chi-restraints excluded: chain R residue 450 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 199 CYS Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain X residue 373 VAL Chi-restraints excluded: chain X residue 402 LEU Chi-restraints excluded: chain X residue 409 CYS Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 445 THR Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 212 LEU Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 296 GLN Chi-restraints excluded: chain Y residue 300 LEU Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 324 VAL Chi-restraints excluded: chain Y residue 329 CYS Chi-restraints excluded: chain Y residue 350 PHE Chi-restraints excluded: chain Y residue 373 VAL Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 476 ILE Chi-restraints excluded: chain Y residue 505 ASN Chi-restraints excluded: chain Y residue 507 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 485 optimal weight: 2.9990 chunk 782 optimal weight: 5.9990 chunk 477 optimal weight: 3.9990 chunk 371 optimal weight: 30.0000 chunk 544 optimal weight: 20.0000 chunk 820 optimal weight: 2.9990 chunk 755 optimal weight: 0.9980 chunk 653 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 504 optimal weight: 2.9990 chunk 400 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 GLN A 426 GLN ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 ASN ** F 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 HIS ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 GLN ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 541 ASN ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 531 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 296 GLN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.6380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 66864 Z= 0.271 Angle : 0.791 17.864 90576 Z= 0.396 Chirality : 0.043 0.309 10188 Planarity : 0.005 0.123 11506 Dihedral : 6.165 87.380 9097 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.43 % Favored : 94.03 % Rotamer: Outliers : 3.80 % Allowed : 27.89 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.43 % Twisted Proline : 0.66 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.09), residues: 8183 helix: 1.09 (0.07), residues: 5354 sheet: -0.56 (0.22), residues: 562 loop : -2.02 (0.13), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP C 54 HIS 0.030 0.001 HIS N 327 PHE 0.043 0.002 PHE P 233 TYR 0.034 0.002 TYR X 360 ARG 0.009 0.001 ARG P 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16366 Ramachandran restraints generated. 8183 Oldfield, 0 Emsley, 8183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 769 time to evaluate : 5.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6315 (tt) REVERT: A 165 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8571 (tm-30) REVERT: A 167 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8113 (mtpt) REVERT: A 250 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.6819 (t0) REVERT: A 667 MET cc_start: 0.8765 (tpp) cc_final: 0.8505 (mmm) REVERT: A 808 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7700 (ttt90) REVERT: A 1268 HIS cc_start: 0.6361 (t-90) cc_final: 0.6043 (t-170) REVERT: A 1317 SER cc_start: 0.8097 (m) cc_final: 0.7732 (p) REVERT: A 1329 MET cc_start: 0.8632 (ttm) cc_final: 0.8221 (tmm) REVERT: A 1527 MET cc_start: 0.8743 (ptm) cc_final: 0.7975 (ppp) REVERT: A 1606 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.5568 (tp) REVERT: A 1609 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8663 (mp) REVERT: A 1623 ASP cc_start: 0.8466 (t0) cc_final: 0.8091 (t70) REVERT: A 1652 MET cc_start: 0.7004 (tpt) cc_final: 0.5864 (mpp) REVERT: A 1782 GLU cc_start: 0.6502 (mp0) cc_final: 0.6156 (tp30) REVERT: A 1805 MET cc_start: 0.1343 (OUTLIER) cc_final: 0.1139 (mtt) REVERT: A 1850 CYS cc_start: 0.9552 (OUTLIER) cc_final: 0.9255 (t) REVERT: B 1 MET cc_start: 0.5406 (tpp) cc_final: 0.4999 (tpp) REVERT: C 245 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8500 (pp20) REVERT: C 303 PHE cc_start: 0.7428 (t80) cc_final: 0.7179 (t80) REVERT: C 360 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8060 (mp) REVERT: C 436 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8480 (mm) REVERT: C 441 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8140 (pm20) REVERT: C 455 CYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8649 (t) REVERT: C 466 GLU cc_start: 0.8088 (tm-30) cc_final: 0.6599 (mm-30) REVERT: C 522 LYS cc_start: 0.6317 (OUTLIER) cc_final: 0.6043 (mttp) REVERT: D 47 LYS cc_start: 0.8524 (tmtt) cc_final: 0.7921 (tptt) REVERT: E 100 GLU cc_start: 0.8083 (mp0) cc_final: 0.7764 (mm-30) REVERT: F 584 ASP cc_start: 0.7761 (m-30) cc_final: 0.7355 (p0) REVERT: F 646 TYR cc_start: 0.7378 (t80) cc_final: 0.6922 (t80) REVERT: H 145 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7207 (t0) REVERT: H 655 GLU cc_start: 0.8319 (tp30) cc_final: 0.7924 (mm-30) REVERT: H 660 LYS cc_start: 0.8695 (mtmt) cc_final: 0.8484 (tptt) REVERT: H 702 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.7831 (t0) REVERT: I 80 LEU cc_start: 0.7646 (mt) cc_final: 0.7279 (mm) REVERT: I 93 CYS cc_start: 0.7568 (t) cc_final: 0.6879 (p) REVERT: I 99 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8567 (tm-30) REVERT: I 117 GLU cc_start: 0.8961 (pm20) cc_final: 0.8587 (tt0) REVERT: I 263 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7833 (mp10) REVERT: I 309 LEU cc_start: 0.4661 (OUTLIER) cc_final: 0.4378 (mp) REVERT: I 322 MET cc_start: 0.7070 (tpt) cc_final: 0.6492 (ptm) REVERT: I 569 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5691 (mp) REVERT: I 601 LEU cc_start: 0.8826 (tp) cc_final: 0.8547 (pp) REVERT: J 133 CYS cc_start: 0.8264 (m) cc_final: 0.7714 (t) REVERT: J 192 LYS cc_start: 0.8524 (mttt) cc_final: 0.8246 (mmmt) REVERT: J 258 MET cc_start: 0.7992 (mmm) cc_final: 0.7731 (mmm) REVERT: J 259 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8236 (tt0) REVERT: J 311 MET cc_start: 0.7561 (mtp) cc_final: 0.7140 (ptp) REVERT: J 354 MET cc_start: 0.9095 (mtt) cc_final: 0.8892 (mmt) REVERT: J 371 MET cc_start: 0.7871 (mmm) cc_final: 0.7510 (mmm) REVERT: J 395 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8138 (mm) REVERT: J 478 ASN cc_start: 0.7254 (m110) cc_final: 0.6887 (m110) REVERT: J 525 MET cc_start: 0.8059 (mmm) cc_final: 0.7643 (tpp) REVERT: K 13 TYR cc_start: 0.8878 (m-80) cc_final: 0.8617 (m-80) REVERT: K 64 LYS cc_start: 0.8800 (mttt) cc_final: 0.8507 (mmmt) REVERT: K 143 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8225 (mm) REVERT: K 258 MET cc_start: 0.6502 (mmp) cc_final: 0.6188 (mmp) REVERT: K 282 ASN cc_start: 0.7928 (m-40) cc_final: 0.7360 (p0) REVERT: K 327 THR cc_start: 0.5987 (t) cc_final: 0.5565 (p) REVERT: K 331 LYS cc_start: 0.6861 (mttm) cc_final: 0.6500 (tppt) REVERT: K 349 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5668 (mm-30) REVERT: K 364 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7217 (mtm) REVERT: K 367 CYS cc_start: 0.8565 (t) cc_final: 0.8062 (p) REVERT: K 430 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8867 (tp30) REVERT: K 482 TYR cc_start: 0.6198 (m-80) cc_final: 0.5743 (m-80) REVERT: L 12 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7572 (t0) REVERT: L 45 LEU cc_start: 0.7874 (tt) cc_final: 0.7417 (tp) REVERT: L 103 HIS cc_start: 0.7470 (OUTLIER) cc_final: 0.7162 (p90) REVERT: L 136 MET cc_start: 0.8616 (ttp) cc_final: 0.7912 (ptm) REVERT: L 150 ASP cc_start: 0.5835 (m-30) cc_final: 0.5478 (m-30) REVERT: L 153 MET cc_start: 0.6109 (tmm) cc_final: 0.5704 (tmm) REVERT: L 163 GLU cc_start: 0.7925 (tt0) cc_final: 0.7421 (pm20) REVERT: L 178 MET cc_start: 0.9028 (mtm) cc_final: 0.8819 (mtt) REVERT: N 79 LEU cc_start: 0.8866 (pt) cc_final: 0.8604 (tp) REVERT: N 92 TRP cc_start: 0.6856 (OUTLIER) cc_final: 0.5849 (m-90) REVERT: N 172 MET cc_start: 0.8798 (mmm) cc_final: 0.8563 (mmm) REVERT: N 213 TYR cc_start: 0.8660 (t80) cc_final: 0.8337 (p90) REVERT: N 299 TRP cc_start: 0.6392 (OUTLIER) cc_final: 0.4997 (t-100) REVERT: N 392 ASN cc_start: 0.7318 (t0) cc_final: 0.6612 (m-40) REVERT: N 422 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7608 (mm-30) REVERT: N 515 PHE cc_start: 0.8353 (m-80) cc_final: 0.7530 (m-10) REVERT: N 543 GLU cc_start: 0.8209 (pt0) cc_final: 0.7911 (mm-30) REVERT: N 546 LYS cc_start: 0.8172 (tttt) cc_final: 0.7845 (tmtt) REVERT: N 584 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.6096 (tm-30) REVERT: N 670 PHE cc_start: -0.0825 (OUTLIER) cc_final: -0.1406 (t80) REVERT: N 727 MET cc_start: 0.0227 (tpt) cc_final: -0.0519 (mmm) REVERT: O 100 MET cc_start: 0.8698 (mtp) cc_final: 0.8462 (tpt) REVERT: O 150 GLN cc_start: 0.8711 (mt0) cc_final: 0.8464 (mm110) REVERT: O 256 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8023 (tm) REVERT: O 397 LYS cc_start: 0.7265 (mttm) cc_final: 0.6896 (mmmt) REVERT: O 447 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8337 (p) REVERT: O 531 LEU cc_start: 0.8814 (tp) cc_final: 0.8537 (tp) REVERT: O 579 MET cc_start: 0.8704 (mmm) cc_final: 0.8391 (mmm) REVERT: O 603 MET cc_start: 0.7634 (mmm) cc_final: 0.7248 (mtt) REVERT: O 670 CYS cc_start: 0.9378 (t) cc_final: 0.9108 (t) REVERT: O 708 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7882 (mm-30) REVERT: O 754 HIS cc_start: 0.6510 (p-80) cc_final: 0.5523 (p-80) REVERT: P 300 MET cc_start: 0.8199 (mmt) cc_final: 0.7861 (mmm) REVERT: R 78 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7459 (tpt-90) REVERT: R 174 ARG cc_start: 0.8075 (mtm-85) cc_final: 0.7463 (mtp85) REVERT: R 222 MET cc_start: 0.4194 (ttt) cc_final: 0.3915 (ttt) REVERT: R 259 LYS cc_start: 0.4862 (tptt) cc_final: 0.4228 (ptmm) REVERT: R 277 ASN cc_start: 0.1702 (t0) cc_final: 0.1105 (p0) REVERT: R 317 TRP cc_start: 0.3218 (m100) cc_final: 0.2456 (m100) REVERT: R 351 PHE cc_start: 0.1972 (m-80) cc_final: 0.1660 (m-80) REVERT: R 355 GLN cc_start: 0.7558 (mm110) cc_final: 0.7249 (mp10) REVERT: R 403 CYS cc_start: 0.3523 (OUTLIER) cc_final: 0.1752 (t) REVERT: W 4 ARG cc_start: 0.7711 (tmm-80) cc_final: 0.7459 (tmm-80) REVERT: X 269 ASP cc_start: 0.7788 (m-30) cc_final: 0.7519 (p0) REVERT: X 347 CYS cc_start: 0.8960 (m) cc_final: 0.8655 (p) REVERT: X 388 ARG cc_start: 0.8572 (mmm160) cc_final: 0.8364 (mmm160) REVERT: X 409 CYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8648 (p) REVERT: X 423 ILE cc_start: 0.7999 (pt) cc_final: 0.7788 (mt) REVERT: X 459 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6850 (pm20) REVERT: X 475 TYR cc_start: 0.3952 (t80) cc_final: 0.3620 (t80) REVERT: Y 69 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8481 (tp30) REVERT: Y 99 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8021 (mmmm) REVERT: Y 145 CYS cc_start: 0.7543 (m) cc_final: 0.7160 (t) REVERT: Y 173 MET cc_start: 0.8085 (ttp) cc_final: 0.7747 (tpp) REVERT: Y 222 MET cc_start: 0.8974 (tpt) cc_final: 0.8373 (mtt) REVERT: Y 292 LEU cc_start: 0.8589 (tt) cc_final: 0.8275 (mt) REVERT: Y 300 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7551 (mm) REVERT: Y 301 ASP cc_start: 0.7031 (t0) cc_final: 0.6769 (t0) outliers start: 261 outliers final: 194 residues processed: 969 average time/residue: 0.5735 time to fit residues: 971.4904 Evaluate side-chains 979 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 749 time to evaluate : 5.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 808 ARG Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1316 MET Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1397 ASP Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1433 ILE Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1606 LEU Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1674 TRP Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1800 LEU Chi-restraints excluded: chain A residue 1805 MET Chi-restraints excluded: chain A residue 1814 ILE Chi-restraints excluded: chain A residue 1850 CYS Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 115 TYR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 429 ARG Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 455 CYS Chi-restraints excluded: chain C residue 522 LYS Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 721 SER Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 594 ILE Chi-restraints excluded: chain H residue 617 LEU Chi-restraints excluded: chain H residue 702 ASN Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 263 GLN Chi-restraints excluded: chain I residue 265 ILE Chi-restraints excluded: chain I residue 280 LEU Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 372 TRP Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 501 LEU Chi-restraints excluded: chain I residue 529 MET Chi-restraints excluded: chain I residue 569 LEU Chi-restraints excluded: chain I residue 609 GLN Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 289 HIS Chi-restraints excluded: chain J residue 395 LEU Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain J residue 485 ILE Chi-restraints excluded: chain J residue 513 THR Chi-restraints excluded: chain J residue 523 ILE Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 288 SER Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 349 GLU Chi-restraints excluded: chain K residue 358 PHE Chi-restraints excluded: chain K residue 364 MET Chi-restraints excluded: chain K residue 510 ARG Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 162 PHE Chi-restraints excluded: chain N residue 239 GLN Chi-restraints excluded: chain N residue 299 TRP Chi-restraints excluded: chain N residue 346 SER Chi-restraints excluded: chain N residue 364 CYS Chi-restraints excluded: chain N residue 394 CYS Chi-restraints excluded: chain N residue 414 MET Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 501 ILE Chi-restraints excluded: chain N residue 517 ASN Chi-restraints excluded: chain N residue 584 GLU Chi-restraints excluded: chain N residue 626 TYR Chi-restraints excluded: chain N residue 640 THR Chi-restraints excluded: chain N residue 670 PHE Chi-restraints excluded: chain N residue 685 VAL Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 129 THR Chi-restraints excluded: chain O residue 208 SER Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 217 SER Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 350 LEU Chi-restraints excluded: chain O residue 356 ASP Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 436 THR Chi-restraints excluded: chain O residue 447 SER Chi-restraints excluded: chain O residue 581 ILE Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 621 SER Chi-restraints excluded: chain O residue 632 LEU Chi-restraints excluded: chain O residue 634 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 694 LEU Chi-restraints excluded: chain O residue 708 GLU Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 154 LEU Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 286 PHE Chi-restraints excluded: chain P residue 302 THR Chi-restraints excluded: chain P residue 335 CYS Chi-restraints excluded: chain P residue 364 TYR Chi-restraints excluded: chain P residue 365 LEU Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 450 VAL Chi-restraints excluded: chain P residue 455 CYS Chi-restraints excluded: chain R residue 78 ARG Chi-restraints excluded: chain R residue 116 TRP Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 326 SER Chi-restraints excluded: chain R residue 403 CYS Chi-restraints excluded: chain R residue 433 MET Chi-restraints excluded: chain R residue 450 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain X residue 168 THR Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 199 CYS Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain X residue 373 VAL Chi-restraints excluded: chain X residue 402 LEU Chi-restraints excluded: chain X residue 409 CYS Chi-restraints excluded: chain X residue 445 THR Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 212 LEU Chi-restraints excluded: chain Y residue 230 VAL Chi-restraints excluded: chain Y residue 277 LEU Chi-restraints excluded: chain Y residue 296 GLN Chi-restraints excluded: chain Y residue 300 LEU Chi-restraints excluded: chain Y residue 314 LEU Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain Y residue 324 VAL Chi-restraints excluded: chain Y residue 329 CYS Chi-restraints excluded: chain Y residue 350 PHE Chi-restraints excluded: chain Y residue 373 VAL Chi-restraints excluded: chain Y residue 389 VAL Chi-restraints excluded: chain Y residue 476 ILE Chi-restraints excluded: chain Y residue 507 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 519 optimal weight: 1.9990 chunk 696 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 602 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 654 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 chunk 672 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 GLN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1558 HIS ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 HIS ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.096900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.078277 restraints weight = 324337.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.079529 restraints weight = 186700.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.079595 restraints weight = 119797.125| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.6402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.318 66864 Z= 0.377 Angle : 0.852 59.200 90576 Z= 0.441 Chirality : 0.045 0.790 10188 Planarity : 0.005 0.142 11506 Dihedral : 6.152 87.412 9095 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.45 % Favored : 94.02 % Rotamer: Outliers : 3.57 % Allowed : 28.02 % Favored : 68.41 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.43 % Twisted Proline : 0.66 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.09), residues: 8183 helix: 1.10 (0.07), residues: 5354 sheet: -0.56 (0.22), residues: 562 loop : -2.02 (0.13), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.159 0.003 TRP X 342 HIS 0.026 0.001 HIS N 327 PHE 0.037 0.002 PHE Y 294 TYR 0.134 0.002 TYR A1287 ARG 0.025 0.001 ARG N 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19703.35 seconds wall clock time: 339 minutes 49.09 seconds (20389.09 seconds total)