Starting phenix.real_space_refine (version: dev) on Tue Dec 13 04:47:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g04_3385/12_2022/5g04_3385_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g04_3385/12_2022/5g04_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_3385/12_2022/5g04_3385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g04_3385/12_2022/5g04_3385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g04_3385/12_2022/5g04_3385_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5g04_3385/12_2022/5g04_3385_neut.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 1631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 126": "OD1" <-> "OD2" Residue "O TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 28.56, per 1000 atoms: 0.44 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 - 3.50 Amino acid : False - 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: 21.79 Conformation dependent library (CDL) restraints added in 7.6 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: 3.24 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: 27.23 Time building geometry restraints manager: 23.85 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: 85.99 - 96.38: 9 96.38 - 106.78: 2216 106.78 - 117.18: 46930 117.18 - 127.58: 40632 127.58 - 137.98: 789 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 2.520 nonbonded pdb=" O THR A1225 " pdb=" N SER A1229 " model vdw 1.957 2.520 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 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 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. 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 9.330 Check model and map are aligned: 0.770 Convert atoms to be neutral: 0.440 Process input model: 150.800 Find NCS groups from input model: 2.810 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 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 : 1.881 36.334 90576 Z= 1.208 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 : 17.81 Ramachandran Plot: Outliers : 2.24 % Allowed : 6.26 % Favored : 91.50 % Rotamer Outliers : 13.63 % 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 *********************** 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 : 6.091 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 outliers start: 938 outliers final: 220 residues processed: 2629 average time/residue: 0.6368 time to fit residues: 2775.4915 Evaluate side-chains 1257 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1037 time to evaluate : 6.070 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 220 outliers final: 3 residues processed: 220 average time/residue: 0.5352 time to fit residues: 218.0714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 695 optimal weight: 4.9990 chunk 624 optimal weight: 0.8980 chunk 346 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 421 optimal weight: 0.9980 chunk 333 optimal weight: 5.9990 chunk 645 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 392 optimal weight: 0.9990 chunk 480 optimal weight: 6.9990 chunk 748 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 242 HIS A 263 GLN A 266 HIS A 643 ASN A 658 ASN A 666 ASN ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 ASN A1020 ASN A1021 HIS A1124 ASN ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1351 GLN ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 305 ASN C 373 HIS C 386 GLN C 407 GLN D 37 HIS D 49 ASN F 100 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 323 ASN I 351 HIS I 471 ASN I 535 GLN J 45 GLN J 80 HIS J 207 ASN J 228 GLN ** J 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 271 HIS J 316 ASN J 342 HIS J 350 HIS J 362 GLN J 449 ASN J 453 HIS ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 503 HIS K 16 GLN K 17 GLN K 20 GLN K 52 GLN ** K 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 198 GLN ** K 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 282 ASN ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 GLN ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 HIS ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN N 174 GLN N 186 GLN N 266 HIS ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS N 373 GLN N 388 HIS N 571 ASN N 663 GLN N 702 GLN N 726 ASN O 62 GLN O 138 HIS ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 242 ASN O 247 ASN O 319 GLN ** 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 717 GLN O 722 HIS O 754 HIS ** P 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 HIS ** P 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 287 ASN P 305 ASN P 347 HIS P 361 ASN R 87 GLN R 99 ASN ** R 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 369 ASN R 410 HIS X 50 HIS X 151 GLN X 298 GLN X 367 GLN X 374 GLN ** Y 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 298 GLN Y 385 ASN Y 395 HIS Y 471 GLN Y 490 GLN Y 505 ASN Y 531 GLN Total number of N/Q/H flips: 98 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.122 66864 Z= 0.299 Angle : 0.937 26.805 90576 Z= 0.469 Chirality : 0.047 0.260 10188 Planarity : 0.006 0.129 11506 Dihedral : 6.024 54.517 9018 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.94 % Allowed : 4.75 % Favored : 94.31 % Rotamer Outliers : 5.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.45 % Twisted Proline : 0.99 % Twisted General : 0.05 % 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: -0.58 (0.09), residues: 8183 helix: 0.49 (0.07), residues: 5335 sheet: -0.61 (0.22), residues: 516 loop : -2.29 (0.12), residues: 2332 *********************** 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 1544 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1166 time to evaluate : 6.225 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 outliers start: 378 outliers final: 143 residues processed: 1456 average time/residue: 0.5897 time to fit residues: 1469.8802 Evaluate side-chains 985 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 842 time to evaluate : 6.144 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 143 outliers final: 1 residues processed: 143 average time/residue: 0.4907 time to fit residues: 137.9866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 622 optimal weight: 7.9990 chunk 509 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 749 optimal weight: 9.9990 chunk 809 optimal weight: 8.9990 chunk 667 optimal weight: 4.9990 chunk 743 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 601 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 162 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 HIS ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 ASN ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1268 HIS ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1558 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** ** A1892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 ASN B 53 HIS ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 GLN C 495 GLN F 100 GLN ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 517 GLN F 599 ASN ** F 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 HIS H 545 HIS H 583 HIS H 599 ASN H 609 HIS ** H 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 HIS ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 696 GLN ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 289 HIS J 318 HIS ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 HIS K 271 HIS K 414 GLN ** L 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 174 GLN N 245 GLN ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS ** N 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 702 GLN N 726 ASN O 110 GLN O 159 GLN ** O 219 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 693 ASN P 50 HIS ** P 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 346 GLN P 427 GLN P 448 GLN P 477 HIS P 485 GLN R 218 GLN R 323 HIS ** X 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 89 HIS X 105 GLN X 338 HIS X 421 ASN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 296 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.084 66864 Z= 0.388 Angle : 0.891 27.099 90576 Z= 0.447 Chirality : 0.046 0.255 10188 Planarity : 0.006 0.123 11506 Dihedral : 5.779 55.757 9018 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.75 % Allowed : 5.65 % Favored : 93.60 % Rotamer Outliers : 4.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.47 % Twisted Proline : 0.99 % Twisted General : 0.04 % 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: -0.41 (0.09), residues: 8183 helix: 0.58 (0.07), residues: 5343 sheet: -0.75 (0.22), residues: 544 loop : -2.10 (0.13), residues: 2296 *********************** 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 1200 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 866 time to evaluate : 6.274 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 outliers start: 334 outliers final: 141 residues processed: 1117 average time/residue: 0.5950 time to fit residues: 1155.1806 Evaluate side-chains 861 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 720 time to evaluate : 6.148 Switching outliers to nearest non-outliers outliers start: 141 outliers final: 0 residues processed: 141 average time/residue: 0.5003 time to fit residues: 140.3810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 740 optimal weight: 0.9980 chunk 563 optimal weight: 20.0000 chunk 389 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 357 optimal weight: 5.9990 chunk 503 optimal weight: 0.9990 chunk 752 optimal weight: 0.9980 chunk 796 optimal weight: 5.9990 chunk 393 optimal weight: 0.7980 chunk 713 optimal weight: 5.9990 chunk 214 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1379 ASN A1537 GLN A1558 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** C 292 GLN C 305 ASN ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN F 100 GLN ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 679 GLN ** H 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 455 HIS ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 264 HIS J 352 GLN ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 HIS K 497 ASN ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN N 174 GLN ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 639 HIS ** O 219 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 ** O 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 211 ASN X 66 ASN X 75 GLN X 105 GLN X 367 GLN X 421 ASN ** Y 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 66864 Z= 0.223 Angle : 0.789 27.127 90576 Z= 0.386 Chirality : 0.042 0.282 10188 Planarity : 0.005 0.116 11506 Dihedral : 5.419 52.527 9018 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.00 % Favored : 94.31 % Rotamer Outliers : 2.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.47 % Twisted Proline : 0.99 % Twisted General : 0.04 % 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: -0.04 (0.09), residues: 8183 helix: 0.89 (0.07), residues: 5359 sheet: -0.69 (0.22), residues: 562 loop : -2.03 (0.13), residues: 2262 *********************** 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 1082 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 899 time to evaluate : 6.182 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 outliers start: 183 outliers final: 50 residues processed: 1036 average time/residue: 0.5744 time to fit residues: 1034.2853 Evaluate side-chains 798 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 748 time to evaluate : 6.115 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.4798 time to fit residues: 52.8640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 663 optimal weight: 6.9990 chunk 452 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 593 optimal weight: 8.9990 chunk 328 optimal weight: 7.9990 chunk 679 optimal weight: 9.9990 chunk 550 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 406 optimal weight: 0.9980 chunk 714 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 426 GLN ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1309 HIS ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1558 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** ** A1892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 HIS ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN F 100 GLN F 480 ASN ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 716 ASN H 36 HIS ** H 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 708 HIS H 716 ASN I 577 ASN I 676 ASN ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 HIS ** K 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 GLN ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN O 731 ASN ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 426 HIS R 289 HIS R 310 GLN X 105 GLN X 367 GLN X 385 ASN X 421 ASN X 531 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 232 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 66864 Z= 0.367 Angle : 0.827 27.204 90576 Z= 0.412 Chirality : 0.044 0.224 10188 Planarity : 0.005 0.119 11506 Dihedral : 5.452 53.768 9018 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.67 % Allowed : 5.90 % Favored : 93.43 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % Cis-general : 0.45 % Twisted Proline : 0.99 % Twisted General : 0.04 % 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: 0.79 (0.07), residues: 5360 sheet: -0.86 (0.21), residues: 564 loop : -2.05 (0.13), residues: 2259 *********************** 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 987 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 767 time to evaluate : 6.126 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 outliers start: 220 outliers final: 115 residues processed: 925 average time/residue: 0.6191 time to fit residues: 996.1922 Evaluate side-chains 798 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 683 time to evaluate : 6.137 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 115 outliers final: 1 residues processed: 115 average time/residue: 0.5284 time to fit residues: 120.2101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 267 optimal weight: 7.9990 chunk 717 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 467 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 chunk 797 optimal weight: 2.9990 chunk 661 optimal weight: 0.9990 chunk 369 optimal weight: 20.0000 chunk 66 optimal weight: 0.5980 chunk 263 optimal weight: 4.9990 chunk 418 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 GLN ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 HIS ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1558 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** C 427 GLN D 32 GLN ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 577 ASN ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 HIS K 352 GLN ** K 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 152 HIS ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 426 HIS X 367 GLN X 421 ASN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.6090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 66864 Z= 0.220 Angle : 0.786 27.324 90576 Z= 0.381 Chirality : 0.042 0.200 10188 Planarity : 0.005 0.118 11506 Dihedral : 5.251 49.820 9018 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.04 % Favored : 94.28 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.96 % Cis-general : 0.45 % Twisted Proline : 0.33 % Twisted General : 0.05 % 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: 0.01 (0.09), residues: 8183 helix: 0.97 (0.07), residues: 5347 sheet: -0.83 (0.21), residues: 558 loop : -2.05 (0.13), residues: 2278 *********************** 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 972 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 818 time to evaluate : 6.391 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 outliers start: 154 outliers final: 54 residues processed: 932 average time/residue: 0.6045 time to fit residues: 982.6109 Evaluate side-chains 772 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 718 time to evaluate : 6.134 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 54 outliers final: 1 residues processed: 54 average time/residue: 0.5107 time to fit residues: 59.3187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 768 optimal weight: 8.9990 chunk 89 optimal weight: 0.0000 chunk 454 optimal weight: 0.9990 chunk 582 optimal weight: 8.9990 chunk 451 optimal weight: 0.9990 chunk 671 optimal weight: 3.9990 chunk 445 optimal weight: 1.9990 chunk 794 optimal weight: 1.9990 chunk 497 optimal weight: 4.9990 chunk 484 optimal weight: 5.9990 chunk 366 optimal weight: 0.0470 overall best weight: 0.8088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1184 HIS ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1351 GLN ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1558 HIS ** 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 540 ASN ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 GLN ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 HIS K 54 HIS ** K 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS O 127 HIS ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 HIS ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 426 HIS X 421 ASN Y 151 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 66864 Z= 0.211 Angle : 0.779 27.229 90576 Z= 0.375 Chirality : 0.042 0.230 10188 Planarity : 0.005 0.118 11506 Dihedral : 5.130 46.655 9018 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.31 % Favored : 94.03 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.96 % Cis-general : 0.44 % Twisted Proline : 0.33 % Twisted General : 0.05 % 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: 0.08 (0.09), residues: 8183 helix: 1.01 (0.07), residues: 5358 sheet: -0.68 (0.21), residues: 559 loop : -2.05 (0.13), residues: 2266 *********************** 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 906 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 812 time to evaluate : 6.213 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 outliers start: 94 outliers final: 46 residues processed: 874 average time/residue: 0.5976 time to fit residues: 910.3371 Evaluate side-chains 774 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 728 time to evaluate : 6.097 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 46 outliers final: 1 residues processed: 46 average time/residue: 0.5207 time to fit residues: 52.0648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 491 optimal weight: 0.6980 chunk 317 optimal weight: 0.0870 chunk 474 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 chunk 504 optimal weight: 4.9990 chunk 541 optimal weight: 3.9990 chunk 392 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 624 optimal weight: 0.9980 overall best weight: 1.3360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 HIS ** K 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 539 ASN ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 258 GLN R 331 ASN X 105 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.6420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 66864 Z= 0.225 Angle : 0.781 27.136 90576 Z= 0.377 Chirality : 0.042 0.229 10188 Planarity : 0.005 0.119 11506 Dihedral : 5.077 46.768 9018 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.48 % Favored : 93.90 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.96 % Cis-general : 0.44 % Twisted Proline : 0.33 % Twisted General : 0.05 % 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: 0.12 (0.09), residues: 8183 helix: 1.04 (0.07), residues: 5357 sheet: -0.64 (0.21), residues: 555 loop : -2.03 (0.13), residues: 2271 *********************** 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 844 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 772 time to evaluate : 6.622 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 outliers start: 72 outliers final: 37 residues processed: 818 average time/residue: 0.6085 time to fit residues: 871.1251 Evaluate side-chains 748 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 711 time to evaluate : 6.179 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 37 outliers final: 1 residues processed: 37 average time/residue: 0.5202 time to fit residues: 43.7820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 722 optimal weight: 10.0000 chunk 760 optimal weight: 0.8980 chunk 694 optimal weight: 7.9990 chunk 740 optimal weight: 0.8980 chunk 445 optimal weight: 0.9980 chunk 322 optimal weight: 4.9990 chunk 581 optimal weight: 3.9990 chunk 227 optimal weight: 0.4980 chunk 668 optimal weight: 7.9990 chunk 699 optimal weight: 0.9990 chunk 737 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 HIS ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 759 ASN ** I 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 HIS ** K 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 561 HIS ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 ASN X 421 ASN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.6580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 66864 Z= 0.205 Angle : 0.785 27.055 90576 Z= 0.377 Chirality : 0.042 0.480 10188 Planarity : 0.005 0.121 11506 Dihedral : 5.007 39.329 9018 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.38 % Favored : 94.01 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.96 % Cis-general : 0.44 % Twisted Proline : 0.33 % Twisted General : 0.05 % 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: 0.15 (0.09), residues: 8183 helix: 1.07 (0.07), residues: 5359 sheet: -0.60 (0.21), residues: 559 loop : -2.03 (0.13), residues: 2265 *********************** 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 852 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 804 time to evaluate : 6.205 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 outliers start: 48 outliers final: 17 residues processed: 836 average time/residue: 0.5929 time to fit residues: 861.6035 Evaluate side-chains 724 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 707 time to evaluate : 6.075 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.5134 time to fit residues: 24.0652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 485 optimal weight: 4.9990 chunk 782 optimal weight: 10.0000 chunk 477 optimal weight: 4.9990 chunk 371 optimal weight: 20.0000 chunk 544 optimal weight: 20.0000 chunk 820 optimal weight: 3.9990 chunk 755 optimal weight: 1.9990 chunk 653 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 504 optimal weight: 8.9990 chunk 400 optimal weight: 0.0980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 HIS ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 ASN ** H 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 GLN J 449 ASN J 453 HIS K 54 HIS ** K 415 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 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 505 GLN ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 ASN X 105 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.6707 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= 0.272 Angle : 0.810 26.986 90576 Z= 0.395 Chirality : 0.043 0.351 10188 Planarity : 0.005 0.124 11506 Dihedral : 5.069 37.953 9018 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.76 % Favored : 93.65 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.96 % Cis-general : 0.44 % Twisted Proline : 0.33 % 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: 0.10 (0.09), residues: 8183 helix: 1.02 (0.07), residues: 5353 sheet: -0.67 (0.21), residues: 566 loop : -2.01 (0.13), residues: 2264 ********************** 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 759 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 725 time to evaluate : 6.105 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 outliers start: 34 outliers final: 15 residues processed: 746 average time/residue: 0.5924 time to fit residues: 770.6739 Evaluate side-chains 702 residues out of total 7282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 687 time to evaluate : 6.099 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.4913 time to fit residues: 21.9292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 519 optimal weight: 6.9990 chunk 696 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 602 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 654 optimal weight: 0.0970 chunk 274 optimal weight: 8.9990 chunk 672 optimal weight: 4.9990 chunk 82 optimal weight: 0.0030 chunk 120 optimal weight: 3.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 GLN ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN F 480 ASN ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 HIS ** K 415 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 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 HIS ** N 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 ASN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.098341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.079733 restraints weight = 317984.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.081271 restraints weight = 188525.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.081225 restraints weight = 119822.343| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3870 r_free = 0.3870 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.6818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 66864 Z= 0.213 Angle : 0.812 26.990 90576 Z= 0.388 Chirality : 0.043 0.384 10188 Planarity : 0.005 0.124 11506 Dihedral : 5.033 43.348 9018 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.50 % Favored : 93.93 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.96 % Cis-general : 0.44 % Twisted Proline : 0.33 % Twisted General : 0.05 % 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: 0.15 (0.09), residues: 8183 helix: 1.05 (0.07), residues: 5351 sheet: -0.56 (0.21), residues: 563 loop : -1.99 (0.13), residues: 2269 =============================================================================== Job complete usr+sys time: 17310.29 seconds wall clock time: 304 minutes 16.13 seconds (18256.13 seconds total)