Starting phenix.real_space_refine on Thu Nov 16 05:21:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ui9_2924/11_2023/4ui9_2924.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ui9_2924/11_2023/4ui9_2924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ui9_2924/11_2023/4ui9_2924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ui9_2924/11_2023/4ui9_2924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ui9_2924/11_2023/4ui9_2924.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ui9_2924/11_2023/4ui9_2924.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 5 6.06 5 S 396 5.16 5 C 42477 2.51 5 N 11404 2.21 5 O 12171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 715": "OE1" <-> "OE2" Residue "K ASP 232": "OD1" <-> "OD2" Residue "K TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 66453 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 10947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1441, 10947 Classifications: {'peptide': 1441} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 79, 'TRANS': 1357} Chain breaks: 20 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 398 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 24, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 241 Chain: "B" Number of atoms: 650 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 84, 645 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, 645 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: 661 Chain: "C" Number of atoms: 4305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4305 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: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 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': 22} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 482} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 76 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: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 214 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': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 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: 161 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 108 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': 6} Link IDs: {'PTRANS': 14, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 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': 2, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 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: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4831 Classifications: {'peptide': 631} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'CIS': 15, 'PCIS': 3, 'PTRANS': 25, 'TRANS': 587} Chain breaks: 9 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 480 Unresolved non-hydrogen dihedrals: 300 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': 9} Unresolved non-hydrogen planarities: 200 Chain: "O" Number of atoms: 5396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5396 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 665} Chain breaks: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 4042 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 477} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3003 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 5, 'PTRANS': 12, 'TRANS': 369} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 648 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 88} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "T" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 109 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'TRANS': 18} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 20} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 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: 3770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3770 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "Y" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3865 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 480} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 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} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11123 SG CYS B 23 134.280 50.930 152.578 1.00370.06 S ATOM 11141 SG CYS B 26 135.517 54.703 151.653 1.00349.21 S ATOM 11386 SG CYS B 59 132.027 55.249 153.440 1.00371.88 S ATOM 11495 SG CYS B 73 129.545 42.933 150.724 1.00451.97 S ATOM 11516 SG CYS B 76 129.219 38.848 149.464 1.00467.29 S Time building chain proxies: 28.56, per 1000 atoms: 0.43 Number of scatterers: 66453 At special positions: 0 Unit cell: (233.92, 193.12, 220.32, 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 5 29.99 S 396 16.00 O 12171 8.00 N 11404 7.00 C 42477 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: 22.11 Conformation dependent library (CDL) restraints added in 9.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 23 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 26 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 59 " pdb="ZN ZN B 101 " - pdb=" ND1 HIS B 56 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" ND1 HIS B 53 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 76 " Number of angles added : 3 16642 Ramachandran restraints generated. 8321 Oldfield, 0 Emsley, 8321 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16200 Finding SS restraints... Secondary structure from input PDB file: 389 helices and 33 sheets defined 68.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.89 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 removed outlier: 4.124A pdb=" N ASP A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 294 removed outlier: 5.750A pdb=" N GLN A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 289 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 631 through 647 removed outlier: 4.009A pdb=" N ALA A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 667 removed outlier: 3.598A pdb=" N MET A 667 " --> pdb=" O CYS A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 777 removed outlier: 3.750A pdb=" N ILE A 762 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 798 removed outlier: 3.666A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 942 through 946 Processing helix chain 'A' and resid 948 through 965 Proline residue: A 954 - end of helix removed outlier: 3.777A pdb=" N GLN A 965 " --> pdb=" O HIS A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 978 Processing helix chain 'A' and resid 980 through 984 removed outlier: 3.612A pdb=" N LEU A 983 " --> pdb=" O ARG A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1032 through 1041 removed outlier: 3.701A pdb=" N ASP A1036 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1088 removed outlier: 3.773A pdb=" N GLU A1064 " --> pdb=" O HIS A1060 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A1076 " --> pdb=" O GLN A1072 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A1079 " --> pdb=" O GLN A1075 " (cutoff:3.500A) Proline residue: A1081 - end of helix removed outlier: 3.607A pdb=" N MET A1086 " --> pdb=" O VAL A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1146 removed outlier: 3.530A pdb=" N LYS A1146 " --> pdb=" O ALA A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1161 Processing helix chain 'A' and resid 1168 through 1183 removed outlier: 3.543A pdb=" N TYR A1172 " --> pdb=" O LEU A1168 " (cutoff:3.500A) removed outlier: 3.528A 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 1200 removed outlier: 3.523A pdb=" N ASP A1195 " --> pdb=" O LEU A1191 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A1200 " --> pdb=" O TYR A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1217 Processing helix chain 'A' and resid 1221 through 1232 removed outlier: 3.833A pdb=" N HIS A1231 " --> pdb=" O LEU A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1261 removed outlier: 3.558A pdb=" N ALA A1252 " --> pdb=" O ASN A1248 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A1258 " --> pdb=" O VAL A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1278 removed outlier: 3.531A pdb=" N GLU A1271 " --> pdb=" O ARG A1267 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A1278 " --> pdb=" O LEU A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1307 removed outlier: 3.727A 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: 3.884A 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 Processing helix chain 'A' and resid 1392 through 1399 removed outlier: 3.722A pdb=" N PHE A1398 " --> pdb=" O TYR A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1415 removed outlier: 3.700A pdb=" N LEU A1406 " --> pdb=" O GLU A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 4.198A pdb=" N VAL A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A1429 " --> pdb=" O TRP A1425 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A1430 " --> pdb=" O VAL A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1437 removed outlier: 3.901A 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: 3.530A pdb=" N SER A1500 " --> pdb=" O MET A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1508 removed outlier: 3.581A pdb=" N THR A1507 " --> pdb=" O ASN A1503 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1527 removed outlier: 3.545A pdb=" N MET A1527 " --> pdb=" O LEU A1523 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1546 removed outlier: 3.844A 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 1578 through 1588 Processing helix chain 'A' and resid 1603 through 1608 Processing helix chain 'A' and resid 1609 through 1613 removed outlier: 3.947A 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 Processing helix chain 'A' and resid 1747 through 1758 Processing helix chain 'A' and resid 1767 through 1784 removed outlier: 3.667A pdb=" N LEU A1771 " --> pdb=" O LYS A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1806 removed outlier: 4.117A pdb=" N ALA A1792 " --> pdb=" O GLU A1788 " (cutoff:3.500A) Processing helix chain 'A' and resid 1811 through 1825 removed outlier: 3.692A pdb=" N TRP A1815 " --> pdb=" O THR A1811 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A1816 " --> pdb=" O SER A1812 " (cutoff:3.500A) Processing helix chain 'A' and resid 1847 through 1866 Processing helix chain 'A' and resid 1867 through 1876 Processing helix chain 'A' and resid 1881 through 1896 removed outlier: 3.649A pdb=" N SER A1886 " --> pdb=" O GLU A1882 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET A1887 " --> pdb=" O SER A1883 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS A1890 " --> pdb=" O SER A1886 " (cutoff:3.500A) Processing helix chain 'A' and resid 1911 through 1921 removed outlier: 3.640A pdb=" N ALA A1915 " --> pdb=" O SER A1911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1925 through 1935 removed outlier: 3.972A pdb=" N ARG A1929 " --> pdb=" O LYS A1925 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 68 Processing helix chain 'C' and resid 28 through 47 removed outlier: 4.137A pdb=" N LYS C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 62 Processing helix chain 'C' and resid 77 through 97 removed outlier: 4.985A pdb=" N ASP C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ALA C 86 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 111 through 137 removed outlier: 3.692A pdb=" N VAL C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP C 136 " --> pdb=" O ASP C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 165 removed outlier: 3.849A pdb=" N VAL C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 182 Processing helix chain 'C' and resid 184 through 199 removed outlier: 3.503A pdb=" N ASP C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.688A 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 Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 278 through 293 removed outlier: 3.508A 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 345 Processing helix chain 'C' and resid 346 through 361 Processing helix chain 'C' and resid 365 through 378 removed outlier: 3.555A 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 removed outlier: 3.546A pdb=" N TRP C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 429 removed outlier: 4.165A pdb=" N TYR C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR C 421 " --> pdb=" O TYR C 417 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 447 removed outlier: 3.627A pdb=" N LEU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 463 Processing helix chain 'C' and resid 468 through 480 Processing helix chain 'C' and resid 483 through 500 Processing helix chain 'C' and resid 509 through 523 Processing helix chain 'C' and resid 525 through 540 Processing helix chain 'C' and resid 543 through 557 removed outlier: 3.762A pdb=" N ARG C 557 " --> pdb=" O ILE C 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 46 Processing helix chain 'E' and resid 52 through 92 removed outlier: 3.919A pdb=" N GLU E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU E 88 " --> pdb=" O GLY E 84 " (cutoff:3.500A) 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: 3.585A pdb=" N GLN F 90 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE F 91 " --> pdb=" O GLU F 87 " (cutoff:3.500A) removed outlier: 3.685A 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: 3.707A pdb=" N GLU F 136 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER F 141 " --> pdb=" O CYS F 137 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 158 removed outlier: 3.933A pdb=" N PHE F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 479 removed outlier: 4.229A pdb=" N ALA F 458 " --> pdb=" O LEU F 454 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA F 459 " --> pdb=" O GLN F 455 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY F 461 " --> pdb=" O ALA F 457 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU F 462 " --> pdb=" O ALA F 458 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU F 465 " --> pdb=" O GLY F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 490 removed outlier: 3.550A pdb=" N HIS F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 512 Processing helix chain 'F' and resid 514 through 529 Processing helix chain 'F' and resid 535 through 547 Processing helix chain 'F' and resid 548 through 563 Processing helix chain 'F' and resid 566 through 580 removed outlier: 3.655A pdb=" N TRP F 570 " --> pdb=" O SER F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 597 Processing helix chain 'F' and resid 600 through 615 removed outlier: 4.186A pdb=" N TYR F 604 " --> pdb=" O TYR F 600 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR F 605 " --> pdb=" O ALA F 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 631 removed outlier: 3.538A pdb=" N ALA F 622 " --> pdb=" O ASP F 618 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS F 623 " --> pdb=" O LYS F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 648 removed outlier: 3.717A 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: 3.517A pdb=" N GLU F 728 " --> pdb=" O GLN F 724 " (cutoff:3.500A) Processing helix chain 'F' and resid 736 through 751 removed outlier: 3.712A pdb=" N TYR F 740 " --> pdb=" O GLU F 736 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 767 Processing helix chain 'F' and resid 769 through 819 removed outlier: 3.626A pdb=" N LYS F 813 " --> pdb=" O ASN F 778 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 816 " --> pdb=" O ILE F 812 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 25 removed outlier: 3.838A pdb=" N GLU G 18 " --> pdb=" O GLU G 14 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE G 19 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 3.726A 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: 3.730A pdb=" N ILE H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 3.650A 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: 3.654A pdb=" N GLU H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER H 141 " --> pdb=" O CYS H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 158 removed outlier: 3.903A pdb=" N PHE H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 169 removed outlier: 4.483A pdb=" N THR H 167 " --> pdb=" O ASP H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 479 removed outlier: 3.626A pdb=" N GLY H 461 " --> pdb=" O ALA H 457 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU H 462 " --> pdb=" O ALA H 458 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 465 " --> pdb=" O GLY H 461 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 490 removed outlier: 3.527A pdb=" N HIS H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 512 Processing helix chain 'H' and resid 514 through 529 Processing helix chain 'H' and resid 535 through 547 Processing helix chain 'H' and resid 548 through 563 Processing helix chain 'H' and resid 566 through 580 removed outlier: 3.633A pdb=" N TRP H 570 " --> pdb=" O SER H 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 597 Processing helix chain 'H' and resid 600 through 615 removed outlier: 4.196A pdb=" N TYR H 604 " --> pdb=" O TYR H 600 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 605 " --> pdb=" O ALA H 601 " (cutoff:3.500A) Processing helix chain 'H' and resid 616 through 631 removed outlier: 3.540A pdb=" N ALA H 622 " --> pdb=" O ASP H 618 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS H 623 " --> pdb=" O LYS H 619 " (cutoff:3.500A) Processing helix chain 'H' and resid 634 through 648 removed outlier: 3.701A 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 removed outlier: 3.640A pdb=" N LYS H 706 " --> pdb=" O ASN H 702 " (cutoff:3.500A) Processing helix chain 'H' and resid 718 through 733 removed outlier: 3.537A pdb=" N GLU H 728 " --> pdb=" O GLN H 724 " (cutoff:3.500A) Processing helix chain 'H' and resid 736 through 751 removed outlier: 3.684A pdb=" N TYR H 740 " --> pdb=" O GLU H 736 " (cutoff:3.500A) Processing helix chain 'H' and resid 752 through 771 Processing helix chain 'I' and resid 49 through 52 Processing helix chain 'I' and resid 132 through 137 removed outlier: 4.167A pdb=" N ASN I 136 " --> pdb=" O GLU I 132 " (cutoff:3.500A) removed outlier: 3.558A 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: 3.902A pdb=" N ALA I 275 " --> pdb=" O CYS I 271 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP I 276 " --> pdb=" O MET I 272 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU I 277 " --> pdb=" O CYS I 273 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLU I 278 " --> pdb=" O GLU I 274 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE I 279 " --> pdb=" O ALA I 275 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU I 280 " --> pdb=" O TRP I 276 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N MET I 281 " --> pdb=" O GLU I 277 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN I 282 " --> pdb=" O GLU I 278 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N MET I 283 " --> pdb=" O ILE I 279 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP I 284 " --> pdb=" O LEU I 280 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER I 285 " --> pdb=" O MET I 281 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG I 286 " --> pdb=" O GLN I 282 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU I 287 " --> pdb=" O MET I 283 " (cutoff:3.500A) removed outlier: 3.768A 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: 3.745A pdb=" N GLN I 324 " --> pdb=" O LEU I 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 351 Processing helix chain 'I' and resid 351 through 372 removed outlier: 3.510A 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: 3.512A 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 481 removed outlier: 4.323A pdb=" N TYR I 478 " --> pdb=" O ARG I 474 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU I 479 " --> pdb=" O VAL I 475 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP I 481 " --> pdb=" O GLN I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 503 Processing helix chain 'I' and resid 505 through 510 removed outlier: 3.833A pdb=" N GLU I 509 " --> pdb=" O SER I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 521 through 548 Proline residue: I 540 - end of helix removed outlier: 3.710A 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: 3.504A pdb=" N TRP J 42 " --> pdb=" O GLN J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 63 removed outlier: 3.836A pdb=" N ARG J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 70 removed outlier: 3.533A pdb=" N GLU J 70 " --> pdb=" O ASP J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 84 Processing helix chain 'J' and resid 87 through 94 Processing helix chain 'J' and resid 124 through 144 Processing helix chain 'J' and resid 145 through 161 Processing helix chain 'J' and resid 163 through 173 removed outlier: 4.044A pdb=" N PHE J 167 " --> pdb=" O CYS J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 188 Processing helix chain 'J' and resid 194 through 209 removed outlier: 3.522A 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 Processing helix chain 'J' and resid 266 through 278 removed outlier: 4.488A 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: 3.936A pdb=" N TRP J 302 " --> pdb=" O ASN J 298 " (cutoff:3.500A) removed outlier: 3.694A 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: 3.793A pdb=" N TRP J 337 " --> pdb=" O TYR J 333 " (cutoff:3.500A) removed outlier: 3.720A 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: 3.579A pdb=" N ALA J 434 " --> pdb=" O GLU J 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 444 through 458 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 removed outlier: 3.541A pdb=" N ASP J 500 " --> pdb=" O GLU J 496 " (cutoff:3.500A) 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 Processing helix chain 'K' and resid 52 through 62 Processing helix chain 'K' and resid 64 through 69 Processing helix chain 'K' and resid 69 through 83 Processing helix chain 'K' and resid 87 through 93 Processing helix chain 'K' and resid 128 through 144 removed outlier: 3.639A pdb=" N CYS K 133 " --> pdb=" O LYS K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 161 Processing helix chain 'K' and resid 163 through 172 removed outlier: 4.024A 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: 3.665A pdb=" N LYS K 208 " --> pdb=" O LEU K 204 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS K 211 " --> pdb=" O ASN K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 225 removed outlier: 3.574A 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 278 removed outlier: 4.488A 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: 3.971A pdb=" N TRP K 302 " --> pdb=" O ASN K 298 " (cutoff:3.500A) removed outlier: 3.728A 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: 3.632A 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 368 through 381 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 Processing helix chain 'K' and resid 440 through 458 removed outlier: 4.027A 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: 3.583A 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 removed outlier: 3.535A pdb=" N ASP K 500 " --> pdb=" O GLU K 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 512 through 527 Processing helix chain 'L' and resid 12 through 20 removed outlier: 3.555A pdb=" N LEU L 16 " --> pdb=" O ASP L 12 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY L 20 " --> pdb=" O LEU L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 Processing helix chain 'L' and resid 145 through 148 removed outlier: 3.712A 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 182 removed outlier: 4.144A pdb=" N TYR L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER L 182 " --> pdb=" O MET L 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 16 removed outlier: 3.773A pdb=" N ASP M 16 " --> pdb=" O LEU M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 56 Processing helix chain 'N' and resid 15 through 29 Processing helix chain 'N' and resid 53 through 63 Processing helix chain 'N' and resid 79 through 92 removed outlier: 3.886A 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 123 through 139 removed outlier: 4.293A pdb=" N SER N 128 " --> pdb=" O PRO N 124 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LEU N 129 " --> pdb=" O TYR N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 162 Processing helix chain 'N' and resid 166 through 191 Processing helix chain 'N' and resid 203 through 215 Processing helix chain 'N' and resid 234 through 250 Processing helix chain 'N' and resid 252 through 278 removed outlier: 4.117A pdb=" N VAL N 256 " --> pdb=" O LEU N 252 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA N 258 " --> pdb=" O GLU N 254 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU N 259 " --> pdb=" O ARG N 255 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG N 276 " --> pdb=" O ARG N 272 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG N 278 " --> pdb=" O GLU N 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 304 removed outlier: 3.537A pdb=" N LYS N 291 " --> pdb=" O ARG N 287 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE N 293 " --> pdb=" O PHE N 289 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU N 300 " --> pdb=" O VAL N 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 349 removed outlier: 3.506A pdb=" N ILE N 335 " --> pdb=" O PHE N 331 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE N 345 " --> pdb=" O ILE N 341 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER N 346 " --> pdb=" O GLU N 342 " (cutoff:3.500A) Processing helix chain 'N' and resid 354 through 367 Processing helix chain 'N' and resid 370 through 386 Processing helix chain 'N' and resid 395 through 409 removed outlier: 3.563A pdb=" N LEU N 399 " --> pdb=" O ASP N 395 " (cutoff:3.500A) Processing helix chain 'N' and resid 414 through 421 removed outlier: 3.624A pdb=" N VAL N 419 " --> pdb=" O VAL N 415 " (cutoff:3.500A) Processing helix chain 'N' and resid 421 through 432 Processing helix chain 'N' and resid 433 through 442 Processing helix chain 'N' and resid 451 through 458 removed outlier: 4.186A pdb=" N LYS N 458 " --> pdb=" O VAL N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 499 through 510 removed outlier: 3.794A pdb=" N GLY N 510 " --> pdb=" O VAL N 506 " (cutoff:3.500A) Processing helix chain 'N' and resid 512 through 530 Processing helix chain 'N' and resid 536 through 549 Processing helix chain 'N' and resid 554 through 563 Processing helix chain 'N' and resid 564 through 580 Processing helix chain 'N' and resid 581 through 584 Processing helix chain 'N' and resid 612 through 629 removed outlier: 4.058A pdb=" N ALA N 617 " --> pdb=" O GLU N 613 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA N 618 " --> pdb=" O ASP N 614 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 642 removed outlier: 3.500A pdb=" N LEU N 641 " --> pdb=" O LYS N 638 " (cutoff:3.500A) Processing helix chain 'N' and resid 660 through 672 removed outlier: 3.674A 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 Processing helix chain 'O' and resid 31 through 45 Processing helix chain 'O' and resid 53 through 70 removed outlier: 3.575A pdb=" N ARG O 58 " --> pdb=" O LEU O 54 " (cutoff:3.500A) Proline residue: O 66 - end of helix Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'O' and resid 88 through 103 Processing helix chain 'O' and resid 104 through 121 removed outlier: 3.838A pdb=" N MET O 108 " --> pdb=" O GLU O 104 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER O 120 " --> pdb=" O SER O 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 146 removed outlier: 3.590A pdb=" N LEU O 146 " --> pdb=" O ALA O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 169 removed outlier: 3.814A pdb=" N LYS O 169 " --> pdb=" O ASP O 165 " (cutoff:3.500A) Processing helix chain 'O' and resid 208 through 226 Processing helix chain 'O' and resid 232 through 247 removed outlier: 3.709A pdb=" N PHE O 246 " --> pdb=" O ASN O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 251 through 265 removed outlier: 3.771A pdb=" N TYR O 255 " --> pdb=" O ALA O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 281 removed outlier: 3.686A pdb=" N SER O 270 " --> pdb=" O ASP O 266 " (cutoff:3.500A) Processing helix chain 'O' and resid 297 through 314 removed outlier: 4.303A pdb=" N ARG O 301 " --> pdb=" O GLY O 297 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR O 302 " --> pdb=" O ARG O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 316 through 335 Processing helix chain 'O' and resid 336 through 351 removed outlier: 3.528A pdb=" N LEU O 340 " --> pdb=" O ASP O 336 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS O 342 " --> pdb=" O VAL O 338 " (cutoff:3.500A) Processing helix chain 'O' and resid 357 through 370 removed outlier: 3.922A pdb=" N LEU O 361 " --> pdb=" O SER O 357 " (cutoff:3.500A) Processing helix chain 'O' and resid 373 through 392 Processing helix chain 'O' and resid 394 through 413 removed outlier: 3.571A pdb=" N LEU O 408 " --> pdb=" O ASP O 404 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 432 removed outlier: 3.682A pdb=" N ILE O 418 " --> pdb=" O LEU O 414 " (cutoff:3.500A) Processing helix chain 'O' and resid 434 through 448 Processing helix chain 'O' and resid 462 through 480 removed outlier: 3.859A pdb=" N PHE O 466 " --> pdb=" O ASN O 462 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA O 467 " --> pdb=" O THR O 463 " (cutoff:3.500A) Processing helix chain 'O' and resid 482 through 497 Processing helix chain 'O' and resid 503 through 523 Processing helix chain 'O' and resid 524 through 540 removed outlier: 3.559A pdb=" N THR O 533 " --> pdb=" O ASP O 529 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY O 534 " --> pdb=" O SER O 530 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU O 538 " --> pdb=" O GLY O 534 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 555 Processing helix chain 'O' and resid 556 through 575 Processing helix chain 'O' and resid 576 through 594 removed outlier: 3.950A pdb=" N ARG O 593 " --> pdb=" O GLU O 589 " (cutoff:3.500A) Processing helix chain 'O' and resid 596 through 598 No H-bonds generated for 'chain 'O' and resid 596 through 598' Processing helix chain 'O' and resid 599 through 614 removed outlier: 4.310A pdb=" N MET O 603 " --> pdb=" O ILE O 599 " (cutoff:3.500A) Processing helix chain 'O' and resid 616 through 634 removed outlier: 3.510A pdb=" N GLU O 622 " --> pdb=" O TYR O 618 " (cutoff:3.500A) Processing helix chain 'O' and resid 636 through 654 removed outlier: 4.154A pdb=" N MET O 646 " --> pdb=" O SER O 642 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA O 647 " --> pdb=" O LEU O 643 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU O 649 " --> pdb=" O HIS O 645 " (cutoff:3.500A) Proline residue: O 650 - end of helix removed outlier: 3.662A pdb=" N ASP O 654 " --> pdb=" O PRO O 650 " (cutoff:3.500A) Processing helix chain 'O' and resid 657 through 678 removed outlier: 3.517A pdb=" N MET O 664 " --> pdb=" O LYS O 660 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER O 677 " --> pdb=" O ALA O 673 " (cutoff:3.500A) Processing helix chain 'O' and resid 682 through 705 removed outlier: 3.607A pdb=" N ALA O 689 " --> pdb=" O GLU O 685 " (cutoff:3.500A) Processing helix chain 'O' and resid 707 through 725 removed outlier: 4.093A pdb=" N ASP O 712 " --> pdb=" O GLU O 708 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL O 713 " --> pdb=" O ARG O 709 " (cutoff:3.500A) Processing helix chain 'O' and resid 726 through 741 removed outlier: 3.771A 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: 4.970A pdb=" N ASP P 85 " --> pdb=" O ALA P 81 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ALA P 86 " --> pdb=" O GLN P 82 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS P 97 " --> pdb=" O TYR P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 107 Processing helix chain 'P' and resid 111 through 134 Processing helix chain 'P' and resid 148 through 165 removed outlier: 3.537A pdb=" N GLU P 153 " --> pdb=" O GLU P 149 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU P 154 " --> pdb=" O ALA P 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 182 Processing helix chain 'P' and resid 184 through 199 removed outlier: 3.502A pdb=" N ASP P 190 " --> pdb=" O LYS P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 213 removed outlier: 3.715A 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 Processing helix chain 'P' and resid 243 through 257 Processing helix chain 'P' and resid 262 through 276 removed outlier: 3.697A pdb=" N VAL P 266 " --> pdb=" O SER P 262 " (cutoff:3.500A) Processing helix chain 'P' and resid 278 through 293 removed outlier: 3.558A 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 345 Processing helix chain 'P' and resid 346 through 361 Processing helix chain 'P' and resid 364 through 378 removed outlier: 3.908A pdb=" N TRP P 368 " --> pdb=" O TYR P 364 " (cutoff:3.500A) removed outlier: 3.630A 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 removed outlier: 3.542A pdb=" N TRP P 402 " --> pdb=" O ASP P 398 " (cutoff:3.500A) Processing helix chain 'P' and resid 415 through 429 Processing helix chain 'P' and resid 432 through 447 removed outlier: 3.566A 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 Processing helix chain 'P' and resid 482 through 500 removed outlier: 3.561A pdb=" N ALA P 486 " --> pdb=" O GLU P 482 " (cutoff:3.500A) Processing helix chain 'P' and resid 511 through 523 Processing helix chain 'P' and resid 525 through 538 Processing helix chain 'R' and resid 56 through 63 Processing helix chain 'R' and resid 88 through 100 Processing helix chain 'R' and resid 154 through 163 removed outlier: 3.622A pdb=" N LEU R 160 " --> pdb=" O LYS R 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 358 through 366 Processing helix chain 'S' and resid 423 through 432 Processing helix chain 'U' and resid 6 through 21 Proline residue: U 16 - end of helix removed outlier: 4.067A pdb=" N ALA U 21 " --> pdb=" O PRO U 17 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 25 removed outlier: 3.803A pdb=" N GLU W 18 " --> pdb=" O ASP W 14 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE W 19 " --> pdb=" O ASP W 15 " (cutoff:3.500A) removed outlier: 3.775A 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 161 removed outlier: 3.667A pdb=" N ALA X 155 " --> pdb=" O GLN X 151 " (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 Processing helix chain 'X' and resid 235 through 249 Processing helix chain 'X' and resid 250 through 264 removed outlier: 3.599A pdb=" N ALA X 254 " --> pdb=" O ASP X 250 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 285 Processing helix chain 'X' and resid 286 through 301 removed outlier: 3.534A pdb=" N VAL X 291 " --> pdb=" O ASN X 287 " (cutoff:3.500A) Processing helix chain 'X' and resid 304 through 319 removed outlier: 3.952A pdb=" N ASP X 309 " --> pdb=" O ILE X 305 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL X 310 " --> pdb=" O LYS X 306 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR X 313 " --> pdb=" O ASP X 309 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU X 314 " --> pdb=" O VAL X 310 " (cutoff:3.500A) Processing helix chain 'X' and resid 320 through 335 Processing helix chain 'X' and resid 338 through 353 removed outlier: 3.954A pdb=" N TRP X 342 " --> pdb=" O HIS X 338 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE X 350 " --> pdb=" O GLY X 346 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR X 351 " --> pdb=" O CYS X 347 " (cutoff:3.500A) Processing helix chain 'X' and resid 354 through 369 Processing helix chain 'X' and resid 373 through 387 removed outlier: 3.568A pdb=" N ALA X 382 " --> pdb=" O LEU X 378 " (cutoff:3.500A) Processing helix chain 'X' and resid 388 through 403 removed outlier: 3.878A pdb=" N HIS X 395 " --> pdb=" O GLU X 391 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG X 401 " --> pdb=" O ARG X 397 " (cutoff:3.500A) Processing helix chain 'X' and resid 406 through 421 Processing helix chain 'X' and resid 422 through 438 Processing helix chain 'X' and resid 441 through 454 removed outlier: 3.570A pdb=" N THR X 445 " --> pdb=" O ALA X 441 " (cutoff:3.500A) Processing helix chain 'X' and resid 457 through 472 removed outlier: 3.897A pdb=" N LEU X 464 " --> pdb=" O LYS X 460 " (cutoff:3.500A) Processing helix chain 'X' and resid 475 through 490 Processing helix chain 'X' and resid 491 through 506 removed outlier: 3.607A pdb=" N GLY X 495 " --> pdb=" O LYS X 491 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN X 505 " --> pdb=" O ASN X 501 " (cutoff:3.500A) Processing helix chain 'X' and resid 509 through 523 removed outlier: 3.837A pdb=" N ARG X 513 " --> pdb=" O CYS X 509 " (cutoff:3.500A) removed outlier: 3.514A 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 90 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: 3.670A pdb=" N ALA Y 155 " --> pdb=" O GLN Y 151 " (cutoff:3.500A) removed outlier: 3.762A 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 removed outlier: 3.940A pdb=" N CYS Y 199 " --> pdb=" O VAL Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 202 through 213 Processing helix chain 'Y' and resid 214 through 229 Processing helix chain 'Y' and resid 235 through 249 Processing helix chain 'Y' and resid 250 through 264 removed outlier: 3.579A pdb=" N ALA Y 254 " --> pdb=" O ASP Y 250 " (cutoff:3.500A) Processing helix chain 'Y' and resid 270 through 285 Processing helix chain 'Y' and resid 286 through 301 removed outlier: 3.532A pdb=" N VAL Y 291 " --> pdb=" O ASN Y 287 " (cutoff:3.500A) Processing helix chain 'Y' and resid 304 through 319 removed outlier: 3.618A pdb=" N MET Y 308 " --> pdb=" O LEU Y 304 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP Y 309 " --> pdb=" O ILE Y 305 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL Y 310 " --> pdb=" O LYS Y 306 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR Y 313 " --> pdb=" O ASP Y 309 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU Y 314 " --> pdb=" O VAL Y 310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 320 through 335 Processing helix chain 'Y' and resid 338 through 353 removed outlier: 3.951A pdb=" N TRP Y 342 " --> pdb=" O HIS Y 338 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE Y 350 " --> pdb=" O GLY Y 346 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR Y 351 " --> pdb=" O CYS Y 347 " (cutoff:3.500A) Processing helix chain 'Y' and resid 354 through 369 Processing helix chain 'Y' and resid 372 through 387 removed outlier: 3.710A pdb=" N LEU Y 376 " --> pdb=" O SER Y 372 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA Y 382 " --> pdb=" O LEU Y 378 " (cutoff:3.500A) Processing helix chain 'Y' and resid 388 through 403 removed outlier: 3.875A pdb=" N HIS Y 395 " --> pdb=" O GLU Y 391 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG Y 401 " --> pdb=" O ARG Y 397 " (cutoff:3.500A) Processing helix chain 'Y' and resid 406 through 421 Processing helix chain 'Y' and resid 422 through 438 Processing helix chain 'Y' and resid 441 through 454 removed outlier: 3.592A pdb=" N THR Y 445 " --> pdb=" O ALA Y 441 " (cutoff:3.500A) Processing helix chain 'Y' and resid 457 through 472 removed outlier: 3.916A pdb=" N LEU Y 464 " --> pdb=" O LYS Y 460 " (cutoff:3.500A) Processing helix chain 'Y' and resid 475 through 490 Processing helix chain 'Y' and resid 491 through 506 removed outlier: 3.620A pdb=" N GLY Y 495 " --> pdb=" O LYS Y 491 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN Y 501 " --> pdb=" O ALA Y 497 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN Y 505 " --> pdb=" O ASN Y 501 " (cutoff:3.500A) Processing helix chain 'Y' and resid 509 through 523 removed outlier: 3.843A pdb=" N ARG Y 513 " --> pdb=" O CYS Y 509 " (cutoff:3.500A) removed outlier: 3.532A 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: 3.777A pdb=" N GLY Y 548 " --> pdb=" O LYS Y 544 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET Y 549 " --> pdb=" O SER Y 545 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET Y 552 " --> pdb=" O GLY Y 548 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 17 through 19 removed outlier: 6.798A pdb=" N ARG A 594 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP A 589 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR A 596 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 587 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLU A 598 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 73 through 78 Processing sheet with id= AC, first strand: chain 'A' and resid 127 through 132 removed outlier: 3.505A pdb=" N LEU A 127 " --> pdb=" O CYS A 152 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 151 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 177 through 180 removed outlier: 6.856A pdb=" N GLU A 190 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL A 180 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 188 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 245 through 250 removed outlier: 6.154A pdb=" N ILE A 246 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR A 259 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 255 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 268 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.978A pdb=" N LYS A 440 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A 452 " --> pdb=" O ASN A 473 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN A 473 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N CYS A 454 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL A 471 " --> pdb=" O CYS A 454 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS A 456 " --> pdb=" O GLY A 469 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A 458 " --> pdb=" O ILE A 467 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 478 through 482 removed outlier: 3.764A pdb=" N ASP A 478 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 482 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 487 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU A 497 " --> pdb=" O LYS A 508 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LYS A 508 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 499 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A' and resid 1108 through 1111 Processing sheet with id= AI, first strand: chain 'A' and resid 1572 through 1574 Processing sheet with id= AJ, first strand: chain 'A' and resid 1620 through 1622 Processing sheet with id= AK, first strand: chain 'A' and resid 1646 through 1652 removed outlier: 3.520A pdb=" N THR A1647 " --> pdb=" O TYR A1638 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A1633 " --> pdb=" O VAL A1668 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A1668 " --> pdb=" O LEU A1633 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU A1635 " --> pdb=" O ILE A1666 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE A1666 " --> pdb=" O GLU A1635 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A1637 " --> pdb=" O LYS A1664 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A1675 " --> pdb=" O VAL A1668 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'B' and resid 3 through 9 removed outlier: 5.302A pdb=" N ILE B 5 " --> pdb=" O ASP N 647 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASP N 647 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS B 7 " --> pdb=" O THR N 645 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU N 655 " --> pdb=" O VAL N 648 " (cutoff:3.500A) Processing sheet with id= BB, 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: 6.902A pdb=" N VAL I 44 " --> pdb=" O SER I 57 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N SER I 57 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 6.653A 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: 4.179A pdb=" N CYS I 70 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS I 93 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS I 102 " --> pdb=" O LEU I 92 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASP I 94 " --> pdb=" O SER I 100 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER I 100 " --> pdb=" O ASP I 94 " (cutoff:3.500A) Processing sheet with id= IC, first strand: chain 'I' and resid 112 through 117 removed outlier: 3.588A pdb=" N TYR I 188 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE I 185 " --> pdb=" O ARG I 197 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG I 197 " --> pdb=" O ILE I 185 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU I 187 " --> pdb=" O ILE I 195 " (cutoff:3.500A) Processing sheet with id= ID, first strand: chain 'I' and resid 204 through 210 removed outlier: 5.734A pdb=" N CYS I 205 " --> pdb=" O GLU I 222 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU I 222 " --> pdb=" O CYS I 205 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA I 207 " --> pdb=" O VAL I 220 " (cutoff:3.500A) Processing sheet with id= IE, first strand: chain 'I' and resid 229 through 230 Processing sheet with id= IF, 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: 8.522A pdb=" N PHE I 620 " --> pdb=" O TYR I 596 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N MET I 598 " --> pdb=" O ILE I 618 " (cutoff:3.500A) 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: 8.522A pdb=" N PHE I 620 " --> pdb=" O TYR I 596 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N MET I 598 " --> pdb=" O ILE I 618 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE I 707 " --> pdb=" O GLY I 621 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE I 623 " --> pdb=" O PHE I 707 " (cutoff:3.500A) Processing sheet with id= IH, first strand: chain 'I' and resid 631 through 632 Processing sheet with id= II, first strand: chain 'I' and resid 636 through 645 removed outlier: 5.623A pdb=" N CYS I 638 " --> pdb=" O LYS I 654 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LYS I 654 " --> pdb=" O CYS I 638 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR I 648 " --> pdb=" O TYR I 644 " (cutoff:3.500A) Processing sheet with id= IJ, 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: 4.162A 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: 12.044A pdb=" N ILE L 66 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N ALA L 140 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N PHE L 68 " --> pdb=" O GLN L 138 " (cutoff:3.500A) removed outlier: 11.322A pdb=" N GLN L 138 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N ARG L 70 " --> pdb=" O MET L 136 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N MET L 136 " --> pdb=" O ARG L 70 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR L 72 " --> pdb=" O THR L 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR L 132 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE L 94 " --> pdb=" O GLN L 110 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLN L 110 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL L 96 " --> pdb=" O ILE L 108 " (cutoff:3.500A) Processing sheet with id= RA, first strand: chain 'R' and resid 177 through 180 removed outlier: 3.611A pdb=" N LYS R 177 " --> pdb=" O PHE R 469 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR R 466 " --> pdb=" O ALA R 462 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA R 462 " --> pdb=" O THR R 466 " (cutoff:3.500A) Processing sheet with id= RB, first strand: chain 'R' and resid 193 through 195 removed outlier: 6.357A pdb=" N VAL R 209 " --> pdb=" O LEU R 222 " (cutoff:3.500A) Processing sheet with id= RC, first strand: chain 'R' and resid 232 through 237 removed outlier: 6.387A pdb=" N VAL R 253 " --> pdb=" O MET R 266 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N MET R 266 " --> pdb=" O VAL R 253 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE R 255 " --> pdb=" O LEU R 264 " (cutoff:3.500A) Processing sheet with id= RD, first strand: chain 'R' and resid 274 through 280 removed outlier: 4.263A pdb=" N MET R 292 " --> pdb=" O SER R 288 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE R 293 " --> pdb=" O ARG R 307 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG R 307 " --> pdb=" O ILE R 293 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN R 295 " --> pdb=" O SER R 305 " (cutoff:3.500A) Processing sheet with id= RE, first strand: chain 'R' and resid 319 through 321 Processing sheet with id= RF, first strand: chain 'R' and resid 360 through 363 removed outlier: 3.896A pdb=" N ALA R 360 " --> pdb=" O GLY R 374 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE R 382 " --> pdb=" O CYS R 395 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N CYS R 395 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE R 384 " --> pdb=" O LEU R 393 " (cutoff:3.500A) Processing sheet with id= RG, first strand: chain 'R' and resid 402 through 407 removed outlier: 3.608A pdb=" N ASN R 404 " --> pdb=" O THR R 417 " (cutoff:3.500A) Processing sheet with id= SA, first strand: chain 'S' and resid 376 through 377 4225 hydrogen bonds defined for protein. 12546 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: 28.48 Time building geometry restraints manager: 24.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.45: 30077 1.45 - 1.71: 37166 1.71 - 1.98: 586 1.98 - 2.25: 4 2.25 - 2.52: 2 Bond restraints: 67835 Sorted by residual: bond pdb=" C ASP N 563 " pdb=" N MET N 564 " ideal model delta sigma weight residual 1.335 2.519 -1.184 1.31e-02 5.83e+03 8.17e+03 bond pdb=" N PRO R 431 " pdb=" CD PRO R 431 " ideal model delta sigma weight residual 1.473 2.227 -0.754 1.40e-02 5.10e+03 2.90e+03 bond pdb=" N PRO R 392 " pdb=" CD PRO R 392 " ideal model delta sigma weight residual 1.473 2.186 -0.713 1.40e-02 5.10e+03 2.60e+03 bond pdb=" N PRO R 302 " pdb=" CD PRO R 302 " ideal model delta sigma weight residual 1.473 2.160 -0.687 1.40e-02 5.10e+03 2.41e+03 bond pdb=" N PRO R 301 " pdb=" CD PRO R 301 " ideal model delta sigma weight residual 1.473 2.139 -0.666 1.40e-02 5.10e+03 2.26e+03 ... (remaining 67830 not shown) Histogram of bond angle deviations from ideal: 39.44 - 62.77: 1 62.77 - 86.10: 6 86.10 - 109.42: 10463 109.42 - 132.75: 81265 132.75 - 156.07: 156 Bond angle restraints: 91891 Sorted by residual: angle pdb=" O PRO R 431 " pdb=" C PRO R 431 " pdb=" N SER R 432 " ideal model delta sigma weight residual 122.64 39.44 83.20 1.35e+00 5.49e-01 3.80e+03 angle pdb=" O GLN R 310 " pdb=" C GLN R 310 " pdb=" N GLY R 311 " ideal model delta sigma weight residual 122.84 73.03 49.81 1.20e+00 6.94e-01 1.72e+03 angle pdb=" N THR R 434 " pdb=" CA THR R 434 " pdb=" CB THR R 434 " ideal model delta sigma weight residual 110.60 156.07 -45.47 1.52e+00 4.33e-01 8.95e+02 angle pdb=" N VAL R 436 " pdb=" CA VAL R 436 " pdb=" CB VAL R 436 " ideal model delta sigma weight residual 112.34 142.56 -30.22 1.30e+00 5.92e-01 5.40e+02 angle pdb=" C VAL R 436 " pdb=" CA VAL R 436 " pdb=" CB VAL R 436 " ideal model delta sigma weight residual 110.41 85.19 25.22 1.14e+00 7.69e-01 4.89e+02 ... (remaining 91886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.04: 37401 26.04 - 52.08: 2989 52.08 - 78.12: 396 78.12 - 104.16: 39 104.16 - 130.21: 1 Dihedral angle restraints: 40826 sinusoidal: 15845 harmonic: 24981 Sorted by residual: dihedral pdb=" CA GLU N 280 " pdb=" C GLU N 280 " pdb=" N TYR N 281 " pdb=" CA TYR N 281 " ideal model delta harmonic sigma weight residual 180.00 49.79 130.21 0 5.00e+00 4.00e-02 6.78e+02 dihedral pdb=" CA CYS N 394 " pdb=" C CYS N 394 " pdb=" N ASP N 395 " pdb=" CA ASP N 395 " ideal model delta harmonic sigma weight residual 180.00 98.07 81.93 0 5.00e+00 4.00e-02 2.68e+02 dihedral pdb=" N THR R 434 " pdb=" C THR R 434 " pdb=" CA THR R 434 " pdb=" CB THR R 434 " ideal model delta harmonic sigma weight residual 123.40 156.24 -32.84 0 2.50e+00 1.60e-01 1.73e+02 ... (remaining 40823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.248: 9972 0.248 - 0.497: 363 0.497 - 0.745: 21 0.745 - 0.994: 5 0.994 - 1.242: 1 Chirality restraints: 10362 Sorted by residual: chirality pdb=" CA THR R 434 " pdb=" N THR R 434 " pdb=" C THR R 434 " pdb=" CB THR R 434 " both_signs ideal model delta sigma weight residual False 2.53 1.28 1.24 2.00e-01 2.50e+01 3.86e+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 1.53 0.98 2.00e-01 2.50e+01 2.42e+01 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 1.61 0.90 2.00e-01 2.50e+01 2.01e+01 ... (remaining 10359 not shown) Planarity restraints: 11673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO R 431 " 0.193 2.00e-02 2.50e+03 2.73e-01 7.46e+02 pdb=" C PRO R 431 " -0.457 2.00e-02 2.50e+03 pdb=" O PRO R 431 " 0.226 2.00e-02 2.50e+03 pdb=" N SER R 432 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN R 310 " -0.156 2.00e-02 2.50e+03 2.37e-01 5.62e+02 pdb=" C GLN R 310 " 0.409 2.00e-02 2.50e+03 pdb=" O GLN R 310 " -0.150 2.00e-02 2.50e+03 pdb=" N GLY R 311 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 430 " 0.202 5.00e-02 4.00e+02 2.59e-01 1.07e+02 pdb=" N PRO R 431 " -0.436 5.00e-02 4.00e+02 pdb=" CA PRO R 431 " 0.188 5.00e-02 4.00e+02 pdb=" CD PRO R 431 " 0.046 5.00e-02 4.00e+02 ... (remaining 11670 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.66: 23 1.66 - 2.47: 346 2.47 - 3.28: 77025 3.28 - 4.09: 165360 4.09 - 4.90: 302492 Warning: very small nonbonded interaction distances. Nonbonded interactions: 545246 Sorted by model distance: nonbonded pdb=" CD GLN R 310 " pdb=" CD2 LEU R 338 " model vdw 0.849 3.690 nonbonded pdb=" CE1 TYR X 355 " pdb=" N ASN X 385 " model vdw 0.943 3.420 nonbonded pdb=" CG GLN R 310 " pdb=" CD2 LEU R 338 " model vdw 0.952 3.860 nonbonded pdb=" CZ TYR X 355 " pdb=" N ASN X 385 " model vdw 0.958 3.340 nonbonded pdb=" SD MET R 292 " pdb=" CD2 LEU R 309 " model vdw 1.028 3.820 ... (remaining 545241 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 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 r \ esid 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 771)) } ncs_group { reference = (chain 'G' and (resid 1 through 13 or resid 15 through 25)) selection = (chain 'W' and (resid 1 through 13 or resid 15 through 25)) } 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 224 or r \ esid 226 through 227 or (resid 228 and (name N or name CA or name C or name O or \ name CB )) or resid 229 through 264 or resid 266 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 224 or resid 226 through 264 or \ resid 266 through 346 or (resid 347 and (name N or name CA or name C or name O o \ r name CB )) or resid 348 through 523 or (resid 524 and (name N or name CA or na \ me C or name O or name CB )) or resid 525 through 527)) } ncs_group { reference = chain 'X' selection = (chain 'Y' and resid 36 through 540) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 6.930 Check model and map are aligned: 0.900 Set scattering table: 0.510 Process input model: 155.550 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 : 0.016 1.184 67835 Z= 1.098 Angle : 1.970 83.198 91891 Z= 1.272 Chirality : 0.111 1.242 10362 Planarity : 0.010 0.273 11673 Dihedral : 17.965 130.206 24626 Min Nonbonded Distance : 0.849 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 1.88 % Allowed : 5.29 % Favored : 92.84 % Rotamer: Outliers : 11.86 % Allowed : 13.54 % Favored : 74.59 % Cbeta Deviations : 1.53 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.28 % Twisted Proline : 1.31 % Twisted General : 0.48 % 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: -1.90 (0.08), residues: 8321 helix: -0.64 (0.06), residues: 5382 sheet: -0.80 (0.21), residues: 574 loop : -2.59 (0.11), residues: 2365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16642 Ramachandran restraints generated. 8321 Oldfield, 0 Emsley, 8321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16642 Ramachandran restraints generated. 8321 Oldfield, 0 Emsley, 8321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1980 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 826 poor density : 1154 time to evaluate : 6.101 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 outliers start: 826 outliers final: 249 residues processed: 1824 average time/residue: 0.6839 time to fit residues: 2078.7232 Evaluate side-chains 940 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 691 time to evaluate : 6.239 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 249 outliers final: 3 residues processed: 249 average time/residue: 0.5408 time to fit residues: 255.7206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 707 optimal weight: 7.9990 chunk 635 optimal weight: 0.2980 chunk 352 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 428 optimal weight: 2.9990 chunk 339 optimal weight: 8.9990 chunk 656 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 chunk 399 optimal weight: 6.9990 chunk 488 optimal weight: 1.9990 chunk 760 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 GLN A 176 GLN A 179 ASN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS A 250 ASN A 266 HIS ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 GLN A 792 GLN A 846 GLN A1184 HIS ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1247 HIS A1262 GLN A1309 HIS A1380 ASN A1453 ASN ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1895 HIS ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN C 107 HIS C 202 HIS C 287 ASN C 299 ASN C 305 ASN C 321 HIS C 361 ASN C 373 HIS ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN F 14 GLN F 64 HIS F 517 GLN F 634 HIS F 636 ASN F 657 HIS H 166 GLN H 517 GLN H 545 HIS H 595 GLN H 599 ASN H 634 HIS H 648 GLN ** H 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 716 ASN H 754 HIS H 759 ASN ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 323 ASN I 374 GLN ** I 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 455 HIS I 523 HIS I 535 GLN J 16 GLN J 38 GLN J 58 HIS J 271 HIS J 316 ASN ** J 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 GLN J 382 ASN J 393 GLN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 GLN K 38 GLN K 45 GLN K 80 HIS K 264 HIS K 271 HIS K 316 ASN K 362 GLN K 393 GLN ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 663 GLN N 671 GLN O 62 GLN O 91 ASN O 219 GLN ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 242 ASN O 247 ASN O 387 GLN O 424 GLN ** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN O 449 ASN O 472 HIS O 539 ASN O 556 GLN O 565 GLN O 671 GLN O 693 ASN O 754 HIS P 71 GLN ** P 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 287 ASN P 299 ASN P 305 ASN P 347 HIS P 355 GLN P 361 ASN P 485 GLN P 495 GLN R 60 ASN ** R 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 242 ASN R 310 GLN R 350 GLN T 6 GLN X 151 GLN X 166 GLN X 337 GLN X 338 HIS ** X 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 471 GLN ** X 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Y 296 GLN Y 326 ASN ** Y 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 432 ASN Y 471 GLN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.167 67835 Z= 0.310 Angle : 0.929 28.088 91891 Z= 0.474 Chirality : 0.048 0.416 10362 Planarity : 0.006 0.197 11673 Dihedral : 6.192 70.207 9172 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.84 % Allowed : 4.59 % Favored : 94.57 % Rotamer: Outliers : 4.19 % Allowed : 18.81 % Favored : 76.99 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.33 % Twisted Proline : 0.65 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.09), residues: 8323 helix: 0.95 (0.07), residues: 5433 sheet: -0.53 (0.20), residues: 582 loop : -2.11 (0.12), residues: 2308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 866 time to evaluate : 6.157 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 outliers start: 292 outliers final: 96 residues processed: 1096 average time/residue: 0.6450 time to fit residues: 1214.2387 Evaluate side-chains 742 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 646 time to evaluate : 6.188 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 0 residues processed: 96 average time/residue: 0.5089 time to fit residues: 100.5520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 422 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 chunk 633 optimal weight: 5.9990 chunk 518 optimal weight: 1.9990 chunk 209 optimal weight: 0.8980 chunk 762 optimal weight: 10.0000 chunk 823 optimal weight: 9.9990 chunk 678 optimal weight: 8.9990 chunk 756 optimal weight: 4.9990 chunk 259 optimal weight: 3.9990 chunk 611 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 451 GLN A 619 GLN ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1486 ASN ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1558 HIS ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN C 197 HIS C 361 ASN C 540 ASN ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 648 GLN H 599 ASN H 657 HIS ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 HIS ** I 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS J 318 HIS J 342 HIS ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 453 HIS J 503 HIS K 352 GLN K 393 GLN ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN N 266 HIS ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 571 ASN ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN O 552 GLN O 556 GLN R 158 GLN R 350 GLN ** X 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 374 GLN ** Y 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 67835 Z= 0.253 Angle : 0.786 18.946 91891 Z= 0.400 Chirality : 0.043 0.277 10362 Planarity : 0.005 0.105 11673 Dihedral : 5.585 57.696 9172 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.13 % Favored : 94.26 % Rotamer: Outliers : 3.33 % Allowed : 19.99 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.37 % Twisted Proline : 0.65 % Twisted General : 0.07 % 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: 0.50 (0.09), residues: 8323 helix: 1.34 (0.07), residues: 5440 sheet: -0.35 (0.21), residues: 569 loop : -1.91 (0.12), residues: 2314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 729 time to evaluate : 6.404 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 outliers start: 232 outliers final: 75 residues processed: 913 average time/residue: 0.6452 time to fit residues: 1021.9444 Evaluate side-chains 673 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 598 time to evaluate : 6.236 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 75 outliers final: 1 residues processed: 75 average time/residue: 0.5239 time to fit residues: 82.0613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 753 optimal weight: 9.9990 chunk 573 optimal weight: 20.0000 chunk 395 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 363 optimal weight: 3.9990 chunk 511 optimal weight: 10.0000 chunk 765 optimal weight: 5.9990 chunk 810 optimal weight: 0.8980 chunk 399 optimal weight: 6.9990 chunk 725 optimal weight: 8.9990 chunk 218 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN A 936 ASN A1124 ASN ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1486 ASN ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1798 GLN A1872 HIS B 78 GLN C 236 HIS C 407 GLN F 90 GLN ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 599 ASN I 257 HIS I 676 ASN ** I 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 GLN J 298 ASN J 314 HIS ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 HIS ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 127 HIS ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 276 HIS O 342 HIS O 387 GLN O 443 GLN O 539 ASN P 339 ASN ** R 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 350 GLN X 78 GLN X 289 ASN X 298 GLN X 348 HIS X 390 GLN X 531 GLN Y 251 ASN Y 326 ASN Y 395 HIS Y 458 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 67835 Z= 0.397 Angle : 0.793 18.855 91891 Z= 0.409 Chirality : 0.044 0.307 10362 Planarity : 0.005 0.094 11673 Dihedral : 5.478 54.943 9172 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.48 % Favored : 93.96 % Rotamer: Outliers : 2.93 % Allowed : 21.48 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.37 % Twisted Proline : 0.65 % 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: 0.52 (0.09), residues: 8323 helix: 1.36 (0.07), residues: 5460 sheet: -0.58 (0.20), residues: 588 loop : -1.90 (0.13), residues: 2275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 599 time to evaluate : 6.192 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 outliers start: 204 outliers final: 65 residues processed: 756 average time/residue: 0.6345 time to fit residues: 834.3804 Evaluate side-chains 613 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 548 time to evaluate : 6.130 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 65 outliers final: 1 residues processed: 65 average time/residue: 0.5238 time to fit residues: 72.4094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 674 optimal weight: 2.9990 chunk 459 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 603 optimal weight: 0.8980 chunk 334 optimal weight: 8.9990 chunk 691 optimal weight: 0.6980 chunk 559 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 413 optimal weight: 0.9990 chunk 727 optimal weight: 10.0000 chunk 204 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1602 HIS A1604 GLN C 355 GLN ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN H 599 ASN H 609 HIS I 696 GLN I 740 HIS J 174 HIS ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 449 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 GLN ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN P 202 HIS X 471 GLN Y 531 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 67835 Z= 0.212 Angle : 0.725 18.866 91891 Z= 0.366 Chirality : 0.041 0.260 10362 Planarity : 0.005 0.092 11673 Dihedral : 5.245 51.959 9172 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.17 % Favored : 94.32 % Rotamer: Outliers : 2.02 % Allowed : 21.94 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.37 % Twisted Proline : 0.65 % Twisted General : 0.07 % 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: 0.73 (0.09), residues: 8323 helix: 1.53 (0.07), residues: 5453 sheet: -0.37 (0.21), residues: 552 loop : -1.84 (0.13), residues: 2318 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 668 time to evaluate : 6.518 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: 141 outliers final: 53 residues processed: 778 average time/residue: 0.6833 time to fit residues: 926.6396 Evaluate side-chains 623 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 570 time to evaluate : 6.160 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 53 outliers final: 1 residues processed: 53 average time/residue: 0.5231 time to fit residues: 60.5420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 272 optimal weight: 0.9980 chunk 729 optimal weight: 30.0000 chunk 160 optimal weight: 4.9990 chunk 475 optimal weight: 0.9980 chunk 199 optimal weight: 30.0000 chunk 810 optimal weight: 9.9990 chunk 673 optimal weight: 10.0000 chunk 375 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 268 optimal weight: 8.9990 chunk 425 optimal weight: 5.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 599 ASN I 235 GLN J 350 HIS ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 530 GLN O 211 GLN ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN O 539 ASN P 202 HIS X 251 ASN ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 367 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 67835 Z= 0.263 Angle : 0.723 18.831 91891 Z= 0.365 Chirality : 0.041 0.304 10362 Planarity : 0.004 0.091 11673 Dihedral : 5.123 50.723 9172 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.40 % Favored : 94.10 % Rotamer: Outliers : 1.69 % Allowed : 22.95 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.37 % Twisted Proline : 0.65 % Twisted General : 0.07 % 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: 0.77 (0.09), residues: 8323 helix: 1.56 (0.07), residues: 5469 sheet: -0.47 (0.21), residues: 558 loop : -1.84 (0.13), residues: 2296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 587 time to evaluate : 6.197 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: 118 outliers final: 47 residues processed: 676 average time/residue: 0.6441 time to fit residues: 754.2871 Evaluate side-chains 596 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 549 time to evaluate : 6.098 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.5309 time to fit residues: 54.2476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 781 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 461 optimal weight: 0.9990 chunk 592 optimal weight: 4.9990 chunk 458 optimal weight: 5.9990 chunk 682 optimal weight: 7.9990 chunk 452 optimal weight: 9.9990 chunk 807 optimal weight: 2.9990 chunk 505 optimal weight: 4.9990 chunk 492 optimal weight: 4.9990 chunk 372 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 GLN ** A1170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 599 ASN I 235 GLN I 374 GLN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 530 GLN ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN O 645 HIS O 671 GLN R 404 ASN ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 458 GLN Y 151 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 67835 Z= 0.316 Angle : 0.739 18.849 91891 Z= 0.375 Chirality : 0.042 0.296 10362 Planarity : 0.005 0.090 11673 Dihedral : 5.120 50.120 9172 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.76 % Favored : 93.80 % Rotamer: Outliers : 1.38 % Allowed : 23.74 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.37 % Twisted Proline : 0.65 % Twisted General : 0.07 % 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: 0.76 (0.09), residues: 8323 helix: 1.56 (0.07), residues: 5468 sheet: -0.56 (0.20), residues: 561 loop : -1.84 (0.13), residues: 2294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 576 time to evaluate : 6.272 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 outliers start: 96 outliers final: 45 residues processed: 640 average time/residue: 0.6549 time to fit residues: 728.7164 Evaluate side-chains 584 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 539 time to evaluate : 6.102 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.5249 time to fit residues: 52.4437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 499 optimal weight: 7.9990 chunk 322 optimal weight: 9.9990 chunk 482 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 513 optimal weight: 10.0000 chunk 550 optimal weight: 10.0000 chunk 399 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 634 optimal weight: 8.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 HIS ** A1170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 HIS ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 599 ASN I 235 GLN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 530 GLN ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN R 314 GLN ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 67835 Z= 0.275 Angle : 0.730 18.840 91891 Z= 0.367 Chirality : 0.041 0.306 10362 Planarity : 0.004 0.090 11673 Dihedral : 5.088 49.010 9172 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.48 % Favored : 94.10 % Rotamer: Outliers : 0.92 % Allowed : 24.36 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.37 % Twisted Proline : 0.65 % Twisted General : 0.07 % 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: 0.77 (0.09), residues: 8323 helix: 1.56 (0.07), residues: 5475 sheet: -0.55 (0.21), residues: 562 loop : -1.85 (0.13), residues: 2286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 580 time to evaluate : 6.128 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 outliers start: 64 outliers final: 30 residues processed: 626 average time/residue: 0.6677 time to fit residues: 726.9502 Evaluate side-chains 577 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 547 time to evaluate : 6.101 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.5425 time to fit residues: 38.5727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 734 optimal weight: 9.9990 chunk 773 optimal weight: 5.9990 chunk 705 optimal weight: 20.0000 chunk 752 optimal weight: 1.9990 chunk 453 optimal weight: 2.9990 chunk 327 optimal weight: 0.7980 chunk 591 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 680 optimal weight: 3.9990 chunk 711 optimal weight: 30.0000 chunk 750 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 ASN ** A1170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 GLN H 599 ASN H 759 ASN ** I 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 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 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 530 GLN ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 67835 Z= 0.210 Angle : 0.728 21.103 91891 Z= 0.361 Chirality : 0.041 0.314 10362 Planarity : 0.004 0.090 11673 Dihedral : 4.973 47.615 9172 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.17 % Favored : 94.42 % Rotamer: Outliers : 0.60 % Allowed : 24.87 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.37 % Twisted Proline : 0.65 % 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: 0.82 (0.09), residues: 8323 helix: 1.60 (0.07), residues: 5491 sheet: -0.49 (0.21), residues: 571 loop : -1.84 (0.13), residues: 2261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 609 time to evaluate : 6.127 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 outliers start: 42 outliers final: 14 residues processed: 639 average time/residue: 0.6808 time to fit residues: 761.9612 Evaluate side-chains 569 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 555 time to evaluate : 6.171 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5880 time to fit residues: 22.9486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 494 optimal weight: 7.9990 chunk 795 optimal weight: 20.0000 chunk 485 optimal weight: 10.0000 chunk 377 optimal weight: 10.0000 chunk 553 optimal weight: 3.9990 chunk 834 optimal weight: 0.0060 chunk 768 optimal weight: 8.9990 chunk 664 optimal weight: 0.0050 chunk 69 optimal weight: 2.9990 chunk 513 optimal weight: 9.9990 chunk 407 optimal weight: 0.9980 overall best weight: 1.6014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 599 ASN H 674 HIS ** I 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 373 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 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 458 GLN ** Y 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 67835 Z= 0.219 Angle : 0.742 20.059 91891 Z= 0.367 Chirality : 0.041 0.316 10362 Planarity : 0.004 0.089 11673 Dihedral : 4.917 47.090 9172 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.36 % Favored : 94.24 % Rotamer: Outliers : 0.26 % Allowed : 25.36 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.37 % Twisted Proline : 0.65 % 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: 0.82 (0.09), residues: 8323 helix: 1.60 (0.07), residues: 5482 sheet: -0.43 (0.21), residues: 569 loop : -1.83 (0.13), residues: 2272 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16646 Ramachandran restraints generated. 8323 Oldfield, 0 Emsley, 8323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 579 time to evaluate : 6.147 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 outliers start: 18 outliers final: 5 residues processed: 591 average time/residue: 0.6563 time to fit residues: 676.4244 Evaluate side-chains 556 residues out of total 7403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 551 time to evaluate : 6.085 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5320 time to fit residues: 13.0821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 528 optimal weight: 0.8980 chunk 708 optimal weight: 0.9980 chunk 203 optimal weight: 9.9990 chunk 612 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 chunk 665 optimal weight: 10.0000 chunk 278 optimal weight: 6.9990 chunk 683 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 GLN ** A1170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 599 ASN I 235 GLN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 373 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 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.068823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.052078 restraints weight = 325367.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.053671 restraints weight = 166897.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.054690 restraints weight = 107054.558| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 67835 Z= 0.212 Angle : 0.737 18.812 91891 Z= 0.364 Chirality : 0.041 0.314 10362 Planarity : 0.004 0.087 11673 Dihedral : 4.869 46.196 9172 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.38 % Favored : 94.22 % Rotamer: Outliers : 0.37 % Allowed : 25.25 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.90 % Cis-general : 0.37 % 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: 0.87 (0.09), residues: 8323 helix: 1.63 (0.07), residues: 5479 sheet: -0.37 (0.21), residues: 567 loop : -1.83 (0.13), residues: 2277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15928.15 seconds wall clock time: 281 minutes 27.39 seconds (16887.39 seconds total)