Starting phenix.real_space_refine on Wed Jan 22 09:20:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9egz_48041/01_2025/9egz_48041.cif Found real_map, /net/cci-nas-00/data/ceres_data/9egz_48041/01_2025/9egz_48041.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/9egz_48041/01_2025/9egz_48041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9egz_48041/01_2025/9egz_48041.map" model { file = "/net/cci-nas-00/data/ceres_data/9egz_48041/01_2025/9egz_48041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9egz_48041/01_2025/9egz_48041.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= 0.003 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 83 atoms to isotropic. 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 12 6.06 5 P 330 5.49 5 Mg 1 5.21 5 S 281 5.16 5 C 41665 2.51 5 N 12605 2.21 5 O 13847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 68741 Number of models: 1 Model: "" Number of chains: 43 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: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} 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: "g" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "h" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "l" Number of atoms: 1993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1993 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 7, 'TRANS': 237} 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} Chain: "l" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 472 SG CYS A 71 82.186 159.639 193.202 1.00195.19 S ATOM 494 SG CYS A 74 85.930 159.754 194.116 1.00179.89 S ATOM 541 SG CYS A 81 84.372 162.610 192.054 1.00159.20 S ATOM 19760 SG CYS B1119 98.154 150.883 189.368 1.00159.94 S ATOM 19782 SG CYS B1122 96.052 149.844 186.339 1.00165.74 S ATOM 19897 SG CYS B1137 94.349 150.594 189.621 1.00160.93 S ATOM 19918 SG CYS B1140 96.402 147.424 188.989 1.00174.03 S ATOM 20884 SG CYS C 88 77.386 227.177 192.200 1.00168.14 S ATOM 20897 SG CYS C 90 75.318 227.063 193.880 1.00180.14 S ATOM 20954 SG CYS C 97 75.550 228.111 189.612 1.00136.55 S ATOM 28204 SG CYS I 17 61.160 140.873 103.967 1.00138.01 S ATOM 28228 SG CYS I 20 60.664 140.287 107.410 1.00126.05 S ATOM 28389 SG CYS I 39 63.495 139.225 107.273 1.00149.07 S ATOM 28766 SG CYS I 86 70.513 183.416 93.617 1.00144.41 S ATOM 28790 SG CYS I 89 67.426 185.457 92.949 1.00140.93 S ATOM 28994 SG CYS I 114 68.346 184.921 96.471 1.00105.70 S ATOM 29029 SG CYS I 119 67.128 181.917 94.329 1.00135.90 S ATOM 29139 SG CYS J 7 75.750 223.028 157.468 1.00110.49 S ATOM 29427 SG CYS J 44 78.483 224.748 154.977 1.00142.30 S ATOM 29433 SG CYS J 45 75.477 226.432 156.351 1.00123.28 S ATOM 55949 SG CYS Y 19 38.232 116.446 177.013 1.00 73.13 S ATOM 67277 SG CYS l1516 121.091 99.082 52.004 1.00 72.21 S ATOM 67378 SG CYS l1529 118.230 97.700 49.743 1.00 57.61 S ATOM 67407 SG CYS l1533 118.902 101.445 50.182 1.00 85.43 S ATOM 67452 SG CYS l1539 121.222 99.483 48.167 1.00 99.70 S ATOM 67151 SG CYS l1499 117.438 98.763 52.911 1.00 66.01 S ATOM 67166 SG CYS l1501 119.988 98.487 55.642 1.00 87.14 S ATOM 67277 SG CYS l1516 121.091 99.082 52.004 1.00 72.21 S ATOM 67304 SG CYS l1520 119.718 95.698 53.132 1.00 82.00 S ATOM 68598 SG CYS l1678 133.166 68.101 30.889 1.00126.80 S ATOM 68615 SG CYS l1680 134.971 67.720 33.744 1.00114.15 S ATOM 68644 SG CYS l1685 134.243 64.592 32.917 1.00130.76 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: 28.31, per 1000 atoms: 0.41 Number of scatterers: 68741 At special positions: 0 Unit cell: (198, 320.1, 293.7, 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 12 29.99 S 281 16.00 P 330 15.00 Mg 1 11.99 O 13847 8.00 N 12605 7.00 C 41665 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: 13.06 Conformation dependent library (CDL) restraints added in 7.7 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 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " 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 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " 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 " pdb=" ZN l2601 " pdb="ZN ZN l2601 " - pdb=" SG CYS l1533 " pdb="ZN ZN l2601 " - pdb=" SG CYS l1539 " pdb="ZN ZN l2601 " - pdb=" SG CYS l1516 " pdb="ZN ZN l2601 " - pdb=" SG CYS l1529 " pdb=" ZN l2602 " pdb="ZN ZN l2602 " - pdb=" SG CYS l1501 " pdb="ZN ZN l2602 " - pdb=" SG CYS l1516 " pdb="ZN ZN l2602 " - pdb=" SG CYS l1499 " pdb="ZN ZN l2602 " - pdb=" SG CYS l1520 " pdb=" ZN l2603 " pdb="ZN ZN l2603 " - pdb=" SG CYS l1685 " pdb="ZN ZN l2603 " - pdb=" SG CYS l1678 " pdb="ZN ZN l2603 " - pdb=" SG CYS l1680 " Number of angles added : 27 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14530 Finding SS restraints... Secondary structure from input PDB file: 321 helices and 93 sheets defined 43.9% alpha, 11.7% beta 158 base pairs and 247 stacking pairs defined. Time for finding SS restraints: 19.97 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: 3.773A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 148 removed outlier: 3.654A pdb=" N CYS A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.586A pdb=" N VAL A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 235 removed outlier: 4.149A 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: 4.252A 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: 3.723A 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: 3.619A pdb=" N LEU A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.730A 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: 4.007A 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 521 through 524 Processing helix chain 'A' and resid 539 through 549 removed outlier: 3.750A pdb=" N THR A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 removed outlier: 3.663A pdb=" N MET A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.942A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) 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: 3.840A pdb=" N ASN A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.201A 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 removed outlier: 3.503A pdb=" N SER A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 785 removed outlier: 3.549A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 866 removed outlier: 4.587A pdb=" N GLY A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (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: 3.825A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.997A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 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 1080 Processing helix chain 'A' and resid 1086 through 1097 removed outlier: 3.505A pdb=" N LEU A1090 " --> pdb=" O MET A1086 " (cutoff:3.500A) 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 1161 removed outlier: 4.228A pdb=" N ASP A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) removed outlier: 4.372A 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 1190 through 1195 removed outlier: 3.812A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 3.782A pdb=" N MET A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1239 removed outlier: 3.884A pdb=" N PHE A1239 " --> pdb=" O ILE A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1295 removed outlier: 3.899A pdb=" N LEU A1285 " --> pdb=" O ASP A1281 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP A1295 " --> pdb=" O ASN A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1348 removed outlier: 3.616A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1367 removed outlier: 4.007A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A1366 " --> pdb=" O ILE A1362 " (cutoff:3.500A) removed outlier: 3.815A 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: 3.844A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 removed outlier: 3.670A pdb=" N ASN A1420 " --> pdb=" O ARG A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1433 removed outlier: 4.001A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1461 Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 3.815A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) removed outlier: 3.551A 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: 3.883A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 3.527A pdb=" N LEU B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.645A 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: 3.593A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.661A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.684A pdb=" N ALA B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 removed outlier: 3.779A 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: 3.655A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 4.082A 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 458 through 462 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.753A pdb=" N TRP B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 562 removed outlier: 4.015A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.792A pdb=" N ASN B 585 " --> pdb=" O GLU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 660 removed outlier: 3.722A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 673 removed outlier: 3.798A pdb=" N VAL B 673 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 684 removed outlier: 4.130A 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: 4.246A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 768 removed outlier: 3.617A pdb=" N LEU B 767 " --> pdb=" O SER B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.283A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.817A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1016 removed outlier: 3.786A 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: 3.936A pdb=" N ILE C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.512A 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: 3.833A pdb=" N THR D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.813A 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: 3.537A pdb=" N ILE D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 removed outlier: 3.844A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU D 100 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS D 104 " --> pdb=" O LEU D 100 " (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: 3.647A pdb=" N LEU D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 3.815A 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: 3.536A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.975A pdb=" N PHE E 40 " --> pdb=" O THR E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 95 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.638A pdb=" N LYS E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.677A 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 removed outlier: 3.617A pdb=" N GLN H 87 " --> pdb=" O ARG H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 68 removed outlier: 4.009A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 74 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: 3.732A pdb=" N GLU J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 removed outlier: 4.245A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.648A pdb=" N ARG J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG J 47 " --> pdb=" O TYR J 43 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.878A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 10 removed outlier: 3.909A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.580A 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: 4.399A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'M' and resid 285 through 291 removed outlier: 3.711A 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: 4.218A pdb=" N GLU M 314 " --> pdb=" O ASP M 310 " (cutoff:3.500A) removed outlier: 3.820A 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: 4.038A 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: 3.563A pdb=" N TYR M 590 " --> pdb=" O GLU M 586 " (cutoff:3.500A) removed outlier: 3.817A 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: 3.664A pdb=" N ASP M 629 " --> pdb=" O ARG M 625 " (cutoff:3.500A) Processing helix chain 'M' and resid 632 through 637 removed outlier: 4.467A pdb=" N PHE M 637 " --> pdb=" O TYR M 633 " (cutoff:3.500A) Processing helix chain 'M' and resid 644 through 650 removed outlier: 3.787A pdb=" N LEU M 648 " --> pdb=" O PRO M 644 " (cutoff:3.500A) Processing helix chain 'M' and resid 651 through 662 removed outlier: 3.574A pdb=" N LYS M 655 " --> pdb=" O ASP M 651 " (cutoff:3.500A) Processing helix chain 'M' and resid 685 through 692 removed outlier: 4.186A pdb=" N ILE M 689 " --> pdb=" O TYR M 685 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS M 690 " --> pdb=" O PHE M 686 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN M 691 " --> pdb=" O GLU M 687 " (cutoff:3.500A) removed outlier: 3.744A 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: 3.753A pdb=" N ARG M 754 " --> pdb=" O TYR M 750 " (cutoff:3.500A) Processing helix chain 'M' and resid 759 through 763 removed outlier: 3.723A pdb=" N GLN M 763 " --> pdb=" O PRO M 760 " (cutoff:3.500A) Processing helix chain 'M' and resid 830 through 843 removed outlier: 3.692A pdb=" N LYS M 843 " --> pdb=" O PHE M 839 " (cutoff:3.500A) Processing helix chain 'M' and resid 854 through 871 Processing helix chain 'M' and resid 888 through 895 removed outlier: 4.137A pdb=" N LEU M 892 " --> pdb=" O GLU M 888 " (cutoff:3.500A) removed outlier: 3.811A 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: 4.260A 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 943 through 949 removed outlier: 4.137A pdb=" N GLU M 947 " --> pdb=" O HIS M 943 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N HIS M 948 " --> pdb=" O PRO M 944 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL M 949 " --> pdb=" O LEU M 945 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 943 through 949' Processing helix chain 'M' and resid 950 through 970 removed outlier: 3.960A pdb=" N LEU M 954 " --> pdb=" O VAL M 950 " (cutoff:3.500A) Processing helix chain 'M' and resid 974 through 979 removed outlier: 4.105A pdb=" N ALA M 978 " --> pdb=" O ASN M 974 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS M 979 " --> pdb=" O ARG M 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 974 through 979' 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: 3.803A 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: 4.189A 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: 3.702A pdb=" N LEU M1245 " --> pdb=" O PRO M1241 " (cutoff:3.500A) Processing helix chain 'M' and resid 1282 through 1287 removed outlier: 3.907A pdb=" N LEU M1286 " --> pdb=" O ARG M1282 " (cutoff:3.500A) removed outlier: 3.668A 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: 3.547A 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: 3.587A pdb=" N LEU M1426 " --> pdb=" O PHE M1422 " (cutoff:3.500A) Processing helix chain 'M' and resid 1434 through 1439 removed outlier: 3.785A pdb=" N ASP M1439 " --> pdb=" O CYS M1435 " (cutoff:3.500A) Processing helix chain 'M' and resid 1441 through 1452 removed outlier: 4.361A pdb=" N GLU M1445 " --> pdb=" O LYS M1441 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU M1446 " --> pdb=" O LYS M1442 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU M1447 " --> pdb=" O LEU M1443 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE M1448 " --> pdb=" O GLU M1444 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS M1452 " --> pdb=" O ILE M1448 " (cutoff:3.500A) Processing helix chain 'M' and resid 1503 through 1512 removed outlier: 4.064A pdb=" N LEU M1507 " --> pdb=" O THR M1503 " (cutoff:3.500A) removed outlier: 3.830A 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: 3.786A 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: 3.683A 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: 3.751A pdb=" N GLU O 636 " --> pdb=" O LYS O 632 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS O 639 " --> pdb=" O GLU O 635 " (cutoff:3.500A) Processing helix chain 'O' and resid 648 through 656 removed outlier: 3.566A 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: 3.737A pdb=" N LYS O 675 " --> pdb=" O SER O 671 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET O 677 " --> pdb=" O SER O 673 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 37 removed outlier: 4.021A pdb=" N ILE Q 31 " --> pdb=" O GLY Q 27 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER Q 32 " --> pdb=" O ASP Q 28 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU Q 37 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 53 removed outlier: 4.139A pdb=" N TRP Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE Q 45 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 64 removed outlier: 3.970A pdb=" N LEU Q 64 " --> pdb=" O PHE Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 69 removed outlier: 3.859A pdb=" N ARG Q 68 " --> pdb=" O GLU Q 65 " (cutoff:3.500A) removed outlier: 3.650A 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: 3.622A pdb=" N GLN Q 82 " --> pdb=" O HIS Q 78 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR Q 88 " --> pdb=" O THR Q 84 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU Q 89 " --> pdb=" O CYS Q 85 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR Q 93 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL Q 94 " --> pdb=" O ALA Q 90 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN Q 95 " --> pdb=" O ALA Q 91 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG Q 98 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS Q 99 " --> pdb=" O GLN Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 121 removed outlier: 3.717A pdb=" N LEU Q 109 " --> pdb=" O ASN Q 105 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN Q 112 " --> pdb=" O ASP Q 108 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU Q 116 " --> pdb=" O GLN Q 112 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR Q 118 " --> pdb=" O THR Q 114 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET Q 119 " --> pdb=" O LEU Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 137 Processing helix chain 'Q' and resid 144 through 159 removed outlier: 3.587A pdb=" N PHE Q 154 " --> pdb=" O ALA Q 150 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL Q 155 " --> pdb=" O GLN Q 151 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU Q 156 " --> pdb=" O PHE Q 152 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN Q 157 " --> pdb=" O HIS Q 153 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER Q 159 " --> pdb=" O VAL Q 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 163 through 176 removed outlier: 3.881A pdb=" N GLY Q 168 " --> pdb=" O PRO Q 164 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LYS Q 169 " --> pdb=" O ALA Q 165 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA Q 170 " --> pdb=" O LEU Q 166 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS Q 171 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE Q 172 " --> pdb=" O GLY Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 178 through 187 Processing helix chain 'Q' and resid 187 through 192 removed outlier: 3.768A pdb=" N ARG Q 191 " --> pdb=" O LYS Q 187 " (cutoff:3.500A) removed outlier: 4.061A 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: 4.004A pdb=" N MET Q 204 " --> pdb=" O VAL Q 200 " (cutoff:3.500A) Processing helix chain 'Q' and resid 213 through 228 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 243 removed outlier: 3.540A pdb=" N GLY Q 237 " --> pdb=" O GLY Q 233 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU Q 238 " --> pdb=" O ALA Q 234 " (cutoff:3.500A) Processing helix chain 'Q' and resid 249 through 255 removed outlier: 3.823A 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: 3.894A pdb=" N PHE Q 281 " --> pdb=" O ASN Q 277 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS Q 282 " --> pdb=" O HIS Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 284 through 295 removed outlier: 3.950A pdb=" N VAL Q 288 " --> pdb=" O ASP Q 284 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN Q 289 " --> pdb=" O TYR Q 285 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N HIS Q 290 " --> pdb=" O SER Q 286 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU Q 293 " --> pdb=" O GLN Q 289 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS Q 294 " --> pdb=" O HIS Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 318 removed outlier: 3.963A pdb=" N GLN Q 305 " --> pdb=" O VAL Q 301 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA Q 306 " --> pdb=" O GLU Q 302 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU Q 307 " --> pdb=" O ALA Q 303 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL Q 318 " --> pdb=" O ARG Q 314 " (cutoff:3.500A) Processing helix chain 'Q' and resid 321 through 336 removed outlier: 3.861A pdb=" N ALA Q 325 " --> pdb=" O ASP Q 321 " (cutoff:3.500A) removed outlier: 3.641A 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 371 removed outlier: 3.759A pdb=" N ALA Q 360 " --> pdb=" O ASP Q 356 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS Q 366 " --> pdb=" O GLN Q 362 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL Q 367 " --> pdb=" O CYS Q 363 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU Q 368 " --> pdb=" O PHE Q 364 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS Q 369 " --> pdb=" O GLU Q 365 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA Q 370 " --> pdb=" O LYS Q 366 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR Q 371 " --> pdb=" O VAL Q 367 " (cutoff:3.500A) Processing helix chain 'Q' and resid 375 through 383 removed outlier: 3.704A pdb=" N LYS Q 379 " --> pdb=" O TYR Q 375 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE Q 380 " --> pdb=" O GLU Q 376 " (cutoff:3.500A) Processing helix chain 'Q' and resid 390 through 407 removed outlier: 3.513A pdb=" N ASP Q 395 " --> pdb=" O GLN Q 391 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ILE Q 396 " --> pdb=" O GLU Q 392 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA Q 397 " --> pdb=" O LYS Q 393 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU Q 406 " --> pdb=" O LYS Q 402 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN Q 407 " --> pdb=" O LYS Q 403 " (cutoff:3.500A) Processing helix chain 'Q' and resid 413 through 423 removed outlier: 3.662A pdb=" N ILE Q 421 " --> pdb=" O GLU Q 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 426 through 440 removed outlier: 3.944A pdb=" N ALA Q 430 " --> pdb=" O ASP Q 426 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG Q 439 " --> pdb=" O GLY Q 435 " (cutoff:3.500A) Processing helix chain 'Q' and resid 450 through 463 removed outlier: 3.732A pdb=" N LEU Q 454 " --> pdb=" O PRO Q 450 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG Q 463 " --> pdb=" O ALA Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 466 through 483 Processing helix chain 'Q' and resid 491 through 510 Processing helix chain 'Q' and resid 512 through 527 removed outlier: 3.799A pdb=" N GLU Q 526 " --> pdb=" O ASN Q 522 " (cutoff:3.500A) Processing helix chain 'Q' and resid 531 through 545 removed outlier: 3.730A pdb=" N GLY Q 538 " --> pdb=" O TYR Q 534 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS Q 544 " --> pdb=" O MET Q 540 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY Q 545 " --> pdb=" O ALA Q 541 " (cutoff:3.500A) Processing helix chain 'Q' and resid 548 through 561 removed outlier: 3.955A pdb=" N ASP Q 552 " --> pdb=" O TYR Q 548 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS Q 555 " --> pdb=" O SER Q 551 " (cutoff:3.500A) Processing helix chain 'Q' and resid 564 through 575 removed outlier: 3.690A pdb=" N HIS Q 575 " --> pdb=" O ILE Q 571 " (cutoff:3.500A) Processing helix chain 'Q' and resid 584 through 590 removed outlier: 4.174A pdb=" N PHE Q 588 " --> pdb=" O GLY Q 584 " (cutoff:3.500A) Processing helix chain 'Q' and resid 600 through 613 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: 4.046A pdb=" N ALA Q 650 " --> pdb=" O ASN Q 646 " (cutoff:3.500A) Processing helix chain 'Q' and resid 665 through 677 removed outlier: 3.871A pdb=" N VAL Q 669 " --> pdb=" O GLU Q 665 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN Q 672 " --> pdb=" O ASP Q 668 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL Q 673 " --> pdb=" O VAL Q 669 " (cutoff:3.500A) Processing helix chain 'Q' and resid 680 through 694 removed outlier: 3.865A pdb=" N TRP Q 684 " --> pdb=" O ILE Q 680 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU Q 685 " --> pdb=" O SER Q 681 " (cutoff:3.500A) Processing helix chain 'Q' and resid 700 through 708 removed outlier: 3.551A pdb=" N LEU Q 708 " --> pdb=" O TYR Q 704 " (cutoff:3.500A) Processing helix chain 'Q' and resid 716 through 724 removed outlier: 3.655A 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: 3.897A pdb=" N VAL Q 746 " --> pdb=" O LYS Q 742 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA Q 747 " --> pdb=" O ALA Q 743 " (cutoff:3.500A) Processing helix chain 'Q' and resid 750 through 770 removed outlier: 3.809A pdb=" N MET Q 754 " --> pdb=" O ASP Q 750 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA Q 758 " --> pdb=" O MET Q 754 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS Q 770 " --> pdb=" O THR Q 766 " (cutoff:3.500A) Processing helix chain 'Q' and resid 775 through 797 removed outlier: 3.714A pdb=" N VAL Q 779 " --> pdb=" O ASN Q 775 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL Q 783 " --> pdb=" O VAL Q 779 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS Q 784 " --> pdb=" O LEU Q 780 " (cutoff:3.500A) removed outlier: 3.537A 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: 4.352A pdb=" N ALA Q 829 " --> pdb=" O GLN Q 825 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG Q 830 " --> pdb=" O TYR Q 826 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU Q 848 " --> pdb=" O LYS Q 844 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU Q 883 " --> pdb=" O ALA Q 879 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS Q 886 " --> pdb=" O VAL Q 882 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN Q 887 " --> pdb=" O GLU Q 883 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR Q 892 " --> pdb=" O ILE Q 888 " (cutoff:3.500A) Processing helix chain 'R' and resid 355 through 360 removed outlier: 3.614A 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 368 through 372 removed outlier: 3.609A pdb=" N TRP R 372 " --> pdb=" O LEU R 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 382 removed outlier: 3.608A 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: 4.148A 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: 4.096A pdb=" N ILE R 479 " --> pdb=" O LYS R 475 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS R 480 " --> pdb=" O GLU R 476 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN R 484 " --> pdb=" O LYS R 480 " (cutoff:3.500A) Processing helix chain 'R' and resid 491 through 503 removed outlier: 3.835A 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: 3.527A pdb=" N LYS R 531 " --> pdb=" O GLY R 527 " (cutoff:3.500A) Processing helix chain 'R' and resid 556 through 585 removed outlier: 3.777A 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: 3.640A 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: 4.259A 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: 3.559A pdb=" N GLN S 249 " --> pdb=" O ILE S 245 " (cutoff:3.500A) Processing helix chain 'U' and resid 379 through 383 Processing helix chain 'U' and resid 411 through 415 Processing helix chain 'V' and resid 63 through 68 Processing helix chain 'V' and resid 101 through 106 Processing helix chain 'V' and resid 122 through 126 Processing helix chain 'V' and resid 172 through 186 removed outlier: 3.799A pdb=" N THR V 177 " --> pdb=" O ASP V 173 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA V 186 " --> pdb=" O THR V 182 " (cutoff:3.500A) Processing helix chain 'X' and resid 219 through 225 removed outlier: 3.528A pdb=" N ILE X 224 " --> pdb=" O VAL X 220 " (cutoff:3.500A) Processing helix chain 'X' and resid 233 through 239 removed outlier: 3.581A pdb=" N LEU X 238 " --> pdb=" O ARG X 234 " (cutoff:3.500A) Processing helix chain 'X' and resid 246 through 260 removed outlier: 3.710A pdb=" N ALA X 251 " --> pdb=" O LYS X 247 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE X 252 " --> pdb=" O ASN X 248 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS X 257 " --> pdb=" O LEU X 253 " (cutoff:3.500A) removed outlier: 3.572A 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 65 through 68 Processing helix chain 'Y' and resid 69 through 76 Processing helix chain 'Y' and resid 97 through 104 removed outlier: 3.780A pdb=" N LEU Y 101 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS Y 102 " --> pdb=" O VAL Y 98 " (cutoff:3.500A) removed outlier: 3.611A 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: 4.056A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 246 through 250 removed outlier: 3.598A pdb=" N TYR Z 249 " --> pdb=" O ARG Z 246 " (cutoff:3.500A) removed outlier: 4.475A 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: 4.207A 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 44 through 57 Processing helix chain 'a' and resid 63 through 79 removed outlier: 3.572A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 131 removed outlier: 3.573A 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: 3.542A 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 18 through 22 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.391A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 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 45 through 57 removed outlier: 3.633A pdb=" N SER e 57 " --> pdb=" O ARG e 53 " (cutoff:3.500A) Processing helix chain 'e' and resid 63 through 77 removed outlier: 3.681A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) removed outlier: 3.683A 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: 3.513A 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 42 Processing helix chain 'f' and resid 47 through 76 removed outlier: 4.133A pdb=" N TYR f 51 " --> pdb=" O SER f 47 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU f 52 " --> pdb=" O GLY f 48 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.235A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU g 65 " --> pdb=" O GLU g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'g' and resid 112 through 116 Processing helix chain 'h' and resid 34 through 46 Processing helix chain 'h' and resid 52 through 81 Processing helix chain 'h' and resid 87 through 99 Processing helix chain 'h' and resid 100 through 121 Processing helix chain 'l' and resid 1520 through 1525 Processing helix chain 'l' and resid 1542 through 1547 Processing helix chain 'l' and resid 1585 through 1598 removed outlier: 3.755A pdb=" N LYS l1590 " --> pdb=" O HIS l1586 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA l1591 " --> pdb=" O LYS l1587 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS l1594 " --> pdb=" O LYS l1590 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG l1598 " --> pdb=" O LYS l1594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 3.591A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.723A pdb=" N LYS A 357 " --> pdb=" O PHE B1086 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 365 removed outlier: 3.989A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET A 501 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.628A 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: 3.722A 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: 4.302A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.870A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.420A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 872 through 874 removed outlier: 3.846A pdb=" N THR A 878 " --> pdb=" O LYS A 874 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 902 through 904 Processing sheet with id=AB3, first strand: chain 'A' and resid 1211 through 1216 removed outlier: 3.537A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 3.718A pdb=" N ARG A1260 " --> pdb=" O ASN A1244 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1308 through 1310 removed outlier: 3.654A pdb=" N GLU A1337 " --> pdb=" O TYR A1308 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE A1335 " --> pdb=" O HIS A1310 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1471 through 1475 removed outlier: 3.553A pdb=" N ASP A1472 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 84 removed outlier: 4.857A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 84 removed outlier: 6.018A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL B 132 " --> pdb=" O GLN B 141 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN B 141 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LYS B 134 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN B 139 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC1, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.579A pdb=" N ASN B 486 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU B 198 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 524 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 205 through 208 Processing sheet with id=AC3, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.995A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 531 through 532 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 572 through 577 removed outlier: 4.563A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU B 611 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 613 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 602 " --> pdb=" O TYR B 615 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 749 through 751 removed outlier: 3.822A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 749 through 751 removed outlier: 3.822A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 922 " --> pdb=" O GLN B 906 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 3.545A 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 776 through 782 removed outlier: 4.124A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 936 " --> pdb=" O GLN B1049 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 776 through 782 removed outlier: 4.124A 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: 4.115A 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 Processing sheet with id=AD6, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.574A 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: 7.213A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.776A 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: 6.434A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.543A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA G 74 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE G 11 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE G 46 " --> pdb=" O ILE G 75 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.543A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA G 74 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE G 11 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU G 67 " --> pdb=" O VAL G 58 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 62 through 63 removed outlier: 3.804A pdb=" N VAL E 62 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE E 73 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.791A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE E 194 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 107 through 109 removed outlier: 7.119A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.505A 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: 3.603A pdb=" N LEU H 41 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 121 through 128 removed outlier: 3.757A pdb=" N ALA H 114 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG H 111 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY H 101 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 24 through 29 Processing sheet with id=AE9, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF1, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF2, first strand: chain 'M' and resid 804 through 809 removed outlier: 4.255A pdb=" N GLU M 804 " --> pdb=" O ASN M 800 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU M 798 " --> pdb=" O THR M 806 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE M 808 " --> pdb=" O CYS M 796 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N CYS M 796 " --> pdb=" O PHE M 808 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL M 848 " --> pdb=" O GLU M 883 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 971 through 972 removed outlier: 5.931A pdb=" N VAL M 971 " --> pdb=" O LYS M1036 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'M' and resid 1237 through 1240 removed outlier: 3.703A pdb=" N CYS M1265 " --> pdb=" O ILE M1167 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG M1266 " --> pdb=" O THR M1280 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 1355 through 1359 removed outlier: 3.790A pdb=" N LEU M1367 " --> pdb=" O VAL M1383 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TRP M1371 " --> pdb=" O GLN M1379 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN M1379 " --> pdb=" O TRP M1371 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 1461 through 1464 removed outlier: 4.187A pdb=" N PHE M1461 " --> pdb=" O GLY M1475 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY M1475 " --> pdb=" O PHE M1461 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 5 through 7 removed outlier: 4.408A pdb=" N ILE Q 6 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU Q 19 " --> pdb=" O ILE Q 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'R' and resid 386 through 387 removed outlier: 3.956A pdb=" N VAL R 387 " --> pdb=" O ALA R 403 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA R 403 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR R 420 " --> pdb=" O LEU R 417 " (cutoff:3.500A) removed outlier: 3.890A 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: 8.130A pdb=" N LYS R 413 " --> pdb=" O LYS R 424 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LEU R 426 " --> pdb=" O THR R 411 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N THR R 411 " --> pdb=" O LEU R 426 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 386 through 387 removed outlier: 3.956A pdb=" N VAL R 387 " --> pdb=" O ALA R 403 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA R 403 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU R 426 " --> pdb=" O PHE R 437 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE R 437 " --> pdb=" O LEU R 426 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU R 428 " --> pdb=" O ARG R 435 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG R 435 " --> pdb=" O LEU R 428 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP R 433 " --> pdb=" O HIS R 430 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 256 through 258 Processing sheet with id=AG2, first strand: chain 'U' and resid 376 through 377 removed outlier: 3.601A pdb=" N PHE V 312 " --> pdb=" O VAL U 376 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 494 through 495 removed outlier: 3.841A pdb=" N HIS U 494 " --> pdb=" O TYR U 460 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR U 460 " --> pdb=" O HIS U 494 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET U 448 " --> pdb=" O VAL U 459 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS U 451 " --> pdb=" O ARG U 439 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG U 439 " --> pdb=" O HIS U 451 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE U 440 " --> pdb=" O VAL V 204 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL V 204 " --> pdb=" O ILE U 440 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS U 442 " --> pdb=" O VAL V 202 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'V' and resid 221 through 222 removed outlier: 3.611A pdb=" N ARG V 331 " --> pdb=" O LYS V 292 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER V 333 " --> pdb=" O LYS V 290 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS V 290 " --> pdb=" O SER V 333 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'V' and resid 250 through 251 removed outlier: 3.933A pdb=" N GLN V 250 " --> pdb=" O VAL V 261 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 6 through 11 removed outlier: 6.461A pdb=" N ILE W 300 " --> pdb=" O LEU W 8 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS W 10 " --> pdb=" O ILE W 298 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE W 298 " --> pdb=" O LYS W 10 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY W 279 " --> pdb=" O VAL W 292 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 19 through 24 removed outlier: 3.518A pdb=" N SER W 21 " --> pdb=" O GLY W 38 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS W 45 " --> pdb=" O THR W 37 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL W 44 " --> pdb=" O SER W 59 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER W 59 " --> pdb=" O VAL W 44 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL W 46 " --> pdb=" O GLN W 57 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 67 through 72 removed outlier: 7.286A pdb=" N SER W 82 " --> pdb=" O VAL W 68 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL W 70 " --> pdb=" O ALA W 80 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA W 80 " --> pdb=" O VAL W 70 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ILE W 72 " --> pdb=" O ILE W 78 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE W 78 " --> pdb=" O ILE W 72 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS W 100 " --> pdb=" O LEU W 90 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP W 92 " --> pdb=" O GLN W 98 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLN W 98 " --> pdb=" O ASP W 92 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 120 through 124 removed outlier: 3.667A pdb=" N VAL W 130 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR W 142 " --> pdb=" O ILE W 132 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY W 134 " --> pdb=" O LYS W 140 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LYS W 140 " --> pdb=" O GLY W 134 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'W' and resid 151 through 156 removed outlier: 6.106A pdb=" N GLY W 166 " --> pdb=" O LEU W 152 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE W 154 " --> pdb=" O ALA W 164 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ALA W 164 " --> pdb=" O ILE W 154 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'W' and resid 172 through 175 Processing sheet with id=AH3, first strand: chain 'W' and resid 195 through 198 removed outlier: 3.714A pdb=" N SER W 195 " --> pdb=" O ALA W 208 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR W 197 " --> pdb=" O VAL W 206 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL W 206 " --> pdb=" O THR W 197 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR W 207 " --> pdb=" O LYS W 215 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS W 215 " --> pdb=" O THR W 207 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY W 226 " --> pdb=" O ILE W 216 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASP W 218 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU W 224 " --> pdb=" O ASP W 218 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'W' and resid 237 through 240 removed outlier: 3.532A pdb=" N LYS W 257 " --> pdb=" O SER W 249 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL W 256 " --> pdb=" O THR W 269 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR W 269 " --> pdb=" O VAL W 256 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL W 258 " --> pdb=" O VAL W 267 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Y' and resid 13 through 15 removed outlier: 3.533A pdb=" N LYS Y 23 " --> pdb=" O ARG Y 14 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Y' and resid 57 through 58 removed outlier: 3.655A pdb=" N SER Y 88 " --> pdb=" O ASP Y 58 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Y' and resid 83 through 85 removed outlier: 4.077A pdb=" N ILE Y 60 " --> pdb=" O ALA Z 217 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Z' and resid 224 through 228 removed outlier: 3.819A pdb=" N GLN Z 253 " --> pdb=" O THR Z 181 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Z' and resid 278 through 280 Processing sheet with id=AI1, first strand: chain 'Z' and resid 302 through 303 Processing sheet with id=AI2, first strand: chain 'Z' and resid 367 through 368 Processing sheet with id=AI3, first strand: chain 'Z' and resid 438 through 439 Processing sheet with id=AI4, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.689A pdb=" N LEU Z 491 " --> pdb=" O PHE Z 503 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE Z 503 " --> pdb=" O LEU Z 491 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.605A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL Z 551 " --> pdb=" O GLN Z 559 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN Z 541 " --> pdb=" O THR Z 576 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR Z 576 " --> pdb=" O GLN Z 541 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Z' and resid 622 through 625 removed outlier: 6.935A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY Z 612 " --> pdb=" O VAL Z 600 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL Z 600 " --> pdb=" O GLY Z 612 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Z' and resid 742 through 746 removed outlier: 3.614A pdb=" N ASP Z 726 " --> pdb=" O ARG Z 733 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU Z 735 " --> pdb=" O VAL Z 724 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL Z 724 " --> pdb=" O GLU Z 735 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.918A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AJ1, first strand: chain 'b' and resid 96 through 98 Processing sheet with id=AJ2, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.464A pdb=" N ARG c 42 " --> pdb=" O ILE d 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AJ4, first strand: chain 'c' and resid 100 through 102 Processing sheet with id=AJ5, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.519A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ5 Processing sheet with id=AJ6, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AJ7, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.159A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AJ9, first strand: chain 'l' and resid 1554 through 1556 removed outlier: 3.606A pdb=" N ILE l1555 " --> pdb=" O GLY l1563 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'l' and resid 1575 through 1578 removed outlier: 7.117A pdb=" N PHE l1650 " --> pdb=" O VAL l1576 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLU l1578 " --> pdb=" O VAL l1648 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL l1648 " --> pdb=" O GLU l1578 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'l' and resid 1575 through 1578 removed outlier: 7.117A pdb=" N PHE l1650 " --> pdb=" O VAL l1576 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLU l1578 " --> pdb=" O VAL l1648 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL l1648 " --> pdb=" O GLU l1578 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'l' and resid 1582 through 1584 removed outlier: 4.018A pdb=" N ILE l1614 " --> pdb=" O LEU l1584 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU l1613 " --> pdb=" O LEU l1609 " (cutoff:3.500A) 2740 hydrogen bonds defined for protein. 7827 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 403 hydrogen bonds 802 hydrogen bond angles 0 basepair planarities 158 basepair parallelities 247 stacking parallelities Total time for adding SS restraints: 42.56 Time building geometry restraints manager: 15.48 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: 19297 1.33 - 1.45: 13072 1.45 - 1.57: 37057 1.57 - 1.69: 661 1.69 - 1.81: 439 Bond restraints: 70526 Sorted by residual: 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 2.86e+01 bond pdb=" OG1 TPO Z 775 " pdb=" P TPO Z 775 " ideal model delta sigma weight residual 1.717 1.615 0.102 2.00e-02 2.50e+03 2.60e+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 1.69e+01 bond pdb=" O3P TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" O3P TPO Z 775 " pdb=" P TPO Z 775 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 70521 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 95550 2.56 - 5.11: 848 5.11 - 7.67: 77 7.67 - 10.22: 10 10.22 - 12.78: 6 Bond angle restraints: 96491 Sorted by residual: angle pdb=" C GLU Q 772 " pdb=" N LYS Q 773 " pdb=" CA LYS Q 773 " ideal model delta sigma weight residual 121.70 134.48 -12.78 1.80e+00 3.09e-01 5.04e+01 angle pdb=" C TYR V 61 " pdb=" N LYS V 62 " pdb=" CA LYS V 62 " ideal model delta sigma weight residual 121.70 132.60 -10.90 1.80e+00 3.09e-01 3.67e+01 angle pdb=" O3' DT N 145 " pdb=" P DA N 146 " pdb=" OP1 DA N 146 " ideal model delta sigma weight residual 108.00 120.26 -12.26 3.00e+00 1.11e-01 1.67e+01 angle pdb=" CB TPO A1525 " pdb=" OG1 TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 119.31 107.25 12.06 3.00e+00 1.11e-01 1.62e+01 angle pdb=" OG1 TPO Z 775 " pdb=" P TPO Z 775 " pdb=" O1P TPO Z 775 " ideal model delta sigma weight residual 100.43 111.72 -11.29 3.00e+00 1.11e-01 1.42e+01 ... (remaining 96486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 39422 35.94 - 71.87: 1281 71.87 - 107.81: 25 107.81 - 143.75: 2 143.75 - 179.69: 7 Dihedral angle restraints: 40737 sinusoidal: 17391 harmonic: 23346 Sorted by residual: dihedral pdb=" CA GLU I 105 " pdb=" C GLU I 105 " pdb=" N ASP I 106 " pdb=" CA ASP I 106 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASP A 120 " pdb=" C ASP A 120 " pdb=" N SER A 121 " pdb=" CA SER A 121 " ideal model delta harmonic sigma weight residual -180.00 -159.37 -20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" O4' U P 13 " pdb=" C1' U P 13 " pdb=" N1 U P 13 " pdb=" C2 U P 13 " ideal model delta sinusoidal sigma weight residual -160.00 -108.04 -51.96 1 1.50e+01 4.44e-03 1.64e+01 ... (remaining 40734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 10005 0.099 - 0.198: 423 0.198 - 0.296: 1 0.296 - 0.395: 2 0.395 - 0.494: 1 Chirality restraints: 10432 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 -2.84 -0.49 2.00e-01 2.50e+01 6.10e+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 -2.73 -0.38 2.00e-01 2.50e+01 3.60e+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 -2.71 -0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 10429 not shown) Planarity restraints: 11763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP Q 684 " 0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C TRP Q 684 " -0.072 2.00e-02 2.50e+03 pdb=" O TRP Q 684 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU Q 685 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA N 61 " 0.026 2.00e-02 2.50e+03 1.87e-02 9.58e+00 pdb=" N9 DA N 61 " -0.052 2.00e-02 2.50e+03 pdb=" C8 DA N 61 " 0.021 2.00e-02 2.50e+03 pdb=" N7 DA N 61 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA N 61 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA N 61 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA N 61 " 0.003 2.00e-02 2.50e+03 pdb=" N1 DA N 61 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA N 61 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA N 61 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DA N 61 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC T -73 " 0.018 2.00e-02 2.50e+03 2.02e-02 9.22e+00 pdb=" N1 DC T -73 " -0.046 2.00e-02 2.50e+03 pdb=" C2 DC T -73 " 0.030 2.00e-02 2.50e+03 pdb=" O2 DC T -73 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DC T -73 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DC T -73 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC T -73 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DC T -73 " 0.015 2.00e-02 2.50e+03 pdb=" C6 DC T -73 " -0.002 2.00e-02 2.50e+03 ... (remaining 11760 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 451 2.54 - 3.13: 54733 3.13 - 3.72: 107239 3.72 - 4.31: 143715 4.31 - 4.90: 233312 Nonbonded interactions: 539450 Sorted by model distance: nonbonded pdb=" OH TYR Q 371 " pdb=" NE2 GLN V 69 " model vdw 1.945 3.120 nonbonded pdb=" O3' C P 26 " pdb="MG MG A2003 " model vdw 1.968 2.170 nonbonded pdb=" N CYS J 45 " pdb="ZN ZN J 101 " model vdw 2.009 2.310 nonbonded pdb=" OG1 THR K 77 " pdb=" O TYR K 81 " model vdw 2.069 3.040 nonbonded pdb=" O MET A 535 " pdb=" OH TYR A 669 " model vdw 2.074 3.040 ... (remaining 539445 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 'a' and resid 39 through 134) selection = (chain 'e' and resid 39 through 134) } ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 16 through 118) } ncs_group { reference = (chain 'd' and resid 29 through 121) selection = chain 'h' } 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: 9.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.330 Construct map_model_manager: 0.060 Extract box with map and model: 2.140 Check model and map are aligned: 0.380 Set scattering table: 0.470 Process input model: 158.380 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5651 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 0.107 70526 Z= 0.279 Angle : 0.657 12.780 96491 Z= 0.348 Chirality : 0.045 0.494 10432 Planarity : 0.004 0.053 11763 Dihedral : 14.203 179.685 26207 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.85 % Favored : 93.07 % Rotamer: Outliers : 0.94 % Allowed : 3.63 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % 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: -1.37 (0.09), residues: 8502 helix: 1.13 (0.10), residues: 3274 sheet: -2.96 (0.16), residues: 824 loop : -2.18 (0.09), residues: 4404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Q 568 HIS 0.009 0.001 HIS d 79 PHE 0.022 0.002 PHE C 21 TYR 0.023 0.002 TYR B 752 ARG 0.012 0.001 ARG Q 763 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 728 time to evaluate : 5.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8930 (m-10) cc_final: 0.8704 (m-10) REVERT: A 329 MET cc_start: 0.8320 (mtt) cc_final: 0.7971 (mmt) REVERT: A 355 MET cc_start: 0.8472 (mmt) cc_final: 0.8229 (mmm) REVERT: A 474 VAL cc_start: 0.8731 (t) cc_final: 0.8304 (p) REVERT: A 520 MET cc_start: 0.7518 (tpt) cc_final: 0.6739 (tpt) REVERT: A 539 GLN cc_start: 0.6231 (mm110) cc_final: 0.5903 (pm20) REVERT: A 1102 MET cc_start: 0.8834 (ptp) cc_final: 0.8615 (ptm) REVERT: A 1133 LYS cc_start: 0.8609 (pttp) cc_final: 0.8182 (mtmm) REVERT: A 1433 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7772 (tt0) REVERT: B 109 MET cc_start: 0.8518 (mmm) cc_final: 0.8296 (mmm) REVERT: B 840 MET cc_start: 0.6871 (ttp) cc_final: 0.6514 (tmm) REVERT: B 1054 MET cc_start: 0.8400 (mmt) cc_final: 0.7878 (mmm) REVERT: C 247 SER cc_start: 0.8988 (m) cc_final: 0.8730 (p) REVERT: C 254 LYS cc_start: 0.8692 (tttm) cc_final: 0.8429 (mmmm) REVERT: C 268 GLN cc_start: 0.8916 (tp40) cc_final: 0.8661 (pt0) REVERT: E 18 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8738 (mmt) REVERT: F 80 MET cc_start: 0.8100 (mmt) cc_final: 0.7834 (mmt) REVERT: H 12 VAL cc_start: 0.9498 (t) cc_final: 0.9250 (m) REVERT: J 1 MET cc_start: 0.7711 (mtm) cc_final: 0.7471 (mtm) REVERT: J 26 GLN cc_start: 0.9051 (tt0) cc_final: 0.8509 (tm-30) REVERT: L 27 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7968 (mm-30) REVERT: L 28 ILE cc_start: 0.8759 (mm) cc_final: 0.8381 (mp) REVERT: L 38 GLU cc_start: 0.7815 (pm20) cc_final: 0.6382 (mp0) REVERT: Q 697 TYR cc_start: 0.1133 (OUTLIER) cc_final: 0.0880 (m-80) REVERT: Q 754 MET cc_start: 0.7184 (mtm) cc_final: 0.6775 (pp-130) REVERT: Q 817 CYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6875 (p) REVERT: Q 881 TYR cc_start: 0.6045 (m-10) cc_final: 0.5334 (m-10) REVERT: R 503 ARG cc_start: 0.0648 (tmm160) cc_final: -0.0025 (ttt180) REVERT: R 563 ILE cc_start: -0.1241 (tp) cc_final: -0.1964 (tp) REVERT: R 567 ASN cc_start: 0.1368 (m-40) cc_final: -0.0852 (t0) REVERT: V 58 PHE cc_start: 0.0750 (p90) cc_final: 0.0327 (t80) REVERT: W 11 GLN cc_start: 0.8476 (tp-100) cc_final: 0.8205 (tm-30) REVERT: W 191 MET cc_start: 0.5831 (mmm) cc_final: 0.5424 (mmt) REVERT: W 234 TRP cc_start: 0.7777 (m-10) cc_final: 0.7474 (m-10) REVERT: W 272 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: a 74 ILE cc_start: 0.8628 (mt) cc_final: 0.7999 (mm) REVERT: a 77 ASP cc_start: 0.8240 (m-30) cc_final: 0.7947 (m-30) REVERT: c 114 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.7876 (t) REVERT: g 90 ASP cc_start: 0.6614 (t70) cc_final: 0.6329 (t70) REVERT: h 99 LEU cc_start: 0.8463 (mt) cc_final: 0.8109 (tp) outliers start: 54 outliers final: 12 residues processed: 768 average time/residue: 1.6381 time to fit residues: 1620.5047 Evaluate side-chains 393 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 376 time to evaluate : 5.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 697 TYR Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 817 CYS Chi-restraints excluded: chain W residue 272 ASP Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 81 ARG Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain l residue 1489 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 744 optimal weight: 5.9990 chunk 668 optimal weight: 7.9990 chunk 370 optimal weight: 0.9980 chunk 228 optimal weight: 0.9990 chunk 450 optimal weight: 30.0000 chunk 357 optimal weight: 4.9990 chunk 691 optimal weight: 9.9990 chunk 267 optimal weight: 0.5980 chunk 420 optimal weight: 50.0000 chunk 514 optimal weight: 30.0000 chunk 800 optimal weight: 8.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 301 HIS A 320 ASN A 341 GLN A 387 ASN A 423 ASN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 GLN A 531 ASN A 673 GLN A 700 GLN A 982 ASN A 991 GLN ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 GLN A1422 GLN A1457 ASN A1462 GLN B 98 HIS B 227 ASN B 319 ASN B 420 GLN B 471 ASN B 582 GLN B 725 GLN B1071 ASN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS H 29 HIS I 41 ASN K 2 ASN L 23 HIS Q 289 GLN Q 305 GLN Q 373 ASN Q 374 ASN Q 407 GLN Q 466 ASN Q 502 ASN Q 527 HIS Q 529 ASN ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 616 HIS Q 628 HIS Q 659 HIS Q 694 GLN Q 714 HIS ** Q 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 775 ASN V 69 GLN V 72 HIS W 11 GLN W 27 ASN W 173 ASN W 273 HIS Y 12 HIS Z 446 ASN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 79 HIS g 31 HIS h 60 ASN h 64 ASN ** l1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l1603 HIS l1628 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.093917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.071595 restraints weight = 420723.141| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 5.84 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3850 r_free = 0.3850 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 393 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3850 r_free = 0.3850 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 393 | |-----------------------------------------------------------------------------| r_final: 0.3850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 70526 Z= 0.293 Angle : 0.625 11.118 96491 Z= 0.330 Chirality : 0.043 0.212 10432 Planarity : 0.005 0.080 11763 Dihedral : 17.509 178.044 12987 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.13 % Favored : 94.82 % Rotamer: Outliers : 1.88 % Allowed : 9.13 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % 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: -1.14 (0.09), residues: 8502 helix: 1.09 (0.09), residues: 3374 sheet: -2.49 (0.16), residues: 853 loop : -1.97 (0.09), residues: 4275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP W 47 HIS 0.007 0.001 HIS W 231 PHE 0.023 0.002 PHE V 53 TYR 0.021 0.002 TYR Q 602 ARG 0.010 0.001 ARG L 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 431 time to evaluate : 5.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8082 (tmt) REVERT: A 329 MET cc_start: 0.8571 (mtt) cc_final: 0.7687 (mmt) REVERT: A 355 MET cc_start: 0.8477 (mmt) cc_final: 0.8245 (mmm) REVERT: A 1102 MET cc_start: 0.8992 (ptp) cc_final: 0.8709 (ptm) REVERT: A 1133 LYS cc_start: 0.8504 (pttp) cc_final: 0.8179 (mtmm) REVERT: A 1309 MET cc_start: 0.7641 (ttp) cc_final: 0.7375 (ttm) REVERT: A 1428 MET cc_start: 0.8523 (tpp) cc_final: 0.8151 (mmt) REVERT: B 297 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8775 (tpp) REVERT: B 347 MET cc_start: 0.8841 (tmm) cc_final: 0.8596 (tmm) REVERT: B 744 MET cc_start: 0.8474 (mmm) cc_final: 0.8273 (mtp) REVERT: B 840 MET cc_start: 0.6548 (ttp) cc_final: 0.5781 (tmm) REVERT: B 1054 MET cc_start: 0.8297 (mmt) cc_final: 0.8030 (mmm) REVERT: B 1075 MET cc_start: 0.8680 (mmm) cc_final: 0.8472 (mmm) REVERT: F 82 GLU cc_start: 0.7499 (tp30) cc_final: 0.7077 (tp30) REVERT: G 1 MET cc_start: 0.8624 (ttp) cc_final: 0.8258 (ttp) REVERT: G 131 MET cc_start: 0.4469 (tmm) cc_final: 0.3971 (tpt) REVERT: J 1 MET cc_start: 0.7688 (mtm) cc_final: 0.7380 (mtm) REVERT: J 26 GLN cc_start: 0.8921 (tt0) cc_final: 0.8587 (tp40) REVERT: L 28 ILE cc_start: 0.9116 (mm) cc_final: 0.8445 (tt) REVERT: Q 378 MET cc_start: 0.4939 (mtt) cc_final: 0.4168 (tmm) REVERT: Q 602 TYR cc_start: 0.7374 (OUTLIER) cc_final: 0.6785 (m-80) REVERT: Q 691 TYR cc_start: 0.8906 (m-10) cc_final: 0.8665 (m-80) REVERT: Q 754 MET cc_start: 0.8473 (mtm) cc_final: 0.7427 (ppp) REVERT: Q 761 LEU cc_start: 0.9069 (mt) cc_final: 0.8637 (tt) REVERT: Q 817 CYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7170 (p) REVERT: Q 881 TYR cc_start: 0.5913 (OUTLIER) cc_final: 0.5417 (m-10) REVERT: R 503 ARG cc_start: -0.0655 (tmm160) cc_final: -0.1151 (ttm170) REVERT: R 567 ASN cc_start: -0.0465 (m-40) cc_final: -0.1301 (t0) REVERT: V 58 PHE cc_start: 0.3626 (p90) cc_final: 0.1683 (t80) REVERT: W 187 GLU cc_start: 0.9103 (pm20) cc_final: 0.8434 (mm-30) REVERT: W 234 TRP cc_start: 0.8532 (m-10) cc_final: 0.8219 (m-10) REVERT: X 238 LEU cc_start: 0.8548 (mt) cc_final: 0.8336 (mt) REVERT: X 245 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8628 (t80) REVERT: X 250 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.6673 (m-80) REVERT: Y 63 MET cc_start: -0.0221 (tpp) cc_final: -0.0959 (tpp) REVERT: Z 307 MET cc_start: -0.0143 (pmt) cc_final: -0.0468 (pmm) REVERT: Z 460 MET cc_start: 0.3258 (ttp) cc_final: 0.2918 (ttm) REVERT: b 54 THR cc_start: 0.8539 (p) cc_final: 0.8211 (t) REVERT: e 74 ILE cc_start: 0.9078 (mt) cc_final: 0.8814 (tp) REVERT: e 90 MET cc_start: 0.7998 (tpt) cc_final: 0.7723 (tpp) REVERT: g 92 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6787 (pt0) REVERT: g 99 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7877 (mtm180) REVERT: h 88 SER cc_start: 0.8576 (p) cc_final: 0.8321 (m) REVERT: h 99 LEU cc_start: 0.8530 (mt) cc_final: 0.8122 (tp) outliers start: 108 outliers final: 26 residues processed: 496 average time/residue: 1.4283 time to fit residues: 943.5289 Evaluate side-chains 391 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 356 time to evaluate : 5.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain Q residue 377 THR Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 602 TYR Chi-restraints excluded: chain Q residue 667 ARG Chi-restraints excluded: chain Q residue 669 VAL Chi-restraints excluded: chain Q residue 817 CYS Chi-restraints excluded: chain Q residue 881 TYR Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain X residue 245 PHE Chi-restraints excluded: chain X residue 250 PHE Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 99 TYR Chi-restraints excluded: chain a residue 110 CYS Chi-restraints excluded: chain a residue 122 LYS Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 76 THR Chi-restraints excluded: chain g residue 92 GLU Chi-restraints excluded: chain g residue 99 ARG Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain l residue 1480 VAL Chi-restraints excluded: chain l residue 1489 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 283 optimal weight: 20.0000 chunk 177 optimal weight: 1.9990 chunk 638 optimal weight: 50.0000 chunk 352 optimal weight: 5.9990 chunk 860 optimal weight: 1.9990 chunk 579 optimal weight: 7.9990 chunk 318 optimal weight: 5.9990 chunk 417 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 413 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 GLN B 980 HIS B1101 GLN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS K 2 ASN L 26 ASN ** Q 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 573 ASN ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 734 GLN ** V 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 221 HIS Z 234 HIS ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 46 HIS ** g 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l1498 GLN ** l1549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.092075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.068849 restraints weight = 418623.626| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 5.95 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 70526 Z= 0.347 Angle : 0.625 9.734 96491 Z= 0.331 Chirality : 0.043 0.183 10432 Planarity : 0.004 0.059 11763 Dihedral : 17.761 174.182 12968 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.63 % Favored : 94.32 % Rotamer: Outliers : 2.12 % Allowed : 10.82 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % 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: -1.02 (0.09), residues: 8502 helix: 1.08 (0.09), residues: 3419 sheet: -2.06 (0.17), residues: 834 loop : -1.92 (0.09), residues: 4249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP W 49 HIS 0.009 0.001 HIS A 804 PHE 0.025 0.002 PHE H 10 TYR 0.035 0.002 TYR B 766 ARG 0.011 0.001 ARG a 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 375 time to evaluate : 5.839 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: A 266 MET cc_start: 0.2307 (OUTLIER) cc_final: 0.2099 (ttp) REVERT: A 520 MET cc_start: 0.7917 (tpp) cc_final: 0.7700 (mmm) REVERT: A 524 MET cc_start: 0.7510 (mtp) cc_final: 0.7229 (mtp) REVERT: A 1102 MET cc_start: 0.9032 (ptp) cc_final: 0.8783 (ptm) REVERT: A 1133 LYS cc_start: 0.8665 (pttp) cc_final: 0.8411 (mtmm) REVERT: A 1228 MET cc_start: 0.8103 (mmm) cc_final: 0.7808 (mmt) REVERT: A 1428 MET cc_start: 0.8607 (tpp) cc_final: 0.8281 (mmt) REVERT: A 1451 MET cc_start: 0.8628 (tpp) cc_final: 0.8417 (mmm) REVERT: B 239 MET cc_start: 0.7544 (ptm) cc_final: 0.7318 (ptm) REVERT: B 347 MET cc_start: 0.8920 (tmm) cc_final: 0.8524 (tmm) REVERT: B 744 MET cc_start: 0.8269 (mmm) cc_final: 0.8052 (mtp) REVERT: B 840 MET cc_start: 0.6733 (ttp) cc_final: 0.5793 (tmm) REVERT: B 1054 MET cc_start: 0.8351 (mmt) cc_final: 0.7971 (mmm) REVERT: B 1075 MET cc_start: 0.8577 (mmm) cc_final: 0.8368 (mmm) REVERT: C 268 GLN cc_start: 0.8999 (mm110) cc_final: 0.8502 (pt0) REVERT: D 74 PHE cc_start: 0.6466 (OUTLIER) cc_final: 0.6207 (p90) REVERT: G 1 MET cc_start: 0.8549 (ttp) cc_final: 0.8220 (ttp) REVERT: G 10 GLU cc_start: 0.8133 (pm20) cc_final: 0.7901 (tp30) REVERT: G 29 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8736 (ttmt) REVERT: J 1 MET cc_start: 0.7669 (mtm) cc_final: 0.7382 (mtm) REVERT: J 26 GLN cc_start: 0.9038 (tt0) cc_final: 0.8697 (tp40) REVERT: K 111 ASP cc_start: 0.9047 (t0) cc_final: 0.8845 (t0) REVERT: Q 378 MET cc_start: 0.4988 (mtt) cc_final: 0.4378 (tmm) REVERT: Q 674 ARG cc_start: 0.8932 (ttp-170) cc_final: 0.8714 (ptp-170) REVERT: Q 691 TYR cc_start: 0.8942 (m-10) cc_final: 0.8714 (m-80) REVERT: Q 761 LEU cc_start: 0.9079 (mt) cc_final: 0.8640 (tt) REVERT: Q 817 CYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8308 (p) REVERT: Q 820 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8893 (mm) REVERT: R 493 GLU cc_start: 0.4585 (OUTLIER) cc_final: 0.4309 (mm-30) REVERT: R 496 VAL cc_start: 0.4194 (m) cc_final: 0.3958 (t) REVERT: R 500 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6975 (pm20) REVERT: R 503 ARG cc_start: 0.0358 (tmm160) cc_final: -0.0755 (ttm-80) REVERT: R 564 ASN cc_start: 0.1192 (t0) cc_final: 0.0948 (m-40) REVERT: R 567 ASN cc_start: 0.0064 (m-40) cc_final: -0.0510 (t0) REVERT: R 568 ARG cc_start: 0.0306 (ppt170) cc_final: 0.0046 (ppt170) REVERT: V 53 PHE cc_start: 0.5270 (t80) cc_final: 0.5066 (t80) REVERT: W 221 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7663 (p90) REVERT: Z 307 MET cc_start: -0.0141 (pmt) cc_final: -0.0457 (pmm) REVERT: b 62 LEU cc_start: 0.8971 (mt) cc_final: 0.8747 (mt) REVERT: b 84 MET cc_start: 0.7677 (mpp) cc_final: 0.7122 (mmt) REVERT: g 92 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6845 (pt0) REVERT: h 68 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7783 (tp30) REVERT: h 99 LEU cc_start: 0.8558 (mt) cc_final: 0.8166 (tp) REVERT: l 1497 MET cc_start: 0.4704 (mpt) cc_final: 0.4277 (mpp) REVERT: l 1526 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6685 (tpt) outliers start: 122 outliers final: 37 residues processed: 463 average time/residue: 1.3773 time to fit residues: 859.4469 Evaluate side-chains 384 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 338 time to evaluate : 5.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain C residue 60 HIS Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 669 VAL Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 817 CYS Chi-restraints excluded: chain Q residue 820 LEU Chi-restraints excluded: chain R residue 493 GLU Chi-restraints excluded: chain V residue 58 PHE Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 221 HIS Chi-restraints excluded: chain W residue 241 CYS Chi-restraints excluded: chain X residue 245 PHE Chi-restraints excluded: chain X residue 250 PHE Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 110 CYS Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 76 THR Chi-restraints excluded: chain g residue 92 GLU Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain l residue 1463 CYS Chi-restraints excluded: chain l residue 1526 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 835 optimal weight: 3.9990 chunk 565 optimal weight: 10.0000 chunk 831 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 137 optimal weight: 0.6980 chunk 594 optimal weight: 9.9990 chunk 633 optimal weight: 5.9990 chunk 861 optimal weight: 0.7980 chunk 209 optimal weight: 0.9990 chunk 774 optimal weight: 30.0000 chunk 808 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1445 HIS ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN ** Q 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 694 GLN ** V 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 239 GLN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.093405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.070735 restraints weight = 424678.094| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 6.13 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 70526 Z= 0.176 Angle : 0.532 11.659 96491 Z= 0.280 Chirality : 0.040 0.186 10432 Planarity : 0.003 0.048 11763 Dihedral : 17.764 174.018 12961 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.78 % Favored : 95.19 % Rotamer: Outliers : 1.55 % Allowed : 12.52 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % 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: -0.70 (0.09), residues: 8502 helix: 1.36 (0.09), residues: 3405 sheet: -1.83 (0.17), residues: 842 loop : -1.76 (0.09), residues: 4255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1192 HIS 0.006 0.001 HIS f 75 PHE 0.033 0.001 PHE a 78 TYR 0.023 0.001 TYR B 766 ARG 0.007 0.000 ARG B1091 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 369 time to evaluate : 5.730 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: A 520 MET cc_start: 0.8040 (tpp) cc_final: 0.7839 (mmm) REVERT: A 1102 MET cc_start: 0.8973 (ptp) cc_final: 0.8730 (ptm) REVERT: A 1133 LYS cc_start: 0.8562 (pttp) cc_final: 0.8242 (mtmm) REVERT: A 1228 MET cc_start: 0.8049 (mmm) cc_final: 0.7781 (mmm) REVERT: A 1309 MET cc_start: 0.8004 (ttm) cc_final: 0.7552 (mtp) REVERT: A 1428 MET cc_start: 0.8575 (tpp) cc_final: 0.8156 (mmt) REVERT: B 239 MET cc_start: 0.7515 (ptm) cc_final: 0.7275 (ptm) REVERT: B 298 MET cc_start: 0.8643 (ttm) cc_final: 0.8262 (ttm) REVERT: B 347 MET cc_start: 0.8904 (tmm) cc_final: 0.8462 (tmm) REVERT: B 744 MET cc_start: 0.8363 (mmm) cc_final: 0.8148 (mtp) REVERT: B 840 MET cc_start: 0.6757 (ttp) cc_final: 0.5811 (tmm) REVERT: B 1054 MET cc_start: 0.8253 (mmt) cc_final: 0.7910 (mmm) REVERT: C 268 GLN cc_start: 0.8992 (mm110) cc_final: 0.8495 (pt0) REVERT: D 74 PHE cc_start: 0.6341 (OUTLIER) cc_final: 0.6070 (p90) REVERT: G 1 MET cc_start: 0.8649 (ttp) cc_final: 0.8362 (ttp) REVERT: G 29 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8770 (ttmt) REVERT: G 131 MET cc_start: 0.4211 (tmm) cc_final: 0.3697 (tpt) REVERT: H 75 TYR cc_start: 0.7979 (t80) cc_final: 0.7673 (t80) REVERT: J 1 MET cc_start: 0.7582 (mtm) cc_final: 0.7241 (mtm) REVERT: J 26 GLN cc_start: 0.8974 (tt0) cc_final: 0.8671 (tp40) REVERT: K 82 SER cc_start: 0.7684 (OUTLIER) cc_final: 0.7405 (t) REVERT: K 111 ASP cc_start: 0.9053 (t0) cc_final: 0.8802 (t0) REVERT: Q 378 MET cc_start: 0.4689 (mtt) cc_final: 0.4078 (tmm) REVERT: Q 402 LYS cc_start: 0.9084 (mptt) cc_final: 0.8725 (tppt) REVERT: Q 405 THR cc_start: 0.7656 (m) cc_final: 0.7299 (p) REVERT: Q 674 ARG cc_start: 0.8901 (ttp-170) cc_final: 0.8409 (tmt-80) REVERT: Q 691 TYR cc_start: 0.8907 (m-10) cc_final: 0.8668 (m-80) REVERT: Q 761 LEU cc_start: 0.9065 (mt) cc_final: 0.8615 (tt) REVERT: Q 817 CYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8241 (p) REVERT: Q 820 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8950 (mm) REVERT: R 493 GLU cc_start: 0.4632 (OUTLIER) cc_final: 0.4369 (mm-30) REVERT: R 496 VAL cc_start: 0.4752 (m) cc_final: 0.4361 (t) REVERT: R 500 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6881 (pm20) REVERT: R 503 ARG cc_start: 0.0094 (tmm160) cc_final: -0.0798 (ttm170) REVERT: R 567 ASN cc_start: -0.0319 (m-40) cc_final: -0.0820 (t0) REVERT: W 221 HIS cc_start: 0.8013 (OUTLIER) cc_final: 0.7560 (p90) REVERT: X 238 LEU cc_start: 0.8711 (mt) cc_final: 0.8211 (pp) REVERT: Z 307 MET cc_start: 0.0168 (pmt) cc_final: -0.0173 (pmm) REVERT: b 84 MET cc_start: 0.7522 (mpp) cc_final: 0.7075 (mmm) REVERT: c 113 SER cc_start: 0.8575 (p) cc_final: 0.8345 (m) REVERT: d 46 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.6965 (m170) REVERT: g 92 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6734 (pt0) REVERT: h 77 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8435 (mp) REVERT: h 99 LEU cc_start: 0.8398 (mt) cc_final: 0.8048 (tp) REVERT: l 1526 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6763 (tpt) REVERT: l 1560 LYS cc_start: -0.1140 (OUTLIER) cc_final: -0.1497 (tmtm) REVERT: l 1627 MET cc_start: 0.1440 (mmt) cc_final: 0.1229 (mmt) outliers start: 89 outliers final: 31 residues processed: 432 average time/residue: 1.4246 time to fit residues: 825.4067 Evaluate side-chains 377 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 334 time to evaluate : 5.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain K residue 2 ASN Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 663 PHE Chi-restraints excluded: chain Q residue 817 CYS Chi-restraints excluded: chain Q residue 820 LEU Chi-restraints excluded: chain R residue 493 GLU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 221 HIS Chi-restraints excluded: chain X residue 245 PHE Chi-restraints excluded: chain X residue 250 PHE Chi-restraints excluded: chain Y residue 48 MET Chi-restraints excluded: chain Z residue 626 CYS Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 100 LEU Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 76 THR Chi-restraints excluded: chain g residue 92 GLU Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain l residue 1526 MET Chi-restraints excluded: chain l residue 1560 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 472 optimal weight: 40.0000 chunk 819 optimal weight: 6.9990 chunk 766 optimal weight: 9.9990 chunk 293 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 320 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 647 optimal weight: 4.9990 chunk 351 optimal weight: 8.9990 chunk 449 optimal weight: 30.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 98 GLN ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.091899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.068969 restraints weight = 417311.647| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 5.71 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 70526 Z= 0.280 Angle : 0.573 11.279 96491 Z= 0.302 Chirality : 0.041 0.198 10432 Planarity : 0.004 0.054 11763 Dihedral : 17.859 173.831 12961 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.40 % Favored : 94.57 % Rotamer: Outliers : 1.70 % Allowed : 13.18 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % 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: -0.67 (0.09), residues: 8502 helix: 1.32 (0.09), residues: 3420 sheet: -1.75 (0.17), residues: 851 loop : -1.71 (0.09), residues: 4231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP W 47 HIS 0.006 0.001 HIS C 60 PHE 0.028 0.001 PHE V 53 TYR 0.036 0.001 TYR B 766 ARG 0.006 0.000 ARG L 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 357 time to evaluate : 5.646 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: A 537 ILE cc_start: 0.6110 (mp) cc_final: 0.5906 (mp) REVERT: A 1102 MET cc_start: 0.9004 (ptp) cc_final: 0.8759 (ptm) REVERT: A 1133 LYS cc_start: 0.8759 (pttp) cc_final: 0.8468 (mtmm) REVERT: A 1228 MET cc_start: 0.8190 (mmm) cc_final: 0.7949 (mmt) REVERT: A 1296 MET cc_start: 0.8713 (tpp) cc_final: 0.8425 (tpp) REVERT: A 1309 MET cc_start: 0.8108 (ttm) cc_final: 0.7797 (mtp) REVERT: A 1428 MET cc_start: 0.8566 (tpp) cc_final: 0.8146 (mmt) REVERT: A 1451 MET cc_start: 0.8555 (tpp) cc_final: 0.8333 (mmm) REVERT: A 1459 MET cc_start: 0.8602 (mtm) cc_final: 0.8295 (mtm) REVERT: B 239 MET cc_start: 0.7642 (ptm) cc_final: 0.7389 (ptm) REVERT: B 297 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8757 (tpp) REVERT: B 298 MET cc_start: 0.8819 (ttm) cc_final: 0.8477 (ttm) REVERT: B 347 MET cc_start: 0.8925 (tmm) cc_final: 0.8502 (tmm) REVERT: B 1054 MET cc_start: 0.8307 (mmt) cc_final: 0.7977 (mmm) REVERT: B 1075 MET cc_start: 0.8640 (mmm) cc_final: 0.8324 (mpt) REVERT: D 74 PHE cc_start: 0.6388 (OUTLIER) cc_final: 0.6146 (p90) REVERT: G 1 MET cc_start: 0.8698 (ttp) cc_final: 0.8464 (ttp) REVERT: J 1 MET cc_start: 0.7764 (mtm) cc_final: 0.7447 (mtm) REVERT: K 82 SER cc_start: 0.8102 (OUTLIER) cc_final: 0.7550 (t) REVERT: K 111 ASP cc_start: 0.9091 (t0) cc_final: 0.8813 (t0) REVERT: L 15 MET cc_start: 0.7726 (tpp) cc_final: 0.7017 (tpp) REVERT: L 31 ARG cc_start: 0.8705 (mmp80) cc_final: 0.8401 (mmm160) REVERT: L 50 LYS cc_start: 0.8819 (mmmm) cc_final: 0.8275 (tppt) REVERT: Q 270 MET cc_start: 0.8011 (mmm) cc_final: 0.7777 (tpt) REVERT: Q 310 TYR cc_start: 0.6098 (OUTLIER) cc_final: 0.5782 (t80) REVERT: Q 350 MET cc_start: 0.4498 (OUTLIER) cc_final: 0.4275 (ttt) REVERT: Q 378 MET cc_start: 0.4944 (mtt) cc_final: 0.4335 (tmm) REVERT: Q 674 ARG cc_start: 0.8970 (ttp-170) cc_final: 0.8444 (tmt-80) REVERT: Q 691 TYR cc_start: 0.8973 (m-10) cc_final: 0.8692 (m-80) REVERT: Q 761 LEU cc_start: 0.9091 (mt) cc_final: 0.8639 (tt) REVERT: Q 817 CYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8219 (p) REVERT: Q 820 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8913 (mm) REVERT: R 496 VAL cc_start: 0.4511 (m) cc_final: 0.4079 (t) REVERT: R 500 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6678 (pm20) REVERT: R 503 ARG cc_start: 0.0156 (tmm160) cc_final: -0.0711 (ttm170) REVERT: R 566 ARG cc_start: 0.0055 (tmt170) cc_final: -0.0162 (tpt-90) REVERT: R 567 ASN cc_start: 0.0444 (m-40) cc_final: 0.0089 (t0) REVERT: X 238 LEU cc_start: 0.8706 (mt) cc_final: 0.8197 (pp) REVERT: X 250 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.6082 (m-80) REVERT: Z 307 MET cc_start: -0.0638 (pmt) cc_final: -0.0985 (pmm) REVERT: b 84 MET cc_start: 0.7727 (mpp) cc_final: 0.7317 (mmm) REVERT: c 113 SER cc_start: 0.8754 (p) cc_final: 0.8552 (m) REVERT: d 46 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.7049 (m170) REVERT: e 90 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7657 (tpp) REVERT: g 92 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6737 (pt0) REVERT: h 99 LEU cc_start: 0.8566 (mt) cc_final: 0.8156 (tp) REVERT: l 1497 MET cc_start: 0.4548 (mpt) cc_final: 0.4217 (mpp) REVERT: l 1526 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6797 (tpt) REVERT: l 1560 LYS cc_start: -0.1730 (OUTLIER) cc_final: -0.2025 (tmtm) outliers start: 98 outliers final: 40 residues processed: 430 average time/residue: 1.4231 time to fit residues: 825.2459 Evaluate side-chains 391 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 338 time to evaluate : 5.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 368 THR 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 719 SER Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain Q residue 310 TYR Chi-restraints excluded: chain Q residue 350 MET Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 417 GLU Chi-restraints excluded: chain Q residue 669 VAL Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 817 CYS Chi-restraints excluded: chain Q residue 820 LEU Chi-restraints excluded: chain V residue 42 ILE Chi-restraints excluded: chain V residue 58 PHE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 241 CYS Chi-restraints excluded: chain X residue 245 PHE Chi-restraints excluded: chain X residue 250 PHE Chi-restraints excluded: chain Y residue 48 MET Chi-restraints excluded: chain Z residue 626 CYS Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 100 LEU Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 87 VAL Chi-restraints excluded: chain g residue 76 THR Chi-restraints excluded: chain g residue 92 GLU Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain l residue 1463 CYS Chi-restraints excluded: chain l residue 1526 MET Chi-restraints excluded: chain l residue 1560 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 87 optimal weight: 0.9980 chunk 793 optimal weight: 5.9990 chunk 541 optimal weight: 0.0030 chunk 703 optimal weight: 20.0000 chunk 624 optimal weight: 5.9990 chunk 544 optimal weight: 9.9990 chunk 304 optimal weight: 2.9990 chunk 691 optimal weight: 30.0000 chunk 7 optimal weight: 0.9990 chunk 767 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 809 HIS A1044 HIS K 2 ASN Q 575 HIS ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 877 GLN W 268 HIS ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.093229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.071025 restraints weight = 424230.774| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 5.86 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 70526 Z= 0.159 Angle : 0.529 14.560 96491 Z= 0.276 Chirality : 0.040 0.187 10432 Planarity : 0.003 0.046 11763 Dihedral : 17.821 173.956 12961 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 1.35 % Allowed : 13.77 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % 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: -0.44 (0.09), residues: 8502 helix: 1.49 (0.09), residues: 3416 sheet: -1.57 (0.18), residues: 823 loop : -1.57 (0.09), residues: 4263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP W 47 HIS 0.006 0.001 HIS f 75 PHE 0.028 0.001 PHE V 53 TYR 0.027 0.001 TYR B 766 ARG 0.012 0.000 ARG R 597 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 384 time to evaluate : 5.633 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: A 467 MET cc_start: 0.7293 (mmp) cc_final: 0.6366 (mmm) REVERT: A 841 MET cc_start: 0.7941 (mtp) cc_final: 0.7483 (mtt) REVERT: A 1133 LYS cc_start: 0.8590 (pttp) cc_final: 0.8302 (mtmm) REVERT: A 1309 MET cc_start: 0.8011 (ttm) cc_final: 0.7763 (mtp) REVERT: A 1344 MET cc_start: 0.8076 (tpp) cc_final: 0.7849 (tpp) REVERT: A 1428 MET cc_start: 0.8567 (tpp) cc_final: 0.8193 (mmt) REVERT: B 298 MET cc_start: 0.8808 (ttm) cc_final: 0.8492 (ttm) REVERT: B 347 MET cc_start: 0.8969 (tmm) cc_final: 0.8522 (tmm) REVERT: B 840 MET cc_start: 0.6809 (ttp) cc_final: 0.6213 (tmm) REVERT: B 1054 MET cc_start: 0.8250 (mmt) cc_final: 0.7911 (mmm) REVERT: B 1075 MET cc_start: 0.8648 (mmm) cc_final: 0.8440 (mpt) REVERT: B 1089 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7541 (mtm) REVERT: D 74 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.6325 (p90) REVERT: G 1 MET cc_start: 0.8699 (ttp) cc_final: 0.8483 (OUTLIER) REVERT: G 131 MET cc_start: 0.4192 (tmm) cc_final: 0.3657 (tpt) REVERT: H 75 TYR cc_start: 0.7756 (t80) cc_final: 0.7403 (t80) REVERT: I 75 ASP cc_start: 0.8422 (t0) cc_final: 0.8127 (t0) REVERT: J 1 MET cc_start: 0.7704 (mtm) cc_final: 0.7359 (mtm) REVERT: K 82 SER cc_start: 0.7714 (OUTLIER) cc_final: 0.7328 (t) REVERT: L 15 MET cc_start: 0.7655 (tpp) cc_final: 0.7041 (tpp) REVERT: L 25 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8594 (mt-10) REVERT: Q 270 MET cc_start: 0.8580 (mmm) cc_final: 0.8374 (tpt) REVERT: Q 310 TYR cc_start: 0.5950 (OUTLIER) cc_final: 0.5562 (t80) REVERT: Q 378 MET cc_start: 0.4848 (mtt) cc_final: 0.4221 (tmt) REVERT: Q 402 LYS cc_start: 0.9062 (mptt) cc_final: 0.8746 (tppt) REVERT: Q 674 ARG cc_start: 0.8987 (ttp-170) cc_final: 0.8764 (ptp-170) REVERT: Q 691 TYR cc_start: 0.8954 (m-10) cc_final: 0.8653 (m-80) REVERT: Q 761 LEU cc_start: 0.9110 (mt) cc_final: 0.8627 (tt) REVERT: Q 817 CYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8199 (p) REVERT: Q 820 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8911 (mm) REVERT: Q 881 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.6633 (m-80) REVERT: R 496 VAL cc_start: 0.4402 (m) cc_final: 0.3410 (t) REVERT: R 503 ARG cc_start: 0.0349 (tmm160) cc_final: -0.0132 (ttm170) REVERT: R 567 ASN cc_start: 0.1137 (m-40) cc_final: 0.0678 (t0) REVERT: W 52 GLU cc_start: 0.8749 (tp30) cc_final: 0.8452 (tp30) REVERT: W 234 TRP cc_start: 0.8775 (m-10) cc_final: 0.8467 (m-10) REVERT: X 238 LEU cc_start: 0.8669 (mt) cc_final: 0.8400 (pp) REVERT: X 250 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6070 (m-80) REVERT: Z 307 MET cc_start: -0.0971 (pmt) cc_final: -0.1262 (pmm) REVERT: a 97 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6846 (tp30) REVERT: b 84 MET cc_start: 0.7577 (mpp) cc_final: 0.7234 (mmm) REVERT: c 115 LEU cc_start: 0.7560 (mm) cc_final: 0.7356 (mm) REVERT: d 46 HIS cc_start: 0.7239 (OUTLIER) cc_final: 0.6965 (m170) REVERT: e 74 ILE cc_start: 0.9093 (mt) cc_final: 0.8825 (OUTLIER) REVERT: e 90 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7614 (tpp) REVERT: g 92 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6796 (pt0) REVERT: h 99 LEU cc_start: 0.8492 (mt) cc_final: 0.8013 (tp) REVERT: l 1497 MET cc_start: 0.4495 (mpt) cc_final: 0.4039 (mpp) REVERT: l 1526 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7108 (tpt) REVERT: l 1560 LYS cc_start: -0.2032 (OUTLIER) cc_final: -0.2279 (tmtm) outliers start: 78 outliers final: 30 residues processed: 446 average time/residue: 1.4098 time to fit residues: 839.2721 Evaluate side-chains 385 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 344 time to evaluate : 5.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain Q residue 310 TYR Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 417 GLU Chi-restraints excluded: chain Q residue 663 PHE Chi-restraints excluded: chain Q residue 817 CYS Chi-restraints excluded: chain Q residue 820 LEU Chi-restraints excluded: chain Q residue 870 GLU Chi-restraints excluded: chain Q residue 881 TYR Chi-restraints excluded: chain R residue 492 ILE Chi-restraints excluded: chain V residue 42 ILE Chi-restraints excluded: chain V residue 58 PHE Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain X residue 245 PHE Chi-restraints excluded: chain X residue 250 PHE Chi-restraints excluded: chain Y residue 48 MET Chi-restraints excluded: chain Z residue 626 CYS Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 92 GLU Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain l residue 1463 CYS Chi-restraints excluded: chain l residue 1526 MET Chi-restraints excluded: chain l residue 1560 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 411 optimal weight: 50.0000 chunk 421 optimal weight: 50.0000 chunk 143 optimal weight: 0.6980 chunk 674 optimal weight: 3.9990 chunk 709 optimal weight: 0.0170 chunk 639 optimal weight: 10.0000 chunk 605 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 577 optimal weight: 9.9990 chunk 509 optimal weight: 10.0000 overall best weight: 2.0822 ------------------------------------------------------------------------------- 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** K 2 ASN ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 706 ASN Q 781 ASN Q 827 HIS ** R 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.091995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.069344 restraints weight = 419435.396| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 5.86 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 70526 Z= 0.243 Angle : 0.565 12.714 96491 Z= 0.295 Chirality : 0.041 0.192 10432 Planarity : 0.004 0.066 11763 Dihedral : 17.831 173.553 12961 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.18 % Favored : 94.80 % Rotamer: Outliers : 1.70 % Allowed : 14.26 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % 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: -0.41 (0.09), residues: 8502 helix: 1.49 (0.09), residues: 3418 sheet: -1.42 (0.18), residues: 834 loop : -1.56 (0.09), residues: 4250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 47 HIS 0.008 0.001 HIS a 113 PHE 0.033 0.001 PHE V 53 TYR 0.016 0.001 TYR H 118 ARG 0.014 0.000 ARG b 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 358 time to evaluate : 5.770 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: A 248 MET cc_start: 0.7677 (ttp) cc_final: 0.7386 (ttt) REVERT: A 1102 MET cc_start: 0.8120 (ptm) cc_final: 0.7583 (ptm) REVERT: A 1133 LYS cc_start: 0.8729 (pttp) cc_final: 0.8470 (mtmm) REVERT: A 1228 MET cc_start: 0.8673 (mmm) cc_final: 0.8436 (mmt) REVERT: A 1309 MET cc_start: 0.8075 (ttm) cc_final: 0.7868 (mtp) REVERT: A 1344 MET cc_start: 0.8138 (tpp) cc_final: 0.7877 (tpp) REVERT: B 239 MET cc_start: 0.7476 (ptm) cc_final: 0.7225 (ptm) REVERT: B 298 MET cc_start: 0.8873 (ttm) cc_final: 0.8588 (ttm) REVERT: B 347 MET cc_start: 0.8936 (tmm) cc_final: 0.8434 (tmm) REVERT: B 733 MET cc_start: 0.8217 (ptm) cc_final: 0.7950 (ptm) REVERT: B 840 MET cc_start: 0.6957 (ttp) cc_final: 0.6159 (tmm) REVERT: B 1054 MET cc_start: 0.8274 (mmt) cc_final: 0.7970 (mmm) REVERT: B 1075 MET cc_start: 0.8629 (mmm) cc_final: 0.8388 (mpt) REVERT: B 1089 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7605 (mtm) REVERT: B 1172 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7997 (mmm) REVERT: D 74 PHE cc_start: 0.6336 (OUTLIER) cc_final: 0.6055 (p90) REVERT: G 29 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8726 (ttmt) REVERT: H 75 TYR cc_start: 0.7876 (t80) cc_final: 0.7502 (t80) REVERT: J 1 MET cc_start: 0.7924 (mtm) cc_final: 0.7612 (mtm) REVERT: L 15 MET cc_start: 0.7691 (tpp) cc_final: 0.7082 (tpp) REVERT: L 25 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8596 (mt-10) REVERT: L 31 ARG cc_start: 0.8595 (mmp80) cc_final: 0.8317 (mmm-85) REVERT: L 50 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8256 (tppt) REVERT: Q 310 TYR cc_start: 0.5888 (OUTLIER) cc_final: 0.5514 (t80) REVERT: Q 378 MET cc_start: 0.4982 (mtt) cc_final: 0.4362 (tmt) REVERT: Q 674 ARG cc_start: 0.9002 (ttp-170) cc_final: 0.8458 (tmt-80) REVERT: Q 691 TYR cc_start: 0.8995 (m-10) cc_final: 0.8675 (m-80) REVERT: Q 754 MET cc_start: 0.8683 (mtm) cc_final: 0.7535 (pp-130) REVERT: Q 755 PHE cc_start: 0.7912 (m-80) cc_final: 0.7189 (m-80) REVERT: Q 761 LEU cc_start: 0.9150 (mt) cc_final: 0.8665 (tt) REVERT: Q 817 CYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8330 (p) REVERT: Q 820 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8905 (mm) REVERT: R 496 VAL cc_start: 0.3807 (m) cc_final: 0.3207 (t) REVERT: R 503 ARG cc_start: 0.0151 (tmm160) cc_final: -0.0270 (ttm170) REVERT: R 567 ASN cc_start: 0.1107 (m-40) cc_final: 0.0457 (t0) REVERT: W 52 GLU cc_start: 0.8707 (tp30) cc_final: 0.8394 (tp30) REVERT: X 238 LEU cc_start: 0.8821 (mt) cc_final: 0.8382 (pp) REVERT: X 250 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6086 (m-80) REVERT: Z 307 MET cc_start: -0.1034 (pmt) cc_final: -0.1322 (pmm) REVERT: Z 460 MET cc_start: 0.1807 (ttm) cc_final: 0.1297 (tpp) REVERT: Z 508 MET cc_start: 0.1286 (mmm) cc_final: 0.0814 (mmm) REVERT: a 97 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6955 (tp30) REVERT: b 84 MET cc_start: 0.7732 (mpp) cc_final: 0.7396 (mmm) REVERT: d 46 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.7124 (m170) REVERT: e 74 ILE cc_start: 0.9115 (mt) cc_final: 0.8900 (OUTLIER) REVERT: e 90 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7603 (tpp) REVERT: f 96 THR cc_start: 0.8324 (m) cc_final: 0.8071 (p) REVERT: g 92 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6734 (pt0) REVERT: h 99 LEU cc_start: 0.8546 (mt) cc_final: 0.8167 (tp) REVERT: l 1497 MET cc_start: 0.4737 (mpt) cc_final: 0.4369 (mpp) REVERT: l 1526 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6999 (tpt) outliers start: 98 outliers final: 41 residues processed: 433 average time/residue: 1.4109 time to fit residues: 820.6018 Evaluate side-chains 389 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 337 time to evaluate : 5.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1172 MET Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain Q residue 310 TYR Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 417 GLU Chi-restraints excluded: chain Q residue 663 PHE Chi-restraints excluded: chain Q residue 817 CYS Chi-restraints excluded: chain Q residue 820 LEU Chi-restraints excluded: chain Q residue 870 GLU Chi-restraints excluded: chain V residue 42 ILE Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 241 CYS Chi-restraints excluded: chain X residue 245 PHE Chi-restraints excluded: chain X residue 250 PHE Chi-restraints excluded: chain Z residue 524 THR Chi-restraints excluded: chain Z residue 626 CYS Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 100 LEU Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 72 ASP Chi-restraints excluded: chain g residue 76 THR Chi-restraints excluded: chain g residue 92 GLU Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain l residue 1463 CYS Chi-restraints excluded: chain l residue 1526 MET Chi-restraints excluded: chain l residue 1576 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 89 optimal weight: 3.9990 chunk 847 optimal weight: 8.9990 chunk 382 optimal weight: 30.0000 chunk 344 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 496 optimal weight: 50.0000 chunk 374 optimal weight: 1.9990 chunk 629 optimal weight: 40.0000 chunk 252 optimal weight: 3.9990 chunk 624 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** A1313 GLN B 56 GLN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 594 GLN Q 880 GLN ** R 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 607 HIS ** c 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.091132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.068266 restraints weight = 417495.705| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 5.73 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 70526 Z= 0.278 Angle : 0.596 13.787 96491 Z= 0.312 Chirality : 0.041 0.198 10432 Planarity : 0.004 0.071 11763 Dihedral : 17.991 173.899 12959 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.28 % Favored : 94.71 % Rotamer: Outliers : 1.58 % Allowed : 15.04 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.06 % Twisted Proline : 0.29 % 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: -0.43 (0.09), residues: 8502 helix: 1.42 (0.09), residues: 3426 sheet: -1.40 (0.17), residues: 846 loop : -1.54 (0.09), residues: 4230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP W 47 HIS 0.007 0.001 HIS a 113 PHE 0.031 0.002 PHE V 53 TYR 0.016 0.001 TYR H 118 ARG 0.016 0.001 ARG W 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 351 time to evaluate : 5.665 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: A 58 MET cc_start: 0.8006 (tpt) cc_final: 0.7642 (tpt) REVERT: A 238 MET cc_start: 0.8471 (mtm) cc_final: 0.7648 (mpt) REVERT: A 501 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.6674 (mmt) REVERT: A 841 MET cc_start: 0.8126 (mtp) cc_final: 0.7574 (mtt) REVERT: A 1102 MET cc_start: 0.8121 (ptm) cc_final: 0.7654 (ptm) REVERT: A 1133 LYS cc_start: 0.8777 (pttp) cc_final: 0.8535 (mtmm) REVERT: B 239 MET cc_start: 0.7508 (ptm) cc_final: 0.7264 (ptm) REVERT: B 298 MET cc_start: 0.8823 (ttm) cc_final: 0.8556 (ttm) REVERT: B 347 MET cc_start: 0.9007 (tmm) cc_final: 0.8518 (tmm) REVERT: B 840 MET cc_start: 0.6942 (ttp) cc_final: 0.6146 (tmm) REVERT: B 901 THR cc_start: 0.9322 (OUTLIER) cc_final: 0.9083 (p) REVERT: B 1054 MET cc_start: 0.8259 (mmt) cc_final: 0.7929 (mmm) REVERT: B 1075 MET cc_start: 0.8639 (mmm) cc_final: 0.8426 (mpt) REVERT: B 1089 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7641 (mtm) REVERT: B 1145 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8008 (pp30) REVERT: D 74 PHE cc_start: 0.6463 (OUTLIER) cc_final: 0.6124 (p90) REVERT: G 17 TYR cc_start: 0.8578 (m-10) cc_final: 0.8122 (m-10) REVERT: G 29 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8779 (ttmt) REVERT: G 131 MET cc_start: 0.3999 (tmm) cc_final: 0.3407 (tpt) REVERT: H 75 TYR cc_start: 0.7954 (t80) cc_final: 0.7688 (t80) REVERT: J 1 MET cc_start: 0.7813 (mtm) cc_final: 0.7524 (mtm) REVERT: L 15 MET cc_start: 0.7778 (tpp) cc_final: 0.7182 (tpp) REVERT: L 25 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8576 (mt-10) REVERT: L 31 ARG cc_start: 0.8678 (mmp80) cc_final: 0.8381 (mmm160) REVERT: L 50 LYS cc_start: 0.8812 (mmmm) cc_final: 0.8243 (tppt) REVERT: Q 310 TYR cc_start: 0.6027 (OUTLIER) cc_final: 0.5658 (t80) REVERT: Q 350 MET cc_start: 0.3450 (mtt) cc_final: 0.3248 (ttt) REVERT: Q 378 MET cc_start: 0.4988 (mtt) cc_final: 0.4358 (tmt) REVERT: Q 691 TYR cc_start: 0.9113 (m-10) cc_final: 0.8815 (m-80) REVERT: Q 754 MET cc_start: 0.8734 (mtm) cc_final: 0.8520 (mtt) REVERT: Q 761 LEU cc_start: 0.9176 (mt) cc_final: 0.8688 (tt) REVERT: Q 817 CYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8283 (p) REVERT: Q 820 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9004 (mm) REVERT: R 496 VAL cc_start: 0.4314 (m) cc_final: 0.3988 (t) REVERT: R 503 ARG cc_start: 0.0159 (tmm160) cc_final: -0.0346 (ttm170) REVERT: R 567 ASN cc_start: 0.1117 (m-40) cc_final: 0.0475 (t0) REVERT: X 238 LEU cc_start: 0.8874 (mt) cc_final: 0.8438 (pp) REVERT: Z 307 MET cc_start: -0.0918 (pmt) cc_final: -0.1212 (pmm) REVERT: Z 460 MET cc_start: 0.2231 (ttm) cc_final: 0.1728 (tpp) REVERT: Z 508 MET cc_start: 0.1697 (mmm) cc_final: 0.1194 (mmm) REVERT: a 97 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6976 (tp30) REVERT: a 117 VAL cc_start: 0.8448 (m) cc_final: 0.8159 (p) REVERT: b 84 MET cc_start: 0.7821 (mpp) cc_final: 0.7338 (mmt) REVERT: e 90 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7590 (tpp) REVERT: f 96 THR cc_start: 0.8367 (m) cc_final: 0.8114 (p) REVERT: g 92 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6723 (pt0) REVERT: h 99 LEU cc_start: 0.8572 (mt) cc_final: 0.8182 (tp) REVERT: l 1497 MET cc_start: 0.4701 (mpt) cc_final: 0.4391 (mpp) REVERT: l 1526 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6826 (tpt) outliers start: 91 outliers final: 43 residues processed: 418 average time/residue: 1.3701 time to fit residues: 772.2604 Evaluate side-chains 386 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 331 time to evaluate : 5.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1145 GLN Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain Q residue 310 TYR Chi-restraints excluded: chain Q residue 340 PHE Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 417 GLU Chi-restraints excluded: chain Q residue 817 CYS Chi-restraints excluded: chain Q residue 820 LEU Chi-restraints excluded: chain Q residue 870 GLU Chi-restraints excluded: chain V residue 42 ILE Chi-restraints excluded: chain V residue 58 PHE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 241 CYS Chi-restraints excluded: chain X residue 245 PHE Chi-restraints excluded: chain X residue 250 PHE Chi-restraints excluded: chain Y residue 48 MET Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain Z residue 524 THR Chi-restraints excluded: chain Z residue 626 CYS Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 72 ASP Chi-restraints excluded: chain g residue 76 THR Chi-restraints excluded: chain g residue 92 GLU Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain l residue 1526 MET Chi-restraints excluded: chain l residue 1576 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 646 optimal weight: 4.9990 chunk 569 optimal weight: 3.9990 chunk 871 optimal weight: 6.9990 chunk 622 optimal weight: 4.9990 chunk 459 optimal weight: 40.0000 chunk 196 optimal weight: 0.7980 chunk 201 optimal weight: 4.9990 chunk 364 optimal weight: 2.9990 chunk 668 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 558 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 854 GLN ** Q 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 272 ASN Z 625 HIS Z 632 ASN ** c 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 79 HIS ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l1603 HIS ** l1622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.090044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.067060 restraints weight = 415577.307| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 5.80 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 70526 Z= 0.360 Angle : 0.653 12.921 96491 Z= 0.343 Chirality : 0.043 0.220 10432 Planarity : 0.004 0.055 11763 Dihedral : 18.229 174.276 12959 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.81 % Favored : 94.18 % Rotamer: Outliers : 1.44 % Allowed : 15.47 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.06 % Twisted Proline : 0.29 % 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: -0.60 (0.09), residues: 8502 helix: 1.23 (0.09), residues: 3442 sheet: -1.39 (0.17), residues: 832 loop : -1.63 (0.09), residues: 4228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Q 684 HIS 0.007 0.001 HIS B1097 PHE 0.033 0.002 PHE V 53 TYR 0.027 0.002 TYR B 84 ARG 0.006 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 351 time to evaluate : 5.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7867 (mtp) cc_final: 0.6848 (mmt) REVERT: A 1102 MET cc_start: 0.8243 (ptm) cc_final: 0.7783 (ptm) REVERT: A 1133 LYS cc_start: 0.8807 (pttp) cc_final: 0.8590 (mtmm) REVERT: A 1428 MET cc_start: 0.8540 (tpp) cc_final: 0.8182 (mmt) REVERT: B 239 MET cc_start: 0.7686 (ptm) cc_final: 0.7444 (ptm) REVERT: B 298 MET cc_start: 0.8910 (ttm) cc_final: 0.8651 (ttm) REVERT: B 347 MET cc_start: 0.9003 (tmm) cc_final: 0.8492 (tmm) REVERT: B 744 MET cc_start: 0.8116 (mtp) cc_final: 0.7893 (ttp) REVERT: B 840 MET cc_start: 0.6922 (ttp) cc_final: 0.5981 (tmm) REVERT: B 901 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.9069 (p) REVERT: B 954 MET cc_start: 0.8018 (tpp) cc_final: 0.7714 (mpp) REVERT: B 1054 MET cc_start: 0.8293 (mmt) cc_final: 0.7966 (mmm) REVERT: B 1075 MET cc_start: 0.8627 (mmm) cc_final: 0.8419 (mpt) REVERT: B 1089 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7564 (mtm) REVERT: B 1145 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7993 (pp30) REVERT: D 74 PHE cc_start: 0.6642 (OUTLIER) cc_final: 0.6243 (p90) REVERT: E 111 THR cc_start: 0.7082 (OUTLIER) cc_final: 0.6844 (p) REVERT: G 29 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8716 (ttmt) REVERT: H 75 TYR cc_start: 0.7868 (t80) cc_final: 0.7627 (t80) REVERT: J 1 MET cc_start: 0.7992 (mtm) cc_final: 0.7740 (mtm) REVERT: L 25 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8552 (mt-10) REVERT: L 31 ARG cc_start: 0.8663 (mmp80) cc_final: 0.8352 (mmm-85) REVERT: L 44 MET cc_start: 0.7977 (tmm) cc_final: 0.7759 (tpp) REVERT: L 50 LYS cc_start: 0.8882 (mmmm) cc_final: 0.8242 (tppt) REVERT: Q 310 TYR cc_start: 0.6067 (OUTLIER) cc_final: 0.5702 (t80) REVERT: Q 378 MET cc_start: 0.5089 (mtt) cc_final: 0.4420 (tmm) REVERT: Q 402 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8806 (tppt) REVERT: Q 604 MET cc_start: 0.7759 (mtt) cc_final: 0.7524 (ptp) REVERT: Q 674 ARG cc_start: 0.8905 (ttp-170) cc_final: 0.8394 (tmt-80) REVERT: Q 691 TYR cc_start: 0.9106 (m-10) cc_final: 0.8800 (m-80) REVERT: Q 754 MET cc_start: 0.8742 (mtm) cc_final: 0.8522 (mtt) REVERT: Q 817 CYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8188 (p) REVERT: Q 820 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9026 (mm) REVERT: R 503 ARG cc_start: 0.0548 (tmm160) cc_final: 0.0234 (ttm170) REVERT: R 567 ASN cc_start: 0.1151 (m-40) cc_final: 0.0518 (t0) REVERT: V 49 ILE cc_start: 0.9467 (mm) cc_final: 0.9164 (tp) REVERT: W 52 GLU cc_start: 0.8776 (tp30) cc_final: 0.8501 (tp30) REVERT: X 238 LEU cc_start: 0.8916 (mt) cc_final: 0.8476 (pp) REVERT: X 253 LEU cc_start: 0.9254 (mp) cc_final: 0.8757 (pp) REVERT: Z 260 MET cc_start: 0.5462 (mtp) cc_final: 0.5005 (mpt) REVERT: Z 307 MET cc_start: -0.1010 (pmt) cc_final: -0.1317 (pmm) REVERT: Z 460 MET cc_start: 0.2133 (ttm) cc_final: 0.1622 (tpp) REVERT: Z 508 MET cc_start: 0.2024 (mmm) cc_final: 0.1566 (mmm) REVERT: a 97 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7051 (tp30) REVERT: a 117 VAL cc_start: 0.8546 (m) cc_final: 0.8253 (p) REVERT: b 84 MET cc_start: 0.7894 (mpp) cc_final: 0.7438 (mmt) REVERT: e 90 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7693 (tpp) REVERT: f 95 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.6502 (mtp-110) REVERT: f 96 THR cc_start: 0.8329 (m) cc_final: 0.8091 (p) REVERT: g 92 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6711 (pt0) REVERT: h 64 ASN cc_start: 0.8179 (m110) cc_final: 0.7879 (m110) REVERT: h 99 LEU cc_start: 0.8638 (mt) cc_final: 0.8338 (tp) REVERT: l 1497 MET cc_start: 0.4876 (mpt) cc_final: 0.4625 (mpp) REVERT: l 1526 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6990 (tpp) outliers start: 83 outliers final: 44 residues processed: 411 average time/residue: 1.4009 time to fit residues: 771.2986 Evaluate side-chains 391 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 333 time to evaluate : 5.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1210 TRP Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1145 GLN Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain Q residue 310 TYR Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 402 LYS Chi-restraints excluded: chain Q residue 417 GLU Chi-restraints excluded: chain Q residue 817 CYS Chi-restraints excluded: chain Q residue 820 LEU Chi-restraints excluded: chain Q residue 870 GLU Chi-restraints excluded: chain R residue 572 ILE Chi-restraints excluded: chain V residue 42 ILE Chi-restraints excluded: chain V residue 58 PHE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 241 CYS Chi-restraints excluded: chain X residue 245 PHE Chi-restraints excluded: chain X residue 250 PHE Chi-restraints excluded: chain Y residue 48 MET Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Z residue 524 THR Chi-restraints excluded: chain Z residue 626 CYS Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 95 ARG Chi-restraints excluded: chain g residue 72 ASP Chi-restraints excluded: chain g residue 76 THR Chi-restraints excluded: chain g residue 92 GLU Chi-restraints excluded: chain h residue 88 SER Chi-restraints excluded: chain l residue 1526 MET Chi-restraints excluded: chain l residue 1576 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 399 optimal weight: 20.0000 chunk 299 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 292 optimal weight: 0.9990 chunk 732 optimal weight: 3.9990 chunk 411 optimal weight: 40.0000 chunk 313 optimal weight: 0.8980 chunk 807 optimal weight: 2.9990 chunk 534 optimal weight: 50.0000 chunk 613 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN A 320 ASN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 594 GLN Q 706 ASN ** R 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l1541 ASN ** l1622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.090941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.068393 restraints weight = 418735.305| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 5.62 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 70526 Z= 0.227 Angle : 0.597 14.320 96491 Z= 0.311 Chirality : 0.041 0.206 10432 Planarity : 0.004 0.058 11763 Dihedral : 18.217 174.658 12959 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.98 % Favored : 95.01 % Rotamer: Outliers : 1.01 % Allowed : 16.08 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.06 % Twisted Proline : 0.29 % 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: -0.44 (0.09), residues: 8502 helix: 1.40 (0.09), residues: 3431 sheet: -1.33 (0.17), residues: 829 loop : -1.54 (0.09), residues: 4242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 180 HIS 0.006 0.001 HIS a 113 PHE 0.033 0.001 PHE V 53 TYR 0.020 0.001 TYR l1579 ARG 0.016 0.000 ARG L 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17004 Ramachandran restraints generated. 8502 Oldfield, 0 Emsley, 8502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 351 time to evaluate : 5.732 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: A 238 MET cc_start: 0.8564 (mtm) cc_final: 0.7862 (mpp) REVERT: A 248 MET cc_start: 0.8104 (ttt) cc_final: 0.7732 (ttt) REVERT: A 388 MET cc_start: 0.7177 (mtm) cc_final: 0.6924 (mtp) REVERT: A 501 MET cc_start: 0.7822 (mtp) cc_final: 0.6652 (mmt) REVERT: A 1262 MET cc_start: 0.4611 (OUTLIER) cc_final: 0.4263 (mmm) REVERT: A 1428 MET cc_start: 0.8653 (tpp) cc_final: 0.8257 (mmt) REVERT: B 298 MET cc_start: 0.8895 (ttm) cc_final: 0.8639 (ttm) REVERT: B 347 MET cc_start: 0.9024 (tmm) cc_final: 0.8541 (tmm) REVERT: B 744 MET cc_start: 0.8039 (mtp) cc_final: 0.7831 (mtp) REVERT: B 840 MET cc_start: 0.6847 (ttp) cc_final: 0.6003 (tmm) REVERT: B 901 THR cc_start: 0.9322 (OUTLIER) cc_final: 0.9057 (p) REVERT: B 954 MET cc_start: 0.8003 (tpp) cc_final: 0.7755 (mpp) REVERT: B 1054 MET cc_start: 0.8225 (mmt) cc_final: 0.7997 (mmm) REVERT: B 1089 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7435 (mtm) REVERT: B 1145 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8024 (pp30) REVERT: B 1172 MET cc_start: 0.8355 (mpp) cc_final: 0.8056 (mtt) REVERT: D 74 PHE cc_start: 0.6534 (OUTLIER) cc_final: 0.6091 (p90) REVERT: E 111 THR cc_start: 0.6927 (OUTLIER) cc_final: 0.6686 (p) REVERT: G 1 MET cc_start: 0.8875 (ptm) cc_final: 0.8607 (ppp) REVERT: G 29 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8729 (ttmt) REVERT: G 131 MET cc_start: 0.4213 (tmm) cc_final: 0.3453 (tpt) REVERT: G 164 MET cc_start: 0.6977 (mpm) cc_final: 0.6740 (mpm) REVERT: H 75 TYR cc_start: 0.7938 (t80) cc_final: 0.7633 (t80) REVERT: J 1 MET cc_start: 0.7949 (mtm) cc_final: 0.7655 (mtm) REVERT: L 15 MET cc_start: 0.7813 (tpp) cc_final: 0.7286 (tpp) REVERT: L 25 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8549 (mt-10) REVERT: L 31 ARG cc_start: 0.8637 (mmp80) cc_final: 0.8404 (mmm-85) REVERT: Q 310 TYR cc_start: 0.5883 (OUTLIER) cc_final: 0.5464 (t80) REVERT: Q 369 LYS cc_start: 0.7463 (mttp) cc_final: 0.7137 (pttt) REVERT: Q 378 MET cc_start: 0.5065 (mtt) cc_final: 0.4361 (tmm) REVERT: Q 402 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8732 (tppt) REVERT: Q 604 MET cc_start: 0.7718 (mtt) cc_final: 0.7433 (ptp) REVERT: Q 674 ARG cc_start: 0.8908 (ttp-170) cc_final: 0.8368 (tmt-80) REVERT: Q 691 TYR cc_start: 0.9068 (m-10) cc_final: 0.8697 (m-80) REVERT: Q 754 MET cc_start: 0.8711 (mtm) cc_final: 0.8494 (mtt) REVERT: Q 817 CYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8230 (p) REVERT: Q 820 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9043 (mm) REVERT: R 496 VAL cc_start: 0.2615 (m) cc_final: 0.2219 (t) REVERT: R 503 ARG cc_start: 0.0303 (tmm160) cc_final: -0.0442 (ttm170) REVERT: R 567 ASN cc_start: 0.1264 (m-40) cc_final: 0.0578 (t0) REVERT: V 49 ILE cc_start: 0.9397 (mm) cc_final: 0.9052 (tp) REVERT: W 52 GLU cc_start: 0.8665 (tp30) cc_final: 0.8381 (tp30) REVERT: X 238 LEU cc_start: 0.8863 (mt) cc_final: 0.8407 (pp) REVERT: Z 254 MET cc_start: 0.6735 (mmm) cc_final: 0.6482 (tpp) REVERT: Z 260 MET cc_start: 0.5495 (mtp) cc_final: 0.4968 (mpt) REVERT: Z 307 MET cc_start: -0.1314 (pmt) cc_final: -0.1583 (pmm) REVERT: Z 460 MET cc_start: 0.1901 (ttm) cc_final: 0.1383 (tpp) REVERT: a 97 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7008 (tp30) REVERT: a 117 VAL cc_start: 0.8583 (m) cc_final: 0.8302 (p) REVERT: b 84 MET cc_start: 0.7831 (mpp) cc_final: 0.7391 (mmt) REVERT: e 90 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7677 (tpp) REVERT: f 96 THR cc_start: 0.8317 (m) cc_final: 0.8069 (p) REVERT: g 92 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6743 (pt0) REVERT: h 64 ASN cc_start: 0.8107 (m110) cc_final: 0.7820 (m110) REVERT: h 99 LEU cc_start: 0.8562 (mt) cc_final: 0.8188 (tp) REVERT: l 1526 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.7002 (tpt) outliers start: 58 outliers final: 35 residues processed: 394 average time/residue: 1.4424 time to fit residues: 763.6468 Evaluate side-chains 381 residues out of total 7588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 332 time to evaluate : 5.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1145 GLN Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain Q residue 310 TYR Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 402 LYS Chi-restraints excluded: chain Q residue 417 GLU Chi-restraints excluded: chain Q residue 817 CYS Chi-restraints excluded: chain Q residue 820 LEU Chi-restraints excluded: chain Q residue 870 GLU Chi-restraints excluded: chain R residue 572 ILE Chi-restraints excluded: chain V residue 42 ILE Chi-restraints excluded: chain V residue 58 PHE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 16 ASP Chi-restraints excluded: chain W residue 241 CYS Chi-restraints excluded: chain X residue 245 PHE Chi-restraints excluded: chain Y residue 48 MET Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain Z residue 524 THR Chi-restraints excluded: chain Z residue 626 CYS Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain g residue 72 ASP Chi-restraints excluded: chain g residue 76 THR Chi-restraints excluded: chain g residue 92 GLU Chi-restraints excluded: chain l residue 1526 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 882 random chunks: chunk 638 optimal weight: 0.0020 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 802 optimal weight: 0.9990 chunk 602 optimal weight: 4.9990 chunk 526 optimal weight: 50.0000 chunk 137 optimal weight: 0.0370 chunk 283 optimal weight: 3.9990 chunk 752 optimal weight: 40.0000 chunk 204 optimal weight: 1.9990 chunk 730 optimal weight: 50.0000 overall best weight: 0.6248 ------------------------------------------------------------------------------- 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 790 GLN A 982 ASN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l1622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.091897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.069180 restraints weight = 416779.240| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 5.77 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 70526 Z= 0.166 Angle : 0.576 13.494 96491 Z= 0.298 Chirality : 0.040 0.221 10432 Planarity : 0.003 0.049 11763 Dihedral : 18.060 174.279 12959 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.63 % Favored : 95.35 % Rotamer: Outliers : 0.97 % Allowed : 16.22 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % 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: -0.28 (0.09), residues: 8502 helix: 1.51 (0.09), residues: 3431 sheet: -1.21 (0.18), residues: 817 loop : -1.45 (0.09), residues: 4254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q 684 HIS 0.006 0.001 HIS f 75 PHE 0.032 0.001 PHE V 53 TYR 0.025 0.001 TYR B 766 ARG 0.024 0.000 ARG B1131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 48357.00 seconds wall clock time: 825 minutes 43.67 seconds (49543.67 seconds total)