Starting phenix.real_space_refine on Mon Dec 30 22:52:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9egx_48039/12_2024/9egx_48039.cif Found real_map, /net/cci-nas-00/data/ceres_data/9egx_48039/12_2024/9egx_48039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9egx_48039/12_2024/9egx_48039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9egx_48039/12_2024/9egx_48039.map" model { file = "/net/cci-nas-00/data/ceres_data/9egx_48039/12_2024/9egx_48039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9egx_48039/12_2024/9egx_48039.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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: 7 Type Number sf(0) Gaussians Zn 9 6.06 5 P 330 5.49 5 Mg 1 5.21 5 S 257 5.16 5 C 39335 2.51 5 N 11908 2.21 5 O 13163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 65003 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 11210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1426, 11210 Classifications: {'peptide': 1426} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1353} Chain breaks: 7 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'TPO:plan-1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 8980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8980 Classifications: {'peptide': 1122} Link IDs: {'PTRANS': 52, 'TRANS': 1069} Chain breaks: 4 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2072 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "D" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 626 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1333 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1197 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 397 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "M" Number of atoms: 4309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 4309 Classifications: {'peptide': 1002} Incomplete info: {'backbone_only': 747, 'truncation_to_alanine': 161} Link IDs: {'PTRANS': 44, 'TRANS': 957} Chain breaks: 12 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 4067 Unresolved non-hydrogen angles: 5716 Unresolved non-hydrogen dihedrals: 2768 Unresolved non-hydrogen chiralities: 1012 Planarities with less than four sites: {'GLN:plan1': 49, 'HIS:plan': 25, 'TYR:plan': 40, 'ASN:plan1': 36, 'TRP:plan': 11, 'ASP:plan': 61, 'PHE:plan': 46, 'GLU:plan': 95, 'ARG:plan': 68} Unresolved non-hydrogen planarities: 2160 Chain: "N" Number of atoms: 3048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3048 Classifications: {'DNA': 148} Link IDs: {'rna3p': 147} Chain breaks: 1 Chain: "O" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 656 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 7, 'TRANS': 124} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 407 Unresolved non-hydrogen angles: 508 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 181 Chain: "P" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 432 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 5, 'rna3p_pur': 3, 'rna3p_pyr': 12} Link IDs: {'rna2p': 6, 'rna3p': 14} Chain: "Q" Number of atoms: 6427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 6427 Classifications: {'peptide': 890} Incomplete info: {'truncation_to_alanine': 230} Link IDs: {'CIS': 2, 'PTRANS': 19, 'TRANS': 868} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 843 Unresolved non-hydrogen angles: 1069 Unresolved non-hydrogen dihedrals: 693 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 20, 'TYR:plan': 11, 'ASN:plan1': 15, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 8, 'GLU:plan': 18, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 458 Chain: "R" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1428 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 235} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 755 Unresolved non-hydrogen dihedrals: 500 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 8, 'GLU:plan': 19, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 342 Chain: "S" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 657 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 148} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain breaks: 1 Unresolved non-hydrogen bonds: 628 Unresolved non-hydrogen angles: 894 Unresolved non-hydrogen dihedrals: 391 Unresolved non-hydrogen chiralities: 187 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 297 Chain: "T" Number of atoms: 3245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3245 Classifications: {'DNA': 159} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 158} Chain: "U" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 617 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain breaks: 3 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 426 Unresolved non-hydrogen angles: 542 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 8, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 248 Chain: "V" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1378 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'CIS': 2, 'PTRANS': 14, 'TRANS': 227} Chain breaks: 4 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 697 Unresolved non-hydrogen angles: 889 Unresolved non-hydrogen dihedrals: 583 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 7, 'GLU:plan': 23, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 425 Chain: "W" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2333 Classifications: {'peptide': 300} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 291} Chain: "X" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 353 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 4025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4025 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 490} Chain breaks: 5 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "a" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 627 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "b" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "c" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "d" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" 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} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 472 SG CYS A 71 82.430 158.581 168.227 1.00184.52 S ATOM 494 SG CYS A 74 86.230 158.515 168.819 1.00181.13 S ATOM 541 SG CYS A 81 84.633 161.520 166.910 1.00144.87 S ATOM 19760 SG CYS B1119 98.306 149.885 164.197 1.00170.15 S ATOM 19782 SG CYS B1122 96.235 148.847 161.140 1.00170.01 S ATOM 19897 SG CYS B1137 94.498 149.573 164.438 1.00162.36 S ATOM 19918 SG CYS B1140 96.611 146.444 163.919 1.00179.35 S ATOM 20884 SG CYS C 88 77.567 226.083 167.068 1.00174.75 S ATOM 20897 SG CYS C 90 75.498 226.048 168.750 1.00186.13 S ATOM 20954 SG CYS C 97 75.707 227.124 164.403 1.00132.75 S ATOM 28204 SG CYS I 17 61.387 139.740 78.860 1.00134.60 S ATOM 28228 SG CYS I 20 60.844 139.248 82.099 1.00123.55 S ATOM 28389 SG CYS I 39 63.804 137.817 82.215 1.00147.86 S ATOM 28766 SG CYS I 86 70.643 182.467 68.437 1.00140.85 S ATOM 28790 SG CYS I 89 67.505 184.435 67.699 1.00133.42 S ATOM 28994 SG CYS I 114 68.530 183.927 71.270 1.00102.80 S ATOM 29029 SG CYS I 119 67.267 180.942 69.102 1.00127.06 S ATOM 29139 SG CYS J 7 75.899 221.852 132.239 1.00106.72 S ATOM 29427 SG CYS J 44 78.650 223.645 129.722 1.00138.35 S ATOM 29433 SG CYS J 45 75.610 225.290 131.116 1.00117.57 S ATOM 55949 SG CYS Y 19 38.378 115.513 151.883 1.00122.23 S Residues with excluded nonbonded symmetry interactions: 94 residue: pdb=" N ASN M1145 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN M1145 " occ=0.00 residue: pdb=" N THR M1146 " occ=0.00 ... (2 atoms not shown) pdb=" O THR M1146 " occ=0.00 residue: pdb=" N GLU M1147 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1147 " occ=0.00 residue: pdb=" N GLU M1148 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1148 " occ=0.00 residue: pdb=" N ILE M1149 " occ=0.00 ... (2 atoms not shown) pdb=" O ILE M1149 " occ=0.00 residue: pdb=" N PHE M1150 " occ=0.00 ... (2 atoms not shown) pdb=" O PHE M1150 " occ=0.00 residue: pdb=" N ASN M1151 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN M1151 " occ=0.00 residue: pdb=" N MET M1152 " occ=0.00 ... (2 atoms not shown) pdb=" O MET M1152 " occ=0.00 residue: pdb=" N LEU M1153 " occ=0.00 ... (2 atoms not shown) pdb=" O LEU M1153 " occ=0.00 residue: pdb=" N THR M1154 " occ=0.00 ... (2 atoms not shown) pdb=" O THR M1154 " occ=0.00 residue: pdb=" N LYS M1155 " occ=0.00 ... (2 atoms not shown) pdb=" O LYS M1155 " occ=0.00 residue: pdb=" N GLU M1156 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1156 " occ=0.00 ... (remaining 82 not shown) Time building chain proxies: 26.67, per 1000 atoms: 0.41 Number of scatterers: 65003 At special positions: 0 Unit cell: (197.806, 318.687, 269.235, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 9 29.99 S 257 16.00 P 330 15.00 Mg 1 11.99 O 13163 8.00 N 11908 7.00 C 39335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.53 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " Number of angles added : 15 16080 Ramachandran restraints generated. 8040 Oldfield, 0 Emsley, 8040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13658 Finding SS restraints... Secondary structure from input PDB file: 304 helices and 84 sheets defined 43.8% alpha, 11.7% beta 159 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 18.18 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.765A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 148 removed outlier: 3.667A pdb=" N CYS A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.578A pdb=" N VAL A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 235 removed outlier: 4.214A pdb=" N VAL A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 301 through 319 removed outlier: 4.326A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.665A pdb=" N ALA A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.678A pdb=" N LEU A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 439' Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.879A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 539 through 549 removed outlier: 3.741A pdb=" N THR A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.885A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 removed outlier: 3.558A pdb=" N GLU A 613 " --> pdb=" O PRO A 610 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP A 614 " --> pdb=" O ASP A 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 610 through 614' Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.821A pdb=" N ASN A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 697 through 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 785 removed outlier: 3.528A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 830 removed outlier: 3.820A pdb=" N GLY A 830 " --> pdb=" O TYR A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 868 removed outlier: 4.501A pdb=" N GLY A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 918 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.943A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.505A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1039 through 1049 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1151 through 1162 removed outlier: 4.230A pdb=" N ASP A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 3.769A pdb=" N MET A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1239 removed outlier: 3.923A pdb=" N PHE A1239 " --> pdb=" O ILE A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1295 removed outlier: 4.050A pdb=" N LEU A1285 " --> pdb=" O ASP A1281 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A1295 " --> pdb=" O ASN A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1348 removed outlier: 3.846A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1367 removed outlier: 4.090A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A1366 " --> pdb=" O ILE A1362 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR A1367 " --> pdb=" O VAL A1363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1361 through 1367' Processing helix chain 'A' and resid 1370 through 1387 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.889A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 removed outlier: 3.844A pdb=" N ASN A1420 " --> pdb=" O ARG A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1433 removed outlier: 4.058A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 3.826A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A1482 " --> pdb=" O LYS A1479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1478 through 1482' Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.948A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 5.032A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 268 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.656A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.679A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.621A pdb=" N ALA B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 removed outlier: 3.665A pdb=" N ARG B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 425 removed outlier: 3.698A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'B' and resid 474 through 483 removed outlier: 3.529A pdb=" N ARG B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.937A pdb=" N TRP B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.805A pdb=" N ASN B 585 " --> pdb=" O GLU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.515A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 660 removed outlier: 3.727A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 660 " --> pdb=" O LEU B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 673 removed outlier: 3.796A pdb=" N VAL B 673 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 684 removed outlier: 4.197A pdb=" N GLU B 684 " --> pdb=" O ASP B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 4.063A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.226A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.885A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1016 removed outlier: 3.931A pdb=" N ILE B1011 " --> pdb=" O ASN B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1019 No H-bonds generated for 'chain 'B' and resid 1017 through 1019' Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 27 through 40 Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.927A pdb=" N ILE C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.626A pdb=" N SER C 98 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 270 Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.891A pdb=" N THR D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.870A pdb=" N SER D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 69 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.517A pdb=" N ILE D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 removed outlier: 3.841A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU D 100 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.632A pdb=" N LEU D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.548A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 45 Processing helix chain 'E' and resid 84 through 95 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.642A pdb=" N LYS E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 32 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'I' and resid 63 through 68 removed outlier: 3.989A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 74 removed outlier: 3.508A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 28 removed outlier: 3.922A pdb=" N GLU J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 removed outlier: 4.352A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 51 Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.803A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 10 removed outlier: 3.986A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 10' Processing helix chain 'K' and resid 40 through 53 removed outlier: 4.481A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'M' and resid 285 through 291 removed outlier: 3.683A pdb=" N ILE M 289 " --> pdb=" O GLN M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 302 Processing helix chain 'M' and resid 309 through 323 removed outlier: 4.296A pdb=" N GLU M 314 " --> pdb=" O ASP M 310 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU M 315 " --> pdb=" O ASP M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 370 Processing helix chain 'M' and resid 372 through 379 Processing helix chain 'M' and resid 392 through 429 Processing helix chain 'M' and resid 445 through 453 removed outlier: 4.078A pdb=" N GLU M 449 " --> pdb=" O THR M 445 " (cutoff:3.500A) Processing helix chain 'M' and resid 456 through 472 Processing helix chain 'M' and resid 542 through 553 Processing helix chain 'M' and resid 565 through 570 Processing helix chain 'M' and resid 586 through 598 removed outlier: 3.566A pdb=" N TYR M 590 " --> pdb=" O GLU M 586 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET M 591 " --> pdb=" O GLY M 587 " (cutoff:3.500A) Processing helix chain 'M' and resid 599 through 607 Processing helix chain 'M' and resid 623 through 629 removed outlier: 3.644A pdb=" N ASP M 629 " --> pdb=" O ARG M 625 " (cutoff:3.500A) Processing helix chain 'M' and resid 632 through 637 removed outlier: 4.615A pdb=" N PHE M 637 " --> pdb=" O TYR M 633 " (cutoff:3.500A) Processing helix chain 'M' and resid 644 through 650 removed outlier: 3.771A pdb=" N LEU M 648 " --> pdb=" O PRO M 644 " (cutoff:3.500A) Processing helix chain 'M' and resid 651 through 664 removed outlier: 3.621A pdb=" N LYS M 655 " --> pdb=" O ASP M 651 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU M 664 " --> pdb=" O GLU M 660 " (cutoff:3.500A) Processing helix chain 'M' and resid 685 through 692 removed outlier: 4.243A pdb=" N ILE M 689 " --> pdb=" O TYR M 685 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS M 690 " --> pdb=" O PHE M 686 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN M 691 " --> pdb=" O GLU M 687 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE M 692 " --> pdb=" O GLU M 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 685 through 692' Processing helix chain 'M' and resid 700 through 721 Processing helix chain 'M' and resid 721 through 754 removed outlier: 3.586A pdb=" N MET M 725 " --> pdb=" O LEU M 721 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG M 754 " --> pdb=" O TYR M 750 " (cutoff:3.500A) Processing helix chain 'M' and resid 759 through 763 removed outlier: 3.778A pdb=" N GLN M 763 " --> pdb=" O PRO M 760 " (cutoff:3.500A) Processing helix chain 'M' and resid 830 through 843 removed outlier: 3.749A pdb=" N LYS M 843 " --> pdb=" O PHE M 839 " (cutoff:3.500A) Processing helix chain 'M' and resid 854 through 872 Processing helix chain 'M' and resid 888 through 895 removed outlier: 4.150A pdb=" N LEU M 892 " --> pdb=" O GLU M 888 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN M 895 " --> pdb=" O ILE M 891 " (cutoff:3.500A) Processing helix chain 'M' and resid 896 through 903 Processing helix chain 'M' and resid 907 through 920 Processing helix chain 'M' and resid 922 through 929 Processing helix chain 'M' and resid 936 through 940 removed outlier: 4.263A pdb=" N LEU M 940 " --> pdb=" O ASP M 936 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 936 through 940' Processing helix chain 'M' and resid 944 through 949 removed outlier: 4.242A pdb=" N HIS M 948 " --> pdb=" O PRO M 944 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL M 949 " --> pdb=" O LEU M 945 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 944 through 949' Processing helix chain 'M' and resid 950 through 970 removed outlier: 3.976A pdb=" N LEU M 954 " --> pdb=" O VAL M 950 " (cutoff:3.500A) Processing helix chain 'M' and resid 993 through 1008 Processing helix chain 'M' and resid 1015 through 1020 Processing helix chain 'M' and resid 1024 through 1031 Processing helix chain 'M' and resid 1062 through 1075 Processing helix chain 'M' and resid 1086 through 1095 removed outlier: 3.829A pdb=" N ILE M1092 " --> pdb=" O ALA M1088 " (cutoff:3.500A) Processing helix chain 'M' and resid 1103 through 1114 Processing helix chain 'M' and resid 1121 through 1132 removed outlier: 4.214A pdb=" N ASP M1125 " --> pdb=" O ILE M1121 " (cutoff:3.500A) Processing helix chain 'M' and resid 1145 through 1154 Processing helix chain 'M' and resid 1241 through 1246 removed outlier: 3.740A pdb=" N LEU M1245 " --> pdb=" O PRO M1241 " (cutoff:3.500A) Processing helix chain 'M' and resid 1282 through 1287 removed outlier: 3.897A pdb=" N LEU M1286 " --> pdb=" O ARG M1282 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET M1287 " --> pdb=" O THR M1283 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1282 through 1287' Processing helix chain 'M' and resid 1342 through 1347 removed outlier: 3.558A pdb=" N MET M1347 " --> pdb=" O GLU M1344 " (cutoff:3.500A) Processing helix chain 'M' and resid 1402 through 1406 Processing helix chain 'M' and resid 1410 through 1416 Processing helix chain 'M' and resid 1416 through 1428 removed outlier: 3.600A pdb=" N LEU M1426 " --> pdb=" O PHE M1422 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN M1428 " --> pdb=" O ARG M1424 " (cutoff:3.500A) Processing helix chain 'M' and resid 1434 through 1439 removed outlier: 3.814A pdb=" N ASP M1439 " --> pdb=" O CYS M1435 " (cutoff:3.500A) Processing helix chain 'M' and resid 1441 through 1452 removed outlier: 4.384A pdb=" N GLU M1445 " --> pdb=" O LYS M1441 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU M1446 " --> pdb=" O LYS M1442 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU M1447 " --> pdb=" O LEU M1443 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE M1448 " --> pdb=" O GLU M1444 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS M1452 " --> pdb=" O ILE M1448 " (cutoff:3.500A) Processing helix chain 'M' and resid 1503 through 1512 removed outlier: 4.067A pdb=" N LEU M1507 " --> pdb=" O THR M1503 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE M1508 " --> pdb=" O VAL M1504 " (cutoff:3.500A) Processing helix chain 'O' and resid 555 through 580 Processing helix chain 'O' and resid 585 through 590 Processing helix chain 'O' and resid 590 through 599 removed outlier: 3.736A pdb=" N HIS O 597 " --> pdb=" O ALA O 593 " (cutoff:3.500A) Processing helix chain 'O' and resid 600 through 602 No H-bonds generated for 'chain 'O' and resid 600 through 602' Processing helix chain 'O' and resid 603 through 611 removed outlier: 3.695A pdb=" N GLY O 611 " --> pdb=" O PHE O 607 " (cutoff:3.500A) Processing helix chain 'O' and resid 611 through 621 Processing helix chain 'O' and resid 630 through 642 removed outlier: 3.757A pdb=" N GLU O 636 " --> pdb=" O LYS O 632 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS O 639 " --> pdb=" O GLU O 635 " (cutoff:3.500A) Processing helix chain 'O' and resid 648 through 656 removed outlier: 3.545A pdb=" N LEU O 652 " --> pdb=" O SER O 648 " (cutoff:3.500A) Processing helix chain 'O' and resid 656 through 666 Processing helix chain 'O' and resid 671 through 685 removed outlier: 3.736A pdb=" N LYS O 675 " --> pdb=" O SER O 671 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET O 677 " --> pdb=" O SER O 673 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 34 removed outlier: 4.175A pdb=" N ILE Q 31 " --> pdb=" O GLY Q 27 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER Q 32 " --> pdb=" O ASP Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 53 removed outlier: 4.121A pdb=" N TRP Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE Q 45 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 64 removed outlier: 3.923A pdb=" N LEU Q 64 " --> pdb=" O PHE Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 69 removed outlier: 3.886A pdb=" N ARG Q 68 " --> pdb=" O GLU Q 65 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE Q 69 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 65 through 69' Processing helix chain 'Q' and resid 78 through 99 removed outlier: 3.635A pdb=" N GLN Q 82 " --> pdb=" O HIS Q 78 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR Q 88 " --> pdb=" O THR Q 84 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU Q 89 " --> pdb=" O CYS Q 85 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR Q 93 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL Q 94 " --> pdb=" O ALA Q 90 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG Q 98 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS Q 99 " --> pdb=" O GLN Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 121 removed outlier: 3.727A pdb=" N LEU Q 109 " --> pdb=" O ASN Q 105 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN Q 112 " --> pdb=" O ASP Q 108 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU Q 116 " --> pdb=" O GLN Q 112 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR Q 118 " --> pdb=" O THR Q 114 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET Q 119 " --> pdb=" O LEU Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 142 removed outlier: 3.574A pdb=" N PHE Q 137 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N CYS Q 138 " --> pdb=" O ARG Q 134 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU Q 139 " --> pdb=" O ALA Q 135 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU Q 140 " --> pdb=" O CYS Q 136 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU Q 141 " --> pdb=" O PHE Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 removed outlier: 3.580A pdb=" N PHE Q 154 " --> pdb=" O ALA Q 150 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL Q 155 " --> pdb=" O GLN Q 151 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU Q 156 " --> pdb=" O PHE Q 152 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN Q 157 " --> pdb=" O HIS Q 153 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER Q 159 " --> pdb=" O VAL Q 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 163 through 176 removed outlier: 3.766A pdb=" N GLY Q 168 " --> pdb=" O PRO Q 164 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LYS Q 169 " --> pdb=" O ALA Q 165 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA Q 170 " --> pdb=" O LEU Q 166 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS Q 171 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE Q 172 " --> pdb=" O GLY Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 178 through 187 removed outlier: 3.538A pdb=" N ALA Q 182 " --> pdb=" O ASP Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 192 removed outlier: 3.786A pdb=" N ARG Q 191 " --> pdb=" O LYS Q 187 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR Q 192 " --> pdb=" O LYS Q 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 187 through 192' Processing helix chain 'Q' and resid 200 through 208 removed outlier: 3.950A pdb=" N MET Q 204 " --> pdb=" O VAL Q 200 " (cutoff:3.500A) Processing helix chain 'Q' and resid 213 through 228 removed outlier: 3.538A pdb=" N ARG Q 218 " --> pdb=" O LEU Q 214 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU Q 219 " --> pdb=" O GLU Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 242 removed outlier: 3.629A pdb=" N GLY Q 237 " --> pdb=" O GLY Q 233 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU Q 238 " --> pdb=" O ALA Q 234 " (cutoff:3.500A) Processing helix chain 'Q' and resid 249 through 255 removed outlier: 3.814A pdb=" N ASN Q 253 " --> pdb=" O ASP Q 249 " (cutoff:3.500A) Processing helix chain 'Q' and resid 258 through 265 Processing helix chain 'Q' and resid 268 through 282 removed outlier: 3.929A pdb=" N PHE Q 281 " --> pdb=" O ASN Q 277 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS Q 282 " --> pdb=" O HIS Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 284 through 295 removed outlier: 4.047A pdb=" N VAL Q 288 " --> pdb=" O ASP Q 284 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN Q 289 " --> pdb=" O TYR Q 285 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS Q 290 " --> pdb=" O SER Q 286 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU Q 293 " --> pdb=" O GLN Q 289 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS Q 294 " --> pdb=" O HIS Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 318 removed outlier: 4.080A pdb=" N GLN Q 305 " --> pdb=" O VAL Q 301 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA Q 306 " --> pdb=" O GLU Q 302 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU Q 307 " --> pdb=" O ALA Q 303 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL Q 318 " --> pdb=" O ARG Q 314 " (cutoff:3.500A) Processing helix chain 'Q' and resid 321 through 336 removed outlier: 3.963A pdb=" N ALA Q 325 " --> pdb=" O ASP Q 321 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN Q 327 " --> pdb=" O ASP Q 323 " (cutoff:3.500A) Processing helix chain 'Q' and resid 341 through 351 Processing helix chain 'Q' and resid 352 through 355 Processing helix chain 'Q' and resid 356 through 366 removed outlier: 3.813A pdb=" N ALA Q 360 " --> pdb=" O ASP Q 356 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS Q 366 " --> pdb=" O GLN Q 362 " (cutoff:3.500A) Processing helix chain 'Q' and resid 366 through 371 removed outlier: 3.746A pdb=" N ALA Q 370 " --> pdb=" O LYS Q 366 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR Q 371 " --> pdb=" O VAL Q 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 366 through 371' Processing helix chain 'Q' and resid 375 through 383 removed outlier: 3.515A pdb=" N LYS Q 379 " --> pdb=" O TYR Q 375 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE Q 380 " --> pdb=" O GLU Q 376 " (cutoff:3.500A) Processing helix chain 'Q' and resid 390 through 405 removed outlier: 3.653A pdb=" N ASP Q 395 " --> pdb=" O GLN Q 391 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE Q 396 " --> pdb=" O GLU Q 392 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA Q 397 " --> pdb=" O LYS Q 393 " (cutoff:3.500A) Processing helix chain 'Q' and resid 413 through 423 removed outlier: 3.533A pdb=" N ILE Q 421 " --> pdb=" O GLU Q 417 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU Q 422 " --> pdb=" O LEU Q 418 " (cutoff:3.500A) Processing helix chain 'Q' and resid 426 through 441 removed outlier: 4.155A pdb=" N ALA Q 430 " --> pdb=" O ASP Q 426 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU Q 431 " --> pdb=" O ILE Q 427 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG Q 439 " --> pdb=" O GLY Q 435 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU Q 441 " --> pdb=" O ALA Q 437 " (cutoff:3.500A) Processing helix chain 'Q' and resid 450 through 464 removed outlier: 3.726A pdb=" N LEU Q 454 " --> pdb=" O PRO Q 450 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG Q 463 " --> pdb=" O ALA Q 459 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU Q 464 " --> pdb=" O LEU Q 460 " (cutoff:3.500A) Processing helix chain 'Q' and resid 466 through 484 Processing helix chain 'Q' and resid 491 through 510 Processing helix chain 'Q' and resid 512 through 527 removed outlier: 3.620A pdb=" N ALA Q 516 " --> pdb=" O GLU Q 512 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU Q 526 " --> pdb=" O ASN Q 522 " (cutoff:3.500A) Processing helix chain 'Q' and resid 531 through 545 removed outlier: 3.941A pdb=" N GLY Q 538 " --> pdb=" O TYR Q 534 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS Q 544 " --> pdb=" O MET Q 540 " (cutoff:3.500A) Processing helix chain 'Q' and resid 548 through 561 removed outlier: 4.042A pdb=" N ASP Q 552 " --> pdb=" O TYR Q 548 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS Q 555 " --> pdb=" O SER Q 551 " (cutoff:3.500A) Processing helix chain 'Q' and resid 564 through 575 removed outlier: 3.885A pdb=" N HIS Q 575 " --> pdb=" O ILE Q 571 " (cutoff:3.500A) Processing helix chain 'Q' and resid 584 through 590 removed outlier: 4.188A pdb=" N PHE Q 588 " --> pdb=" O GLY Q 584 " (cutoff:3.500A) Processing helix chain 'Q' and resid 600 through 613 removed outlier: 3.519A pdb=" N MET Q 604 " --> pdb=" O ASP Q 600 " (cutoff:3.500A) Processing helix chain 'Q' and resid 619 through 623 Processing helix chain 'Q' and resid 624 through 642 Processing helix chain 'Q' and resid 646 through 660 removed outlier: 3.988A pdb=" N ALA Q 650 " --> pdb=" O ASN Q 646 " (cutoff:3.500A) Processing helix chain 'Q' and resid 663 through 677 removed outlier: 3.748A pdb=" N ARG Q 667 " --> pdb=" O PHE Q 663 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP Q 668 " --> pdb=" O ARG Q 664 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL Q 669 " --> pdb=" O GLU Q 665 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN Q 672 " --> pdb=" O ASP Q 668 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL Q 673 " --> pdb=" O VAL Q 669 " (cutoff:3.500A) Processing helix chain 'Q' and resid 680 through 694 removed outlier: 3.845A pdb=" N TRP Q 684 " --> pdb=" O ILE Q 680 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU Q 685 " --> pdb=" O SER Q 681 " (cutoff:3.500A) Processing helix chain 'Q' and resid 700 through 708 removed outlier: 3.574A pdb=" N CYS Q 707 " --> pdb=" O MET Q 703 " (cutoff:3.500A) Processing helix chain 'Q' and resid 716 through 724 removed outlier: 3.679A pdb=" N VAL Q 720 " --> pdb=" O ASN Q 716 " (cutoff:3.500A) Processing helix chain 'Q' and resid 729 through 732 Processing helix chain 'Q' and resid 733 through 747 removed outlier: 3.923A pdb=" N VAL Q 746 " --> pdb=" O LYS Q 742 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA Q 747 " --> pdb=" O ALA Q 743 " (cutoff:3.500A) Processing helix chain 'Q' and resid 750 through 770 removed outlier: 3.876A pdb=" N MET Q 754 " --> pdb=" O ASP Q 750 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA Q 758 " --> pdb=" O MET Q 754 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS Q 770 " --> pdb=" O THR Q 766 " (cutoff:3.500A) Processing helix chain 'Q' and resid 775 through 797 removed outlier: 3.582A pdb=" N VAL Q 779 " --> pdb=" O ASN Q 775 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL Q 783 " --> pdb=" O VAL Q 779 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS Q 784 " --> pdb=" O LEU Q 780 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER Q 797 " --> pdb=" O PHE Q 793 " (cutoff:3.500A) Processing helix chain 'Q' and resid 807 through 809 No H-bonds generated for 'chain 'Q' and resid 807 through 809' Processing helix chain 'Q' and resid 810 through 892 removed outlier: 4.359A pdb=" N ALA Q 829 " --> pdb=" O GLN Q 825 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG Q 830 " --> pdb=" O TYR Q 826 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU Q 848 " --> pdb=" O LYS Q 844 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU Q 883 " --> pdb=" O ALA Q 879 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS Q 886 " --> pdb=" O VAL Q 882 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN Q 887 " --> pdb=" O GLU Q 883 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR Q 892 " --> pdb=" O ILE Q 888 " (cutoff:3.500A) Processing helix chain 'R' and resid 355 through 360 removed outlier: 3.647A pdb=" N LEU R 359 " --> pdb=" O LEU R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 361 through 363 No H-bonds generated for 'chain 'R' and resid 361 through 363' Processing helix chain 'R' and resid 367 through 372 removed outlier: 3.618A pdb=" N GLU R 370 " --> pdb=" O HIS R 367 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP R 372 " --> pdb=" O LEU R 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 382 removed outlier: 3.657A pdb=" N VAL R 382 " --> pdb=" O PHE R 378 " (cutoff:3.500A) Processing helix chain 'R' and resid 448 through 463 Processing helix chain 'R' and resid 468 through 484 removed outlier: 4.150A pdb=" N LEU R 477 " --> pdb=" O ASN R 473 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER R 478 " --> pdb=" O LYS R 474 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE R 479 " --> pdb=" O LYS R 475 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS R 480 " --> pdb=" O GLU R 476 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN R 484 " --> pdb=" O LYS R 480 " (cutoff:3.500A) Processing helix chain 'R' and resid 491 through 503 removed outlier: 3.899A pdb=" N PHE R 502 " --> pdb=" O GLU R 498 " (cutoff:3.500A) Processing helix chain 'R' and resid 510 through 525 Processing helix chain 'R' and resid 527 through 553 removed outlier: 3.533A pdb=" N LYS R 531 " --> pdb=" O GLY R 527 " (cutoff:3.500A) Processing helix chain 'R' and resid 556 through 585 removed outlier: 3.693A pdb=" N SER R 561 " --> pdb=" O ILE R 557 " (cutoff:3.500A) Processing helix chain 'S' and resid 138 through 153 Processing helix chain 'S' and resid 156 through 162 removed outlier: 3.612A pdb=" N ALA S 160 " --> pdb=" O ASP S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 164 through 181 Processing helix chain 'S' and resid 184 through 199 Processing helix chain 'S' and resid 203 through 212 removed outlier: 4.332A pdb=" N ARG S 207 " --> pdb=" O ASN S 203 " (cutoff:3.500A) Processing helix chain 'S' and resid 216 through 223 Processing helix chain 'S' and resid 224 through 229 Processing helix chain 'S' and resid 230 through 249 removed outlier: 3.650A pdb=" N GLN S 249 " --> pdb=" O ILE S 245 " (cutoff:3.500A) Processing helix chain 'U' and resid 379 through 383 removed outlier: 3.505A pdb=" N SER U 383 " --> pdb=" O ASN U 380 " (cutoff:3.500A) Processing helix chain 'U' and resid 411 through 415 Processing helix chain 'V' and resid 63 through 68 removed outlier: 3.507A pdb=" N LYS V 68 " --> pdb=" O THR V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 106 Processing helix chain 'V' and resid 122 through 126 removed outlier: 3.599A pdb=" N ALA V 125 " --> pdb=" O GLN V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 172 through 186 removed outlier: 3.850A pdb=" N THR V 177 " --> pdb=" O ASP V 173 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA V 186 " --> pdb=" O THR V 182 " (cutoff:3.500A) Processing helix chain 'X' and resid 219 through 226 removed outlier: 3.541A pdb=" N SER X 226 " --> pdb=" O ARG X 222 " (cutoff:3.500A) Processing helix chain 'X' and resid 233 through 239 removed outlier: 3.869A pdb=" N ILE X 237 " --> pdb=" O THR X 233 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU X 238 " --> pdb=" O ARG X 234 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN X 239 " --> pdb=" O THR X 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 233 through 239' Processing helix chain 'X' and resid 246 through 260 removed outlier: 3.769A pdb=" N ALA X 251 " --> pdb=" O LYS X 247 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE X 252 " --> pdb=" O ASN X 248 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS X 257 " --> pdb=" O LEU X 253 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU X 260 " --> pdb=" O VAL X 256 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 31 Processing helix chain 'Y' and resid 46 through 53 Processing helix chain 'Y' and resid 69 through 76 Processing helix chain 'Y' and resid 97 through 104 removed outlier: 3.729A pdb=" N LEU Y 101 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS Y 102 " --> pdb=" O VAL Y 98 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER Y 103 " --> pdb=" O ARG Y 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 231 through 239 removed outlier: 4.043A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 246 through 250 removed outlier: 3.612A pdb=" N TYR Z 249 " --> pdb=" O ARG Z 246 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP Z 250 " --> pdb=" O LEU Z 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 246 through 250' Processing helix chain 'Z' and resid 256 through 261 removed outlier: 4.228A pdb=" N THR Z 261 " --> pdb=" O LYS Z 258 " (cutoff:3.500A) Processing helix chain 'Z' and resid 379 through 381 No H-bonds generated for 'chain 'Z' and resid 379 through 381' Processing helix chain 'Z' and resid 389 through 396 Processing helix chain 'Z' and resid 630 through 634 Processing helix chain 'a' and resid 63 through 79 Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 removed outlier: 3.668A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 77 removed outlier: 3.582A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.347A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.532A pdb=" N LEU c 83 " --> pdb=" O ILE c 79 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 Processing helix chain 'd' and resid 34 through 46 Processing helix chain 'd' and resid 52 through 81 Processing helix chain 'd' and resid 87 through 99 Processing helix chain 'd' and resid 100 through 121 Processing helix chain 'e' and resid 44 through 56 removed outlier: 3.589A pdb=" N LEU e 48 " --> pdb=" O GLY e 44 " (cutoff:3.500A) Processing helix chain 'e' and resid 63 through 77 removed outlier: 3.733A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP e 77 " --> pdb=" O GLU e 73 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 removed outlier: 3.619A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 47 through 76 removed outlier: 4.162A pdb=" N TYR f 51 " --> pdb=" O SER f 47 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU f 52 " --> pdb=" O GLY f 48 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 3.686A pdb=" N VAL A 21 " --> pdb=" O ASP A1449 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 193 removed outlier: 3.505A pdb=" N TYR A 199 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.602A pdb=" N LYS A 357 " --> pdb=" O PHE B1086 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 365 removed outlier: 3.968A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET A 501 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET A 470 " --> pdb=" O PHE A 458 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 369 removed outlier: 3.956A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.170A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA8, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.439A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA H 114 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU H 121 " --> pdb=" O TYR H 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.439A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AB2, first strand: chain 'A' and resid 872 through 874 removed outlier: 3.933A pdb=" N THR A 878 " --> pdb=" O LYS A 874 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB4, first strand: chain 'A' and resid 1211 through 1216 removed outlier: 3.526A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 3.561A pdb=" N ARG A1260 " --> pdb=" O ASN A1244 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1308 through 1310 removed outlier: 3.727A pdb=" N GLU A1337 " --> pdb=" O TYR A1308 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A1310 " --> pdb=" O ILE A1335 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE A1335 " --> pdb=" O HIS A1310 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1471 through 1475 removed outlier: 3.607A pdb=" N ASP A1472 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.517A pdb=" N ARG B 83 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.517A pdb=" N ARG B 83 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N LYS B 134 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N LEU B 140 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 185 through 186 Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.917A pdb=" N GLU B 198 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 205 through 208 Processing sheet with id=AC4, first strand: chain 'B' and resid 205 through 208 removed outlier: 4.093A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC6, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC7, first strand: chain 'B' and resid 572 through 577 removed outlier: 4.532A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 602 " --> pdb=" O TYR B 615 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 749 through 751 removed outlier: 3.950A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG B 922 " --> pdb=" O GLN B 906 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET L 44 " --> pdb=" O VAL B 909 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD1, first strand: chain 'B' and resid 775 through 782 removed outlier: 4.171A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 775 through 782 removed outlier: 4.171A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 826 through 829 removed outlier: 4.094A pdb=" N GLU B 826 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 837 through 839 Processing sheet with id=AD5, first strand: chain 'B' and resid 1115 through 1119 removed outlier: 3.557A pdb=" N SER B1147 " --> pdb=" O VAL B1118 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.587A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 121 through 122 removed outlier: 7.170A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.428A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 62 through 63 removed outlier: 3.753A pdb=" N VAL E 62 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE E 73 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.717A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 194 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR E 203 " --> pdb=" O ARG E 195 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.723A pdb=" N ILE G 11 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE G 46 " --> pdb=" O ILE G 75 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.723A pdb=" N ILE G 11 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU G 67 " --> pdb=" O VAL G 58 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 107 through 109 removed outlier: 6.634A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL G 85 " --> pdb=" O LEU G 145 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 128 through 129 Processing sheet with id=AE6, first strand: chain 'H' and resid 38 through 44 removed outlier: 3.569A pdb=" N LEU H 41 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG H 27 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE H 15 " --> pdb=" O ARG H 27 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS H 13 " --> pdb=" O HIS H 29 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AE8, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE9, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF1, first strand: chain 'M' and resid 804 through 809 removed outlier: 5.625A pdb=" N VAL M 805 " --> pdb=" O ASN M 800 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASN M 800 " --> pdb=" O VAL M 805 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL M 848 " --> pdb=" O GLU M 883 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 971 through 972 removed outlier: 5.953A pdb=" N VAL M 971 " --> pdb=" O LYS M1036 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'M' and resid 1237 through 1240 removed outlier: 3.720A pdb=" N CYS M1265 " --> pdb=" O ILE M1167 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG M1266 " --> pdb=" O THR M1280 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 1355 through 1359 removed outlier: 3.774A pdb=" N LEU M1367 " --> pdb=" O VAL M1383 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP M1371 " --> pdb=" O GLN M1379 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN M1379 " --> pdb=" O TRP M1371 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 1461 through 1464 removed outlier: 4.201A pdb=" N PHE M1461 " --> pdb=" O GLY M1475 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY M1475 " --> pdb=" O PHE M1461 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 386 through 387 removed outlier: 3.959A pdb=" N VAL R 387 " --> pdb=" O ALA R 403 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA R 403 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR R 420 " --> pdb=" O LEU R 417 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR R 415 " --> pdb=" O THR R 422 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LYS R 424 " --> pdb=" O LYS R 413 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N LYS R 413 " --> pdb=" O LYS R 424 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N LEU R 426 " --> pdb=" O THR R 411 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N THR R 411 " --> pdb=" O LEU R 426 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 386 through 387 removed outlier: 3.959A pdb=" N VAL R 387 " --> pdb=" O ALA R 403 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA R 403 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU R 426 " --> pdb=" O PHE R 437 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE R 437 " --> pdb=" O LEU R 426 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU R 428 " --> pdb=" O ARG R 435 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG R 435 " --> pdb=" O LEU R 428 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP R 433 " --> pdb=" O HIS R 430 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 256 through 258 Processing sheet with id=AF9, first strand: chain 'U' and resid 376 through 377 removed outlier: 3.613A pdb=" N PHE V 312 " --> pdb=" O VAL U 376 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 494 through 495 removed outlier: 3.907A pdb=" N HIS U 494 " --> pdb=" O TYR U 460 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR U 460 " --> pdb=" O HIS U 494 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET U 448 " --> pdb=" O VAL U 459 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS U 451 " --> pdb=" O ARG U 439 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG U 439 " --> pdb=" O HIS U 451 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE U 440 " --> pdb=" O VAL V 204 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL V 204 " --> pdb=" O ILE U 440 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS U 442 " --> pdb=" O VAL V 202 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 221 through 222 removed outlier: 3.581A pdb=" N ARG V 331 " --> pdb=" O LYS V 292 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER V 333 " --> pdb=" O LYS V 290 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS V 290 " --> pdb=" O SER V 333 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 250 through 251 removed outlier: 3.861A pdb=" N GLN V 250 " --> pdb=" O VAL V 261 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 6 through 11 removed outlier: 6.441A pdb=" N ILE W 300 " --> pdb=" O LEU W 8 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS W 10 " --> pdb=" O ILE W 298 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE W 298 " --> pdb=" O LYS W 10 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY W 279 " --> pdb=" O VAL W 292 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'W' and resid 19 through 24 removed outlier: 3.569A pdb=" N SER W 21 " --> pdb=" O GLY W 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY W 38 " --> pdb=" O SER W 21 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS W 45 " --> pdb=" O THR W 37 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL W 44 " --> pdb=" O SER W 59 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER W 59 " --> pdb=" O VAL W 44 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL W 46 " --> pdb=" O GLN W 57 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 67 through 72 removed outlier: 7.185A pdb=" N SER W 82 " --> pdb=" O VAL W 68 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL W 70 " --> pdb=" O ALA W 80 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ALA W 80 " --> pdb=" O VAL W 70 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE W 72 " --> pdb=" O ILE W 78 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE W 78 " --> pdb=" O ILE W 72 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS W 100 " --> pdb=" O LEU W 90 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP W 92 " --> pdb=" O GLN W 98 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLN W 98 " --> pdb=" O ASP W 92 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 112 through 114 removed outlier: 3.786A pdb=" N VAL W 130 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR W 142 " --> pdb=" O ILE W 132 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY W 134 " --> pdb=" O LYS W 140 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS W 140 " --> pdb=" O GLY W 134 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 151 through 156 removed outlier: 6.105A pdb=" N GLY W 166 " --> pdb=" O LEU W 152 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE W 154 " --> pdb=" O ALA W 164 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA W 164 " --> pdb=" O ILE W 154 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 172 through 175 Processing sheet with id=AH1, first strand: chain 'W' and resid 195 through 198 removed outlier: 3.879A pdb=" N SER W 195 " --> pdb=" O ALA W 208 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR W 197 " --> pdb=" O VAL W 206 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL W 206 " --> pdb=" O THR W 197 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR W 207 " --> pdb=" O LYS W 215 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS W 215 " --> pdb=" O THR W 207 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY W 226 " --> pdb=" O ILE W 216 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ASP W 218 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEU W 224 " --> pdb=" O ASP W 218 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'W' and resid 237 through 240 removed outlier: 3.791A pdb=" N LYS W 257 " --> pdb=" O SER W 249 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS W 268 " --> pdb=" O VAL W 258 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP W 260 " --> pdb=" O CYS W 266 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS W 266 " --> pdb=" O ASP W 260 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Y' and resid 13 through 15 Processing sheet with id=AH4, first strand: chain 'Y' and resid 57 through 58 removed outlier: 3.623A pdb=" N SER Y 88 " --> pdb=" O ASP Y 58 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Y' and resid 83 through 85 removed outlier: 4.097A pdb=" N ILE Y 60 " --> pdb=" O ALA Z 217 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Z' and resid 224 through 228 removed outlier: 3.786A pdb=" N GLN Z 253 " --> pdb=" O THR Z 181 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Z' and resid 302 through 303 Processing sheet with id=AH8, first strand: chain 'Z' and resid 352 through 354 Processing sheet with id=AH9, first strand: chain 'Z' and resid 367 through 368 Processing sheet with id=AI1, first strand: chain 'Z' and resid 438 through 439 Processing sheet with id=AI2, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.504A pdb=" N GLY Z 490 " --> pdb=" O VAL Z 478 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU Z 491 " --> pdb=" O PHE Z 503 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE Z 503 " --> pdb=" O LEU Z 491 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL Z 500 " --> pdb=" O VAL Z 513 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL Z 513 " --> pdb=" O VAL Z 500 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.657A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL Z 551 " --> pdb=" O GLN Z 559 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN Z 541 " --> pdb=" O THR Z 576 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR Z 576 " --> pdb=" O GLN Z 541 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Z' and resid 638 through 639 removed outlier: 6.655A pdb=" N PHE Z 621 " --> pdb=" O LEU Z 617 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU Z 617 " --> pdb=" O PHE Z 621 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY Z 612 " --> pdb=" O VAL Z 600 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL Z 600 " --> pdb=" O GLY Z 612 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Z' and resid 742 through 746 removed outlier: 3.568A pdb=" N ASP Z 726 " --> pdb=" O ARG Z 733 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLU Z 735 " --> pdb=" O VAL Z 724 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL Z 724 " --> pdb=" O GLU Z 735 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.817A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AI8, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.592A pdb=" N ARG c 42 " --> pdb=" O ILE d 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AJ1, first strand: chain 'c' and resid 100 through 102 Processing sheet with id=AJ2, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.630A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'e' and resid 118 through 119 2566 hydrogen bonds defined for protein. 7341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 406 hydrogen bonds 808 hydrogen bond angles 0 basepair planarities 159 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 42.78 Time building geometry restraints manager: 14.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 18041 1.33 - 1.46: 13311 1.46 - 1.58: 34300 1.58 - 1.70: 667 1.70 - 1.82: 407 Bond restraints: 66726 Sorted by residual: bond pdb=" CG PRO W 106 " pdb=" CD PRO W 106 " ideal model delta sigma weight residual 1.512 1.285 0.227 2.70e-02 1.37e+03 7.07e+01 bond pdb=" OG1 TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" OG1 TPO Z 775 " pdb=" P TPO Z 775 " ideal model delta sigma weight residual 1.717 1.612 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" CA LYS X 243 " pdb=" CB LYS X 243 " ideal model delta sigma weight residual 1.528 1.594 -0.066 1.39e-02 5.18e+03 2.29e+01 bond pdb=" O2P TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 66721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.88: 90966 3.88 - 7.76: 361 7.76 - 11.63: 49 11.63 - 15.51: 9 15.51 - 19.39: 2 Bond angle restraints: 91387 Sorted by residual: angle pdb=" CA PRO W 106 " pdb=" N PRO W 106 " pdb=" CD PRO W 106 " ideal model delta sigma weight residual 111.50 92.11 19.39 1.40e+00 5.10e-01 1.92e+02 angle pdb=" CA PRO A 911 " pdb=" N PRO A 911 " pdb=" CD PRO A 911 " ideal model delta sigma weight residual 112.00 97.24 14.76 1.40e+00 5.10e-01 1.11e+02 angle pdb=" N PRO W 106 " pdb=" CD PRO W 106 " pdb=" CG PRO W 106 " ideal model delta sigma weight residual 103.80 91.55 12.25 1.20e+00 6.94e-01 1.04e+02 angle pdb=" CA PRO A 433 " pdb=" N PRO A 433 " pdb=" CD PRO A 433 " ideal model delta sigma weight residual 112.00 100.06 11.94 1.40e+00 5.10e-01 7.27e+01 angle pdb=" C GLU Q 772 " pdb=" N LYS Q 773 " pdb=" CA LYS Q 773 " ideal model delta sigma weight residual 121.70 135.34 -13.64 1.80e+00 3.09e-01 5.74e+01 ... (remaining 91382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 36928 35.80 - 71.60: 1434 71.60 - 107.39: 27 107.39 - 143.19: 2 143.19 - 178.99: 7 Dihedral angle restraints: 38398 sinusoidal: 16409 harmonic: 21989 Sorted by residual: dihedral pdb=" CA LYS A 910 " pdb=" C LYS A 910 " pdb=" N PRO A 911 " pdb=" CA PRO A 911 " ideal model delta harmonic sigma weight residual 180.00 154.52 25.48 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ARG a 63 " pdb=" C ARG a 63 " pdb=" N LYS a 64 " pdb=" CA LYS a 64 " ideal model delta harmonic sigma weight residual -180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ASN B 650 " pdb=" C ASN B 650 " pdb=" N TYR B 651 " pdb=" CA TYR B 651 " ideal model delta harmonic sigma weight residual -180.00 -159.14 -20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 38395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 9250 0.087 - 0.173: 624 0.173 - 0.260: 7 0.260 - 0.347: 1 0.347 - 0.433: 3 Chirality restraints: 9885 Sorted by residual: chirality pdb=" P DA N 146 " pdb=" OP1 DA N 146 " pdb=" OP2 DA N 146 " pdb=" O5' DA N 146 " both_signs ideal model delta sigma weight residual True 2.35 -2.78 -0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" P DG N 153 " pdb=" OP1 DG N 153 " pdb=" OP2 DG N 153 " pdb=" O5' DG N 153 " both_signs ideal model delta sigma weight residual True 2.35 -2.75 -0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" P DA T-145 " pdb=" OP1 DA T-145 " pdb=" OP2 DA T-145 " pdb=" O5' DA T-145 " both_signs ideal model delta sigma weight residual True 2.35 -2.74 -0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 9882 not shown) Planarity restraints: 11097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 910 " 0.147 5.00e-02 4.00e+02 2.09e-01 6.99e+01 pdb=" N PRO A 911 " -0.360 5.00e-02 4.00e+02 pdb=" CA PRO A 911 " 0.121 5.00e-02 4.00e+02 pdb=" CD PRO A 911 " 0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY W 105 " -0.118 5.00e-02 4.00e+02 1.59e-01 4.06e+01 pdb=" N PRO W 106 " 0.274 5.00e-02 4.00e+02 pdb=" CA PRO W 106 " -0.093 5.00e-02 4.00e+02 pdb=" CD PRO W 106 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 432 " -0.102 5.00e-02 4.00e+02 1.44e-01 3.34e+01 pdb=" N PRO A 433 " 0.249 5.00e-02 4.00e+02 pdb=" CA PRO A 433 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 433 " -0.073 5.00e-02 4.00e+02 ... (remaining 11094 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 583 2.59 - 3.17: 56053 3.17 - 3.75: 102765 3.75 - 4.32: 134769 4.32 - 4.90: 216025 Nonbonded interactions: 510195 Sorted by model distance: nonbonded pdb=" O3' C P 26 " pdb="MG MG A2003 " model vdw 2.018 2.170 nonbonded pdb=" OP1 DG T-126 " pdb=" OH TYR d 39 " model vdw 2.087 3.040 nonbonded pdb=" OH TYR Q 534 " pdb=" OE1 GLU Q 556 " model vdw 2.099 3.040 nonbonded pdb=" OG SER Z 504 " pdb=" O THR Z 507 " model vdw 2.104 3.040 nonbonded pdb=" N CYS J 45 " pdb="ZN ZN J 101 " model vdw 2.105 2.310 ... (remaining 510190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 7.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 2.040 Check model and map are aligned: 0.370 Set scattering table: 0.450 Process input model: 151.560 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.260 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:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5606 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 : 0.004 0.227 66726 Z= 0.242 Angle : 0.693 19.389 91387 Z= 0.360 Chirality : 0.042 0.433 9885 Planarity : 0.005 0.209 11097 Dihedral : 15.382 178.989 24740 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.64 % Favored : 95.30 % Rotamer: Outliers : 0.50 % Allowed : 10.41 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.07 (0.10), residues: 8040 helix: 1.30 (0.10), residues: 3068 sheet: -2.58 (0.17), residues: 764 loop : -1.98 (0.09), residues: 4208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1210 HIS 0.008 0.001 HIS Q 714 PHE 0.030 0.002 PHE B 309 TYR 0.053 0.002 TYR Q 310 ARG 0.017 0.001 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16080 Ramachandran restraints generated. 8040 Oldfield, 0 Emsley, 8040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16080 Ramachandran restraints generated. 8040 Oldfield, 0 Emsley, 8040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 7188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 379 time to evaluate : 5.449 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: A 51 ARG cc_start: 0.8755 (pmt170) cc_final: 0.8553 (pmt170) REVERT: A 501 MET cc_start: 0.7833 (mtp) cc_final: 0.6506 (mtp) REVERT: A 539 GLN cc_start: 0.7537 (pm20) cc_final: 0.7296 (pm20) REVERT: A 1344 MET cc_start: 0.8660 (tpt) cc_final: 0.8398 (tpt) REVERT: B 840 MET cc_start: 0.6972 (ttp) cc_final: 0.6763 (ttp) REVERT: C 3 TYR cc_start: 0.8749 (m-10) cc_final: 0.8510 (m-10) REVERT: E 72 MET cc_start: 0.8171 (ttp) cc_final: 0.7896 (ptm) REVERT: F 80 MET cc_start: 0.7803 (mmm) cc_final: 0.7506 (mmm) REVERT: G 131 MET cc_start: 0.2730 (tmm) cc_final: 0.2106 (tpt) REVERT: H 51 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.7864 (p0) REVERT: L 37 ARG cc_start: 0.8659 (mmp80) cc_final: 0.8439 (mmp80) REVERT: R 486 LYS cc_start: 0.2664 (mmmt) cc_final: 0.2226 (mmpt) REVERT: R 503 ARG cc_start: -0.0267 (tmm160) cc_final: -0.2439 (ttm170) REVERT: R 567 ASN cc_start: 0.0451 (m-40) cc_final: -0.1125 (t0) REVERT: R 576 GLU cc_start: -0.0537 (mt-10) cc_final: -0.0945 (mt-10) REVERT: R 597 ARG cc_start: -0.1685 (ptt-90) cc_final: -0.2193 (ptt180) REVERT: V 58 PHE cc_start: 0.0789 (p90) cc_final: -0.0055 (t80) REVERT: V 61 TYR cc_start: -0.1091 (m-80) cc_final: -0.1829 (t80) outliers start: 27 outliers final: 7 residues processed: 393 average time/residue: 1.4624 time to fit residues: 742.5330 Evaluate side-chains 321 residues out of total 7188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 313 time to evaluate : 6.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain d residue 85 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 705 optimal weight: 9.9990 chunk 633 optimal weight: 5.9990 chunk 351 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 427 optimal weight: 9.9990 chunk 338 optimal weight: 0.8980 chunk 655 optimal weight: 3.9990 chunk 253 optimal weight: 0.5980 chunk 398 optimal weight: 0.0970 chunk 487 optimal weight: 6.9990 chunk 759 optimal weight: 30.0000 overall best weight: 1.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 122 ASN A 288 ASN A 301 HIS A 320 ASN A 387 ASN A 529 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A 700 GLN A 790 GLN A 791 GLN A 804 HIS A 809 HIS A 991 GLN ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 GLN A1457 ASN A1462 GLN B 227 ASN B 319 ASN B 471 ASN B 725 GLN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 HIS ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN L 26 ASN Q 305 GLN Q 311 GLN Q 373 ASN Q 466 ASN Q 502 ASN Q 527 HIS Q 585 GLN Q 616 HIS Q 628 HIS Q 775 ASN ** V 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 69 GLN V 72 HIS W 27 ASN W 173 ASN W 273 HIS ** X 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 446 ASN a 108 ASN d 64 ASN e 68 GLN e 108 ASN ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5659 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 66726 Z= 0.208 Angle : 0.574 10.271 91387 Z= 0.301 Chirality : 0.041 0.197 9885 Planarity : 0.004 0.121 11097 Dihedral : 17.589 174.838 12442 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.94 % Favored : 95.01 % Rotamer: Outliers : 1.51 % Allowed : 9.52 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.06 % Twisted Proline : 0.30 % Twisted General : 0.00 % 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 (0.10), residues: 8040 helix: 1.33 (0.10), residues: 3174 sheet: -2.33 (0.17), residues: 798 loop : -1.83 (0.09), residues: 4068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1210 HIS 0.010 0.001 HIS a 113 PHE 0.024 0.001 PHE Q 296 TYR 0.041 0.001 TYR Q 310 ARG 0.009 0.001 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16080 Ramachandran restraints generated. 8040 Oldfield, 0 Emsley, 8040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16080 Ramachandran restraints generated. 8040 Oldfield, 0 Emsley, 8040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 7188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 323 time to evaluate : 5.169 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: A 329 MET cc_start: 0.8468 (ptm) cc_final: 0.7667 (pp-130) REVERT: A 474 VAL cc_start: 0.8242 (t) cc_final: 0.7964 (m) REVERT: A 510 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7464 (pp20) REVERT: A 535 MET cc_start: 0.8712 (mtm) cc_final: 0.8485 (mtm) REVERT: A 1210 TRP cc_start: 0.6193 (OUTLIER) cc_final: 0.5832 (p90) REVERT: A 1344 MET cc_start: 0.8663 (tpt) cc_final: 0.8200 (tpt) REVERT: B 347 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8680 (ppp) REVERT: B 840 MET cc_start: 0.6859 (ttp) cc_final: 0.6587 (ttp) REVERT: E 110 MET cc_start: 0.4917 (tpp) cc_final: 0.4530 (mmt) REVERT: F 80 MET cc_start: 0.7830 (mmm) cc_final: 0.7333 (mmt) REVERT: H 51 ASP cc_start: 0.8566 (t0) cc_final: 0.7903 (p0) REVERT: J 26 GLN cc_start: 0.8838 (tp40) cc_final: 0.7906 (tp40) REVERT: K 39 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8270 (m-30) REVERT: K 85 GLU cc_start: 0.7931 (mp0) cc_final: 0.7637 (pm20) REVERT: L 37 ARG cc_start: 0.8789 (mmp80) cc_final: 0.8172 (mmp80) REVERT: Q 304 MET cc_start: 0.3142 (mmt) cc_final: 0.2910 (mmp) REVERT: R 500 GLU cc_start: 0.2454 (OUTLIER) cc_final: 0.2051 (mp0) REVERT: R 503 ARG cc_start: -0.0315 (tmm160) cc_final: -0.1745 (ttm170) REVERT: R 563 ILE cc_start: -0.2588 (tp) cc_final: -0.2831 (tp) REVERT: R 567 ASN cc_start: 0.0842 (m-40) cc_final: -0.0582 (t0) REVERT: R 582 GLU cc_start: -0.1712 (pt0) cc_final: -0.2903 (pp20) REVERT: R 596 ARG cc_start: 0.0366 (mmp-170) cc_final: 0.0070 (mmp-170) REVERT: R 597 ARG cc_start: -0.1572 (ptt-90) cc_final: -0.1795 (ptt180) REVERT: V 58 PHE cc_start: 0.0742 (p90) cc_final: -0.0295 (t80) REVERT: V 61 TYR cc_start: -0.1764 (m-80) cc_final: -0.2239 (t80) REVERT: W 250 SER cc_start: 0.4754 (OUTLIER) cc_final: 0.4539 (p) REVERT: Z 378 MET cc_start: 0.1915 (OUTLIER) cc_final: 0.0962 (ptp) outliers start: 81 outliers final: 21 residues processed: 372 average time/residue: 1.4560 time to fit residues: 711.2057 Evaluate side-chains 330 residues out of total 7188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 302 time to evaluate : 5.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1210 TRP Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain Q residue 531 VAL Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 714 HIS Chi-restraints excluded: chain Q residue 717 THR Chi-restraints excluded: chain Q residue 817 CYS Chi-restraints excluded: chain R residue 500 GLU Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain Y residue 36 CYS Chi-restraints excluded: chain Z residue 378 MET Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain d residue 87 THR Chi-restraints excluded: chain e residue 110 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 421 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 631 optimal weight: 0.0870 chunk 516 optimal weight: 0.0470 chunk 209 optimal weight: 0.8980 chunk 760 optimal weight: 4.9990 chunk 821 optimal weight: 10.0000 chunk 677 optimal weight: 50.0000 chunk 754 optimal weight: 20.0000 chunk 259 optimal weight: 9.9990 chunk 610 optimal weight: 20.0000 overall best weight: 2.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 420 GLN B 582 GLN B 789 ASN B1071 ASN B1101 GLN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS I 41 ASN I 118 HIS Q 289 GLN ** Q 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 877 GLN R 567 ASN R 571 ASN V 69 GLN Y 27 GLN Z 337 GLN Z 616 HIS e 113 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5754 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 66726 Z= 0.237 Angle : 0.559 10.419 91387 Z= 0.295 Chirality : 0.041 0.203 9885 Planarity : 0.004 0.098 11097 Dihedral : 17.783 178.470 12435 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 1.92 % Allowed : 9.98 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.06 % Twisted Proline : 0.30 % Twisted General : 0.00 % 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: -0.71 (0.10), residues: 8040 helix: 1.40 (0.10), residues: 3201 sheet: -2.04 (0.17), residues: 798 loop : -1.75 (0.09), residues: 4041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1210 HIS 0.010 0.001 HIS I 118 PHE 0.024 0.002 PHE R 594 TYR 0.041 0.002 TYR Q 310 ARG 0.009 0.001 ARG R 568 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16080 Ramachandran restraints generated. 8040 Oldfield, 0 Emsley, 8040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16080 Ramachandran restraints generated. 8040 Oldfield, 0 Emsley, 8040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 7188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 325 time to evaluate : 5.727 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: A 78 MET cc_start: 0.8873 (tpp) cc_final: 0.8361 (tpp) REVERT: A 388 MET cc_start: 0.7702 (mmt) cc_final: 0.7270 (mmt) REVERT: A 501 MET cc_start: 0.7746 (mtp) cc_final: 0.7379 (mmm) REVERT: A 510 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7630 (pp20) REVERT: A 535 MET cc_start: 0.8923 (mtm) cc_final: 0.8700 (mtm) REVERT: A 565 MET cc_start: 0.8677 (tpt) cc_final: 0.8446 (mmm) REVERT: A 986 MET cc_start: 0.8824 (mmm) cc_final: 0.8267 (mtt) REVERT: A 1210 TRP cc_start: 0.6233 (OUTLIER) cc_final: 0.5986 (p90) REVERT: A 1344 MET cc_start: 0.8711 (tpt) cc_final: 0.8204 (tpt) REVERT: A 1459 MET cc_start: 0.8522 (mtm) cc_final: 0.8285 (mtm) REVERT: B 298 MET cc_start: 0.9020 (ttm) cc_final: 0.8752 (ttm) REVERT: B 508 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8445 (mtt) REVERT: B 840 MET cc_start: 0.7013 (ttp) cc_final: 0.6722 (ttp) REVERT: B 1054 MET cc_start: 0.8464 (mmm) cc_final: 0.8193 (mmm) REVERT: B 1172 MET cc_start: 0.8781 (mmm) cc_final: 0.8550 (mmm) REVERT: F 80 MET cc_start: 0.7993 (mmm) cc_final: 0.7326 (mmt) REVERT: G 131 MET cc_start: 0.3431 (tmm) cc_final: 0.2845 (tpt) REVERT: H 20 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8524 (tttp) REVERT: H 51 ASP cc_start: 0.8696 (t0) cc_final: 0.8057 (p0) REVERT: K 39 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8279 (m-30) REVERT: L 37 ARG cc_start: 0.8585 (mmp80) cc_final: 0.7517 (mmp80) REVERT: R 492 ILE cc_start: 0.0454 (OUTLIER) cc_final: -0.0297 (mp) REVERT: R 493 GLU cc_start: 0.4109 (mm-30) cc_final: 0.3574 (mm-30) REVERT: R 496 VAL cc_start: -0.0544 (m) cc_final: -0.1244 (m) REVERT: R 498 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.5731 (pt0) REVERT: R 500 GLU cc_start: 0.2663 (OUTLIER) cc_final: 0.2123 (mp0) REVERT: R 503 ARG cc_start: -0.0348 (tmm160) cc_final: -0.1647 (ttm-80) REVERT: R 567 ASN cc_start: 0.0528 (m110) cc_final: -0.0633 (t0) REVERT: R 582 GLU cc_start: -0.1353 (pt0) cc_final: -0.3390 (pp20) REVERT: V 61 TYR cc_start: -0.1179 (m-80) cc_final: -0.2061 (t80) REVERT: W 250 SER cc_start: 0.4798 (OUTLIER) cc_final: 0.4561 (p) REVERT: f 84 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.9065 (pmm) outliers start: 103 outliers final: 25 residues processed: 388 average time/residue: 1.4057 time to fit residues: 715.5958 Evaluate side-chains 331 residues out of total 7188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 296 time to evaluate : 5.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1210 TRP Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 531 VAL Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 717 THR Chi-restraints excluded: chain Q residue 817 CYS Chi-restraints excluded: chain R residue 492 ILE Chi-restraints excluded: chain R residue 495 ILE Chi-restraints excluded: chain R residue 498 GLU Chi-restraints excluded: chain R residue 500 GLU Chi-restraints excluded: chain R residue 569 GLU Chi-restraints excluded: chain V residue 58 PHE Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain Y residue 36 CYS Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain d residue 87 THR Chi-restraints excluded: chain e residue 110 CYS Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 751 optimal weight: 40.0000 chunk 571 optimal weight: 9.9990 chunk 394 optimal weight: 50.0000 chunk 84 optimal weight: 5.9990 chunk 362 optimal weight: 3.9990 chunk 510 optimal weight: 40.0000 chunk 763 optimal weight: 0.9980 chunk 808 optimal weight: 10.0000 chunk 398 optimal weight: 5.9990 chunk 723 optimal weight: 0.5980 chunk 217 optimal weight: 0.0060 overall best weight: 2.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN B 789 ASN B1068 GLN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** Q 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 442 GLN ** Q 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 714 HIS R 571 ASN V 69 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5805 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 66726 Z= 0.254 Angle : 0.563 13.855 91387 Z= 0.295 Chirality : 0.041 0.259 9885 Planarity : 0.004 0.085 11097 Dihedral : 17.933 178.103 12431 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.81 % Favored : 95.15 % Rotamer: Outliers : 1.83 % Allowed : 11.38 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.06 % Twisted Proline : 0.30 % Twisted General : 0.00 % 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: -0.59 (0.10), residues: 8040 helix: 1.43 (0.10), residues: 3220 sheet: -1.81 (0.18), residues: 793 loop : -1.67 (0.09), residues: 4027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Z 180 HIS 0.005 0.001 HIS W 231 PHE 0.023 0.002 PHE D 74 TYR 0.032 0.001 TYR Q 310 ARG 0.011 0.000 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16080 Ramachandran restraints generated. 8040 Oldfield, 0 Emsley, 8040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16080 Ramachandran restraints generated. 8040 Oldfield, 0 Emsley, 8040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 7188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 308 time to evaluate : 5.266 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: A 280 LEU cc_start: 0.9268 (mm) cc_final: 0.8995 (mt) REVERT: A 355 MET cc_start: 0.8631 (mmm) cc_final: 0.8381 (mmm) REVERT: A 510 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7651 (pp20) REVERT: A 535 MET cc_start: 0.9041 (mtm) cc_final: 0.8769 (mtm) REVERT: A 561 MET cc_start: 0.8234 (mtt) cc_final: 0.7992 (mtt) REVERT: A 986 MET cc_start: 0.8814 (mmm) cc_final: 0.8223 (mtt) REVERT: A 1344 MET cc_start: 0.8750 (tpt) cc_final: 0.8205 (tpt) REVERT: A 1459 MET cc_start: 0.8556 (mtm) cc_final: 0.8279 (mtm) REVERT: B 297 MET cc_start: 0.9354 (OUTLIER) cc_final: 0.8999 (tpp) REVERT: B 298 MET cc_start: 0.9055 (ttm) cc_final: 0.8777 (ttm) REVERT: B 508 MET cc_start: 0.8954 (mmt) cc_final: 0.8496 (mtt) REVERT: B 840 MET cc_start: 0.6921 (ttp) cc_final: 0.6573 (ttp) REVERT: B 1054 MET cc_start: 0.8500 (mmm) cc_final: 0.8222 (mmm) REVERT: E 121 MET cc_start: 0.6751 (mtt) cc_final: 0.6445 (ttp) REVERT: F 80 MET cc_start: 0.7967 (mmm) cc_final: 0.7382 (mmm) REVERT: F 88 ASP cc_start: 0.8033 (t0) cc_final: 0.7505 (t0) REVERT: H 20 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8572 (ttmp) REVERT: H 51 ASP cc_start: 0.8761 (t0) cc_final: 0.8016 (p0) REVERT: H 80 ASP cc_start: 0.8998 (m-30) cc_final: 0.8777 (p0) REVERT: K 1 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7367 (mpp) REVERT: K 39 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8275 (m-30) REVERT: K 85 GLU cc_start: 0.8098 (mp0) cc_final: 0.7741 (pm20) REVERT: Q 691 TYR cc_start: 0.8982 (m-10) cc_final: 0.8569 (m-80) REVERT: R 488 ASN cc_start: 0.5635 (OUTLIER) cc_final: 0.5390 (m-40) REVERT: R 493 GLU cc_start: 0.4133 (mm-30) cc_final: 0.3833 (mm-30) REVERT: R 498 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5728 (pt0) REVERT: R 500 GLU cc_start: 0.3046 (OUTLIER) cc_final: 0.2481 (mp0) REVERT: R 503 ARG cc_start: -0.0114 (tmm160) cc_final: -0.1588 (ttm-80) REVERT: R 563 ILE cc_start: -0.2461 (tp) cc_final: -0.2687 (tp) REVERT: R 567 ASN cc_start: 0.0452 (m110) cc_final: -0.0558 (t0) REVERT: R 582 GLU cc_start: -0.1634 (pt0) cc_final: -0.3408 (pp20) REVERT: V 61 TYR cc_start: -0.1517 (m-80) cc_final: -0.2223 (t80) REVERT: f 84 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.9076 (pmm) outliers start: 98 outliers final: 29 residues processed: 371 average time/residue: 1.3619 time to fit residues: 666.7372 Evaluate side-chains 334 residues out of total 7188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 296 time to evaluate : 5.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1106 ARG Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 531 VAL Chi-restraints excluded: chain Q residue 602 TYR Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 714 HIS Chi-restraints excluded: chain R residue 488 ASN Chi-restraints excluded: chain R residue 498 GLU Chi-restraints excluded: chain R residue 499 LYS Chi-restraints excluded: chain R residue 500 GLU Chi-restraints excluded: chain V residue 42 ILE Chi-restraints excluded: chain Y residue 36 CYS Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain d residue 87 THR Chi-restraints excluded: chain e residue 110 CYS Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 673 optimal weight: 0.0270 chunk 458 optimal weight: 0.0970 chunk 11 optimal weight: 4.9990 chunk 601 optimal weight: 40.0000 chunk 333 optimal weight: 20.0000 chunk 689 optimal weight: 30.0000 chunk 558 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 412 optimal weight: 30.0000 chunk 725 optimal weight: 20.0000 chunk 203 optimal weight: 0.1980 overall best weight: 2.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 GLN B 731 GLN B 980 HIS ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN ** Q 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 706 ASN V 69 GLN W 98 GLN Y 12 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 66726 Z= 0.299 Angle : 0.591 12.451 91387 Z= 0.310 Chirality : 0.042 0.183 9885 Planarity : 0.004 0.083 11097 Dihedral : 18.183 174.991 12431 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.80 % Favored : 95.16 % Rotamer: Outliers : 2.13 % Allowed : 12.13 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.06 % Twisted Proline : 0.30 % Twisted General : 0.00 % 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: -0.57 (0.10), residues: 8040 helix: 1.37 (0.10), residues: 3226 sheet: -1.78 (0.18), residues: 792 loop : -1.59 (0.09), residues: 4022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 653 HIS 0.045 0.001 HIS Q 714 PHE 0.031 0.002 PHE A 810 TYR 0.023 0.002 TYR B 766 ARG 0.014 0.001 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16080 Ramachandran restraints generated. 8040 Oldfield, 0 Emsley, 8040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16080 Ramachandran restraints generated. 8040 Oldfield, 0 Emsley, 8040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 7188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 300 time to evaluate : 5.351 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: A 47 THR cc_start: 0.7839 (OUTLIER) cc_final: 0.7636 (t) REVERT: A 388 MET cc_start: 0.7865 (mmt) cc_final: 0.7494 (mmt) REVERT: A 467 MET cc_start: 0.8600 (mmp) cc_final: 0.8370 (mmp) REVERT: A 501 MET cc_start: 0.7799 (mtp) cc_final: 0.7430 (mmm) REVERT: A 510 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7658 (pp20) REVERT: A 535 MET cc_start: 0.9005 (mtm) cc_final: 0.8767 (mtm) REVERT: A 986 MET cc_start: 0.8837 (mmm) cc_final: 0.8376 (mtt) REVERT: A 1344 MET cc_start: 0.8758 (tpt) cc_final: 0.8251 (tpp) REVERT: A 1428 MET cc_start: 0.8678 (tmt) cc_final: 0.8452 (tmm) REVERT: A 1459 MET cc_start: 0.8517 (mtm) cc_final: 0.8236 (mtm) REVERT: B 298 MET cc_start: 0.9160 (ttm) cc_final: 0.8856 (ttm) REVERT: B 347 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8567 (ppp) REVERT: B 508 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8555 (mtt) REVERT: B 733 MET cc_start: 0.8640 (ptm) cc_final: 0.8361 (ptp) REVERT: B 840 MET cc_start: 0.7022 (ttp) cc_final: 0.6689 (ttp) REVERT: B 1054 MET cc_start: 0.8469 (mmm) cc_final: 0.8231 (mmm) REVERT: B 1089 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7577 (mtm) REVERT: B 1125 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8050 (mmt) REVERT: B 1172 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8514 (mpp) REVERT: F 80 MET cc_start: 0.8064 (mmm) cc_final: 0.7483 (mmt) REVERT: F 88 ASP cc_start: 0.8214 (t0) cc_final: 0.7670 (t0) REVERT: F 91 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9227 (mm) REVERT: G 29 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8437 (ttmt) REVERT: H 51 ASP cc_start: 0.8771 (t0) cc_final: 0.8130 (p0) REVERT: K 39 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8652 (m-30) REVERT: K 80 ASP cc_start: 0.8640 (p0) cc_final: 0.8406 (p0) REVERT: Q 402 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8463 (tppt) REVERT: Q 691 TYR cc_start: 0.9056 (m-10) cc_final: 0.8626 (m-80) REVERT: R 498 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5605 (pt0) REVERT: R 500 GLU cc_start: 0.2676 (OUTLIER) cc_final: 0.1864 (mm-30) REVERT: R 503 ARG cc_start: 0.0006 (tmm160) cc_final: -0.1503 (ttm-80) REVERT: R 560 ILE cc_start: -0.2878 (mt) cc_final: -0.3698 (tt) REVERT: R 567 ASN cc_start: 0.0432 (m110) cc_final: -0.0457 (t0) REVERT: R 582 GLU cc_start: -0.1493 (pt0) cc_final: -0.3413 (pp20) REVERT: V 61 TYR cc_start: -0.1026 (m-80) cc_final: -0.2400 (t80) REVERT: Z 197 MET cc_start: 0.4352 (tmt) cc_final: 0.4140 (tmt) REVERT: Z 429 CYS cc_start: 0.1480 (OUTLIER) cc_final: 0.0666 (m) REVERT: Z 547 VAL cc_start: 0.2732 (OUTLIER) cc_final: 0.2416 (t) REVERT: f 84 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.9038 (pmm) outliers start: 114 outliers final: 36 residues processed: 378 average time/residue: 1.3557 time to fit residues: 676.5058 Evaluate side-chains 340 residues out of total 7188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 288 time to evaluate : 5.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1210 TRP Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1106 ARG Chi-restraints excluded: chain B residue 1125 MET Chi-restraints excluded: chain B residue 1172 MET Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 402 LYS Chi-restraints excluded: chain Q residue 531 VAL Chi-restraints excluded: chain Q residue 602 TYR Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 714 HIS Chi-restraints excluded: chain R residue 495 ILE Chi-restraints excluded: chain R residue 498 GLU Chi-restraints excluded: chain R residue 500 GLU Chi-restraints excluded: chain V residue 42 ILE Chi-restraints excluded: chain X residue 232 ARG Chi-restraints excluded: chain Y residue 36 CYS Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain Z residue 547 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain d residue 87 THR Chi-restraints excluded: chain e residue 110 CYS Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.451 > 50: distance: 2 - 23: 35.029 distance: 8 - 28: 37.195 distance: 13 - 38: 36.041 distance: 18 - 23: 35.650 distance: 23 - 24: 55.302 distance: 24 - 25: 56.182 distance: 24 - 27: 41.367 distance: 25 - 26: 68.144 distance: 25 - 28: 41.173 distance: 28 - 29: 68.161 distance: 29 - 30: 40.319 distance: 29 - 32: 56.880 distance: 30 - 31: 38.843 distance: 30 - 38: 40.840 distance: 32 - 33: 57.234 distance: 33 - 34: 69.326 distance: 33 - 35: 39.249 distance: 34 - 36: 57.267 distance: 35 - 37: 39.478 distance: 36 - 37: 40.641 distance: 38 - 39: 67.933 distance: 39 - 40: 57.228 distance: 39 - 42: 40.783 distance: 40 - 41: 55.671 distance: 40 - 46: 57.343 distance: 42 - 43: 55.758 distance: 43 - 44: 68.253 distance: 43 - 45: 70.344 distance: 46 - 47: 40.633 distance: 47 - 48: 40.243 distance: 48 - 49: 40.149 distance: 48 - 54: 70.528 distance: 50 - 51: 39.815 distance: 51 - 52: 39.125 distance: 51 - 53: 57.160 distance: 54 - 55: 40.280 distance: 55 - 56: 69.088 distance: 55 - 58: 39.993 distance: 56 - 57: 70.052 distance: 56 - 63: 38.819 distance: 58 - 59: 68.093 distance: 59 - 60: 40.321 distance: 60 - 61: 57.643 distance: 60 - 62: 56.973 distance: 63 - 64: 56.536 distance: 64 - 65: 57.637 distance: 64 - 67: 56.783 distance: 65 - 66: 56.043 distance: 65 - 71: 40.236 distance: 68 - 69: 56.410 distance: 68 - 70: 69.137 distance: 71 - 72: 41.147 distance: 72 - 73: 55.342 distance: 72 - 75: 55.913 distance: 73 - 74: 70.488 distance: 73 - 80: 68.756 distance: 75 - 76: 39.750 distance: 76 - 77: 40.699 distance: 77 - 78: 70.272 distance: 77 - 79: 68.847 distance: 80 - 81: 69.050 distance: 80 - 86: 70.701 distance: 81 - 82: 70.593 distance: 81 - 84: 68.019 distance: 82 - 83: 57.294 distance: 82 - 87: 38.843 distance: 84 - 85: 57.752 distance: 85 - 86: 38.742 distance: 87 - 88: 38.697 distance: 88 - 89: 68.291 distance: 88 - 91: 57.233 distance: 89 - 90: 57.422 distance: 89 - 94: 38.777 distance: 91 - 92: 56.864 distance: 91 - 93: 68.138 distance: 94 - 95: 57.600 distance: 94 - 100: 69.488 distance: 95 - 96: 70.167 distance: 95 - 98: 38.535 distance: 96 - 97: 55.321 distance: 96 - 101: 35.267 distance: 98 - 99: 56.790 distance: 99 - 100: 55.200