Starting phenix.real_space_refine on Sun Jan 26 09:03:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xti_33450/01_2025/7xti_33450.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xti_33450/01_2025/7xti_33450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xti_33450/01_2025/7xti_33450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xti_33450/01_2025/7xti_33450.map" model { file = "/net/cci-nas-00/data/ceres_data/7xti_33450/01_2025/7xti_33450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xti_33450/01_2025/7xti_33450.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 178 5.49 5 Mg 1 5.21 5 S 315 5.16 5 C 49118 2.51 5 N 13765 2.21 5 O 15273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 78660 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 11064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1404, 11064 Classifications: {'peptide': 1404} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1337} Chain breaks: 5 Chain: "B" Number of atoms: 9284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9284 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 52, 'TRANS': 1111} Chain breaks: 4 Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2098 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 12, 'TRANS': 250} Chain: "D" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1349 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 4, 'TRANS': 169} Chain breaks: 1 Chain: "E" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1741 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1325 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1053 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 554 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 932 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 505 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "N" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1516 Classifications: {'DNA': 74} Link IDs: {'rna3p': 73} Chain breaks: 1 Chain: "P" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 14} Chain: "T" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1744 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "V" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "W" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4232 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Chain breaks: 2 Chain: "m" Number of atoms: 9730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1187, 9730 Classifications: {'peptide': 1187} Link IDs: {'PTRANS': 45, 'TRANS': 1141} Chain breaks: 3 Chain: "n" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1115 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "q" Number of atoms: 7552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7552 Classifications: {'peptide': 930} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 910} Chain: "r" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2139 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 259} Chain breaks: 2 Chain: "u" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1707 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "v" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2878 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 22, 'TRANS': 326} Chain breaks: 3 Chain: "x" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Chain: "a" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 606 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} 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: "e" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 620 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} 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: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 715 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "h" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "j" Number of atoms: 3791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3791 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 449} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 9, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "k" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3535 Classifications: {'peptide': 434} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 414} Chain breaks: 1 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: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 527 SG CYS A 67 151.952 91.843 84.203 1.00100.64 S ATOM 549 SG CYS A 70 155.586 90.842 84.743 1.00 80.68 S ATOM 594 SG CYS A 77 154.478 94.428 85.448 1.00 71.87 S ATOM 829 SG CYS A 107 153.202 116.394 42.452 1.00138.55 S ATOM 851 SG CYS A 110 155.213 113.387 41.263 1.00150.89 S ATOM 1157 SG CYS A 148 155.390 116.652 39.399 1.00202.73 S ATOM 1229 SG CYS A 168 152.027 114.702 39.443 1.00216.76 S ATOM 19880 SG CYS B1163 165.179 92.144 71.088 1.00 71.85 S ATOM 19898 SG CYS B1166 163.140 95.285 70.755 1.00 72.69 S ATOM 20021 SG CYS B1182 161.389 91.981 71.498 1.00 90.87 S ATOM 20044 SG CYS B1185 162.938 92.718 68.055 1.00 89.69 S ATOM 20989 SG CYS C 85 168.101 104.550 151.117 1.00125.19 S ATOM 21002 SG CYS C 87 164.721 103.263 149.963 1.00140.94 S ATOM 21037 SG CYS C 91 164.927 105.162 153.063 1.00118.11 S ATOM 21060 SG CYS C 94 165.551 107.136 149.929 1.00 95.98 S ATOM 29206 SG CYS I 78 155.981 197.530 94.294 1.00315.73 S ATOM 29422 SG CYS I 103 156.813 193.171 93.722 1.00262.68 S ATOM 28659 SG CYS I 10 132.813 176.140 55.235 1.00196.93 S ATOM 28822 SG CYS I 29 136.716 176.704 52.951 1.00211.45 S ATOM 28847 SG CYS I 32 134.827 178.319 52.393 1.00208.27 S ATOM 29563 SG CYS J 7 167.727 137.848 139.708 1.00 45.78 S ATOM 29586 SG CYS J 10 170.522 137.088 142.269 1.00 43.83 S ATOM 29862 SG CYS J 44 170.766 140.095 139.835 1.00 53.80 S ATOM 29868 SG CYS J 45 168.521 139.993 142.855 1.00 44.38 S ATOM 31039 SG CYS L 33 127.569 122.397 129.341 1.00 91.02 S ATOM 31054 SG CYS L 36 125.751 122.877 132.668 1.00111.51 S ATOM 31164 SG CYS L 50 124.752 120.031 130.322 1.00119.16 S ATOM 31188 SG CYS L 53 124.159 123.648 129.279 1.00119.40 S ATOM 31445 SG CYS M 25 125.425 138.014 45.033 1.00336.95 S ATOM 31470 SG CYS M 28 125.686 134.285 45.211 1.00357.91 S ATOM 31628 SG CYS M 49 128.519 136.257 43.610 1.00343.92 S ATOM 31652 SG CYS M 52 125.018 135.832 41.913 1.00371.52 S ATOM 35559 SG CYS V 12 98.113 105.140 59.531 1.00281.78 S ATOM 35581 SG CYS V 15 99.066 108.243 57.726 1.00280.80 S ATOM 35683 SG CYS V 29 95.554 108.033 58.658 1.00312.39 S ATOM 35704 SG CYS V 32 96.845 105.796 55.912 1.00336.34 S Time building chain proxies: 33.79, per 1000 atoms: 0.43 Number of scatterers: 78660 At special positions: 0 Unit cell: (287.896, 219.632, 203.308, 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 10 29.99 S 315 16.00 P 178 15.00 Mg 1 11.99 O 15273 8.00 N 13765 7.00 C 49118 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: 14.36 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 28 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 52 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 25 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 49 " pdb=" ZN V 300 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 15 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 29 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 32 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 12 " Number of angles added : 45 18448 Ramachandran restraints generated. 9224 Oldfield, 0 Emsley, 9224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17698 Finding SS restraints... Secondary structure from input PDB file: 362 helices and 87 sheets defined 47.1% alpha, 15.3% beta 82 base pairs and 137 stacking pairs defined. Time for finding SS restraints: 24.75 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.724A pdb=" N ILE A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 removed outlier: 4.526A pdb=" N THR A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 261 through 284 Processing helix chain 'A' and resid 286 through 306 removed outlier: 3.701A pdb=" N MET A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.710A pdb=" N LEU A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.525A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.889A pdb=" N SER A 477 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 507 through 512 removed outlier: 3.679A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 536 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.505A pdb=" N ASN A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.768A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.583A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.726A pdb=" N ILE A 671 " --> pdb=" O GLY A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 700 removed outlier: 3.618A pdb=" N GLU A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 738 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 755 through 764 Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 810 through 847 removed outlier: 4.730A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 924 through 947 Processing helix chain 'A' and resid 961 through 974 Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 1006 through 1017 removed outlier: 3.685A pdb=" N THR A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 Processing helix chain 'A' and resid 1029 through 1036 Processing helix chain 'A' and resid 1040 through 1058 Processing helix chain 'A' and resid 1065 through 1079 Proline residue: A1077 - end of helix Processing helix chain 'A' and resid 1099 through 1109 Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 3.570A pdb=" N LEU A1128 " --> pdb=" O ARG A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1141 Processing helix chain 'A' and resid 1145 through 1148 No H-bonds generated for 'chain 'A' and resid 1145 through 1148' Processing helix chain 'A' and resid 1168 through 1177 Processing helix chain 'A' and resid 1200 through 1207 Processing helix chain 'A' and resid 1210 through 1223 Processing helix chain 'A' and resid 1259 through 1274 Processing helix chain 'A' and resid 1315 through 1321 removed outlier: 3.624A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1343 removed outlier: 3.636A pdb=" N GLY A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1361 Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 3.987A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1393 Processing helix chain 'A' and resid 1398 through 1404 removed outlier: 3.514A pdb=" N SER A1404 " --> pdb=" O LEU A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1418 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.811A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1451 through 1455 Processing helix chain 'B' and resid 13 through 28 Processing helix chain 'B' and resid 31 through 44 Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.662A pdb=" N TYR B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 299 through 314 Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 329 removed outlier: 3.646A pdb=" N ARG B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 351 Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 401 through 430 removed outlier: 4.198A pdb=" N GLU B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.617A pdb=" N THR B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 removed outlier: 3.721A pdb=" N ALA B 465 " --> pdb=" O GLN B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.207A pdb=" N ARG B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 522 through 526 removed outlier: 4.345A pdb=" N ALA B 525 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 560 through 562 No H-bonds generated for 'chain 'B' and resid 560 through 562' Processing helix chain 'B' and resid 585 through 599 removed outlier: 3.577A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 677 through 684 Processing helix chain 'B' and resid 693 through 698 removed outlier: 3.621A pdb=" N ILE B 698 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.620A pdb=" N GLN B 708 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.746A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 755 removed outlier: 3.553A pdb=" N ILE B 755 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.536A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.508A pdb=" N TYR B 811 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 921 through 926 removed outlier: 4.145A pdb=" N GLU B 924 " --> pdb=" O ASP B 921 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 926 " --> pdb=" O GLU B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 999 removed outlier: 3.655A pdb=" N MET B 999 " --> pdb=" O HIS B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.634A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.960A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.532A pdb=" N VAL B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.610A pdb=" N GLU C 210 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.979A pdb=" N ARG C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 85 through 93 removed outlier: 3.994A pdb=" N THR D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 112 Processing helix chain 'D' and resid 117 through 131 removed outlier: 3.607A pdb=" N SER D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 removed outlier: 3.670A pdb=" N VAL D 136 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 removed outlier: 3.716A pdb=" N GLY D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 Processing helix chain 'D' and resid 161 through 166 removed outlier: 4.193A pdb=" N ALA D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS D 166 " --> pdb=" O SER D 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 166' Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 102 Processing helix chain 'E' and resid 116 through 122 removed outlier: 3.589A pdb=" N MET E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 removed outlier: 3.585A pdb=" N VAL E 140 " --> pdb=" O SER E 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 140' Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.638A pdb=" N LEU E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.708A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 19 through 20 No H-bonds generated for 'chain 'G' and resid 19 through 20' Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.530A pdb=" N ASP H 91 " --> pdb=" O LEU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.571A pdb=" N ASP I 65 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.892A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.817A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'M' and resid 65 through 78 Processing helix chain 'V' and resid 20 through 28 Processing helix chain 'V' and resid 31 through 35 removed outlier: 4.046A pdb=" N SER V 34 " --> pdb=" O ASN V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 49 Processing helix chain 'V' and resid 66 through 72 Processing helix chain 'V' and resid 91 through 101 Processing helix chain 'W' and resid 235 through 251 Processing helix chain 'W' and resid 278 through 287 Processing helix chain 'W' and resid 304 through 310 removed outlier: 4.208A pdb=" N ASP W 308 " --> pdb=" O VAL W 304 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU W 310 " --> pdb=" O TYR W 306 " (cutoff:3.500A) Processing helix chain 'W' and resid 395 through 403 Processing helix chain 'W' and resid 443 through 452 Processing helix chain 'W' and resid 453 through 455 No H-bonds generated for 'chain 'W' and resid 453 through 455' Processing helix chain 'W' and resid 460 through 475 Processing helix chain 'W' and resid 515 through 520 Processing helix chain 'W' and resid 692 through 695 Processing helix chain 'W' and resid 760 through 764 removed outlier: 4.297A pdb=" N TYR W 763 " --> pdb=" O GLN W 760 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS W 764 " --> pdb=" O GLY W 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 760 through 764' Processing helix chain 'W' and resid 792 through 794 No H-bonds generated for 'chain 'W' and resid 792 through 794' Processing helix chain 'm' and resid 230 through 242 Processing helix chain 'm' and resid 244 through 259 removed outlier: 4.416A pdb=" N TRP m 249 " --> pdb=" O THR m 245 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N THR m 250 " --> pdb=" O ASP m 246 " (cutoff:3.500A) Processing helix chain 'm' and resid 279 through 284 Processing helix chain 'm' and resid 285 through 293 Processing helix chain 'm' and resid 295 through 304 Processing helix chain 'm' and resid 307 through 314 Processing helix chain 'm' and resid 323 through 342 Processing helix chain 'm' and resid 342 through 353 Processing helix chain 'm' and resid 358 through 377 Processing helix chain 'm' and resid 380 through 388 Processing helix chain 'm' and resid 388 through 393 removed outlier: 3.936A pdb=" N ALA m 392 " --> pdb=" O ARG m 388 " (cutoff:3.500A) Processing helix chain 'm' and resid 410 through 442 removed outlier: 3.943A pdb=" N ASP m 429 " --> pdb=" O HIS m 425 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS m 430 " --> pdb=" O SER m 426 " (cutoff:3.500A) Processing helix chain 'm' and resid 447 through 456 removed outlier: 3.604A pdb=" N SER m 456 " --> pdb=" O GLU m 452 " (cutoff:3.500A) Processing helix chain 'm' and resid 459 through 474 Processing helix chain 'm' and resid 474 through 484 Processing helix chain 'm' and resid 518 through 527 Processing helix chain 'm' and resid 529 through 537 removed outlier: 4.043A pdb=" N ALA m 537 " --> pdb=" O VAL m 533 " (cutoff:3.500A) Processing helix chain 'm' and resid 538 through 549 Processing helix chain 'm' and resid 561 through 573 Processing helix chain 'm' and resid 581 through 599 Processing helix chain 'm' and resid 600 through 615 removed outlier: 3.501A pdb=" N ARG m 604 " --> pdb=" O GLU m 600 " (cutoff:3.500A) Processing helix chain 'm' and resid 622 through 629 removed outlier: 3.520A pdb=" N ILE m 629 " --> pdb=" O GLY m 625 " (cutoff:3.500A) Processing helix chain 'm' and resid 633 through 639 removed outlier: 3.718A pdb=" N ASP m 637 " --> pdb=" O PRO m 634 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS m 639 " --> pdb=" O PHE m 636 " (cutoff:3.500A) Processing helix chain 'm' and resid 648 through 651 Processing helix chain 'm' and resid 652 through 665 removed outlier: 3.911A pdb=" N TYR m 656 " --> pdb=" O THR m 652 " (cutoff:3.500A) Processing helix chain 'm' and resid 676 through 689 Processing helix chain 'm' and resid 694 through 748 Proline residue: m 717 - end of helix Processing helix chain 'm' and resid 802 through 815 removed outlier: 3.568A pdb=" N SER m 806 " --> pdb=" O SER m 802 " (cutoff:3.500A) Processing helix chain 'm' and resid 830 through 847 removed outlier: 4.059A pdb=" N LYS m 834 " --> pdb=" O ILE m 830 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU m 835 " --> pdb=" O HIS m 831 " (cutoff:3.500A) Processing helix chain 'm' and resid 878 through 887 removed outlier: 3.748A pdb=" N HIS m 886 " --> pdb=" O ARG m 882 " (cutoff:3.500A) Processing helix chain 'm' and resid 887 through 894 removed outlier: 3.690A pdb=" N SER m 891 " --> pdb=" O SER m 887 " (cutoff:3.500A) Processing helix chain 'm' and resid 898 through 913 Processing helix chain 'm' and resid 913 through 921 Processing helix chain 'm' and resid 922 through 928 removed outlier: 4.125A pdb=" N MET m 925 " --> pdb=" O ASP m 922 " (cutoff:3.500A) Processing helix chain 'm' and resid 938 through 958 Processing helix chain 'm' and resid 961 through 967 Processing helix chain 'm' and resid 967 through 972 Processing helix chain 'm' and resid 973 through 977 Processing helix chain 'm' and resid 981 through 996 Processing helix chain 'm' and resid 1003 through 1008 Processing helix chain 'm' and resid 1012 through 1020 Processing helix chain 'm' and resid 1030 through 1034 removed outlier: 3.952A pdb=" N ARG m1033 " --> pdb=" O ASP m1030 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN m1034 " --> pdb=" O VAL m1031 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 1030 through 1034' Processing helix chain 'm' and resid 1040 through 1045 Processing helix chain 'm' and resid 1048 through 1050 No H-bonds generated for 'chain 'm' and resid 1048 through 1050' Processing helix chain 'm' and resid 1051 through 1064 Processing helix chain 'm' and resid 1072 through 1085 Processing helix chain 'm' and resid 1097 through 1103 Processing helix chain 'm' and resid 1104 through 1117 removed outlier: 3.559A pdb=" N TYR m1108 " --> pdb=" O ILE m1104 " (cutoff:3.500A) Processing helix chain 'm' and resid 1120 through 1133 Processing helix chain 'm' and resid 1146 through 1156 Processing helix chain 'm' and resid 1194 through 1198 removed outlier: 4.376A pdb=" N LEU m1198 " --> pdb=" O ARG m1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 1194 through 1198' Processing helix chain 'm' and resid 1205 through 1210 Processing helix chain 'm' and resid 1235 through 1240 Processing helix chain 'm' and resid 1256 through 1273 Processing helix chain 'm' and resid 1290 through 1300 removed outlier: 3.706A pdb=" N ALA m1300 " --> pdb=" O ASP m1296 " (cutoff:3.500A) Processing helix chain 'm' and resid 1358 through 1380 removed outlier: 3.930A pdb=" N ASN m1368 " --> pdb=" O VAL m1364 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN m1369 " --> pdb=" O GLU m1365 " (cutoff:3.500A) Processing helix chain 'm' and resid 1387 through 1402 Processing helix chain 'm' and resid 1453 through 1469 Processing helix chain 'n' and resid 153 through 180 Processing helix chain 'n' and resid 185 through 200 Proline residue: n 192 - end of helix removed outlier: 3.551A pdb=" N ARG n 200 " --> pdb=" O ASP n 196 " (cutoff:3.500A) Processing helix chain 'n' and resid 203 through 211 Processing helix chain 'n' and resid 212 through 221 Processing helix chain 'n' and resid 230 through 244 Processing helix chain 'n' and resid 247 through 255 Processing helix chain 'n' and resid 255 through 266 removed outlier: 4.553A pdb=" N VAL n 259 " --> pdb=" O GLY n 255 " (cutoff:3.500A) Processing helix chain 'n' and resid 270 through 289 Proline residue: n 287 - end of helix Processing helix chain 'q' and resid 5 through 13 removed outlier: 3.879A pdb=" N TYR q 9 " --> pdb=" O ASP q 5 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 20 removed outlier: 3.751A pdb=" N GLU q 20 " --> pdb=" O ASP q 16 " (cutoff:3.500A) Processing helix chain 'q' and resid 21 through 23 No H-bonds generated for 'chain 'q' and resid 21 through 23' Processing helix chain 'q' and resid 46 through 58 Processing helix chain 'q' and resid 60 through 74 removed outlier: 3.661A pdb=" N TRP q 64 " --> pdb=" O ARG q 60 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 89 Processing helix chain 'q' and resid 90 through 96 Processing helix chain 'q' and resid 97 through 120 removed outlier: 3.872A pdb=" N THR q 101 " --> pdb=" O SER q 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR q 119 " --> pdb=" O GLU q 115 " (cutoff:3.500A) Processing helix chain 'q' and resid 122 through 141 Processing helix chain 'q' and resid 144 through 158 removed outlier: 3.690A pdb=" N GLY q 148 " --> pdb=" O LEU q 144 " (cutoff:3.500A) Processing helix chain 'q' and resid 160 through 175 Processing helix chain 'q' and resid 178 through 192 Processing helix chain 'q' and resid 194 through 209 removed outlier: 3.535A pdb=" N LEU q 201 " --> pdb=" O GLN q 197 " (cutoff:3.500A) Processing helix chain 'q' and resid 215 through 227 removed outlier: 4.127A pdb=" N GLY q 219 " --> pdb=" O ASP q 215 " (cutoff:3.500A) Processing helix chain 'q' and resid 229 through 244 Processing helix chain 'q' and resid 248 through 267 removed outlier: 3.878A pdb=" N LYS q 252 " --> pdb=" O ASN q 248 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER q 267 " --> pdb=" O CYS q 263 " (cutoff:3.500A) Processing helix chain 'q' and resid 269 through 289 Processing helix chain 'q' and resid 294 through 308 removed outlier: 3.600A pdb=" N SER q 303 " --> pdb=" O MET q 299 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR q 304 " --> pdb=" O VAL q 300 " (cutoff:3.500A) Processing helix chain 'q' and resid 310 through 325 Processing helix chain 'q' and resid 328 through 347 removed outlier: 3.555A pdb=" N VAL q 332 " --> pdb=" O ASN q 328 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS q 345 " --> pdb=" O ARG q 341 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS q 346 " --> pdb=" O VAL q 342 " (cutoff:3.500A) Processing helix chain 'q' and resid 348 through 363 Processing helix chain 'q' and resid 366 through 380 removed outlier: 3.544A pdb=" N LYS q 370 " --> pdb=" O ASN q 366 " (cutoff:3.500A) Processing helix chain 'q' and resid 382 through 397 Processing helix chain 'q' and resid 402 through 417 Processing helix chain 'q' and resid 419 through 438 Processing helix chain 'q' and resid 442 through 454 removed outlier: 3.802A pdb=" N TYR q 446 " --> pdb=" O LEU q 442 " (cutoff:3.500A) Processing helix chain 'q' and resid 457 through 473 Processing helix chain 'q' and resid 474 through 476 No H-bonds generated for 'chain 'q' and resid 474 through 476' Processing helix chain 'q' and resid 477 through 491 Processing helix chain 'q' and resid 493 through 508 Processing helix chain 'q' and resid 509 through 511 No H-bonds generated for 'chain 'q' and resid 509 through 511' Processing helix chain 'q' and resid 512 through 535 removed outlier: 4.232A pdb=" N GLU q 517 " --> pdb=" O PRO q 513 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ALA q 518 " --> pdb=" O GLN q 514 " (cutoff:3.500A) Processing helix chain 'q' and resid 535 through 550 removed outlier: 3.533A pdb=" N ALA q 539 " --> pdb=" O ASN q 535 " (cutoff:3.500A) Processing helix chain 'q' and resid 553 through 569 removed outlier: 4.100A pdb=" N LYS q 557 " --> pdb=" O TYR q 553 " (cutoff:3.500A) Processing helix chain 'q' and resid 572 through 583 Processing helix chain 'q' and resid 586 through 605 removed outlier: 6.252A pdb=" N ARG q 602 " --> pdb=" O LYS q 598 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS q 603 " --> pdb=" O ARG q 599 " (cutoff:3.500A) Processing helix chain 'q' and resid 609 through 622 Processing helix chain 'q' and resid 626 through 644 Processing helix chain 'q' and resid 648 through 673 Processing helix chain 'q' and resid 676 through 690 removed outlier: 3.546A pdb=" N ALA q 680 " --> pdb=" O ASN q 676 " (cutoff:3.500A) Processing helix chain 'q' and resid 692 through 707 Processing helix chain 'q' and resid 709 through 723 Processing helix chain 'q' and resid 725 through 740 Processing helix chain 'q' and resid 745 through 764 removed outlier: 3.788A pdb=" N LEU q 749 " --> pdb=" O ASP q 745 " (cutoff:3.500A) Processing helix chain 'q' and resid 765 through 784 removed outlier: 3.671A pdb=" N TYR q 769 " --> pdb=" O SER q 765 " (cutoff:3.500A) Processing helix chain 'q' and resid 785 through 806 Processing helix chain 'q' and resid 807 through 811 Processing helix chain 'q' and resid 812 through 835 Processing helix chain 'q' and resid 842 through 856 removed outlier: 3.534A pdb=" N THR q 856 " --> pdb=" O MET q 852 " (cutoff:3.500A) Processing helix chain 'q' and resid 856 through 930 removed outlier: 3.778A pdb=" N ARG q 883 " --> pdb=" O LEU q 879 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG q 884 " --> pdb=" O ARG q 880 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS q 885 " --> pdb=" O THR q 881 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU q 917 " --> pdb=" O ILE q 913 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU q 918 " --> pdb=" O LYS q 914 " (cutoff:3.500A) Processing helix chain 'r' and resid 197 through 204 removed outlier: 3.802A pdb=" N ILE r 204 " --> pdb=" O ASP r 200 " (cutoff:3.500A) Processing helix chain 'r' and resid 207 through 215 Processing helix chain 'r' and resid 219 through 225 Processing helix chain 'r' and resid 287 through 289 No H-bonds generated for 'chain 'r' and resid 287 through 289' Processing helix chain 'r' and resid 295 through 310 Processing helix chain 'r' and resid 315 through 332 Processing helix chain 'r' and resid 335 through 350 Processing helix chain 'r' and resid 353 through 374 Processing helix chain 'r' and resid 378 through 391 removed outlier: 3.611A pdb=" N ARG r 382 " --> pdb=" O GLU r 378 " (cutoff:3.500A) Processing helix chain 'r' and resid 398 through 433 removed outlier: 3.828A pdb=" N ARG r 420 " --> pdb=" O ASN r 416 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU r 428 " --> pdb=" O MET r 424 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS r 429 " --> pdb=" O ALA r 425 " (cutoff:3.500A) Processing helix chain 'r' and resid 486 through 490 Processing helix chain 'r' and resid 492 through 497 Processing helix chain 'r' and resid 498 through 505 Processing helix chain 'u' and resid 122 through 129 Processing helix chain 'u' and resid 135 through 149 Processing helix chain 'u' and resid 228 through 242 removed outlier: 3.627A pdb=" N GLN u 242 " --> pdb=" O LEU u 238 " (cutoff:3.500A) Processing helix chain 'u' and resid 258 through 282 Processing helix chain 'v' and resid 32 through 35 Processing helix chain 'v' and resid 36 through 45 Processing helix chain 'v' and resid 47 through 58 Processing helix chain 'v' and resid 64 through 71 removed outlier: 3.573A pdb=" N ASP v 68 " --> pdb=" O GLU v 65 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY v 69 " --> pdb=" O THR v 66 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP v 71 " --> pdb=" O ASP v 68 " (cutoff:3.500A) Processing helix chain 'v' and resid 73 through 77 removed outlier: 3.608A pdb=" N ILE v 77 " --> pdb=" O TYR v 74 " (cutoff:3.500A) Processing helix chain 'v' and resid 85 through 94 Processing helix chain 'v' and resid 103 through 109 Processing helix chain 'v' and resid 158 through 172 Processing helix chain 'v' and resid 178 through 185 Processing helix chain 'v' and resid 218 through 221 Processing helix chain 'v' and resid 225 through 233 Processing helix chain 'v' and resid 244 through 249 Processing helix chain 'v' and resid 271 through 284 Processing helix chain 'v' and resid 345 through 347 No H-bonds generated for 'chain 'v' and resid 345 through 347' Processing helix chain 'v' and resid 348 through 353 Processing helix chain 'v' and resid 368 through 380 Processing helix chain 'x' and resid 136 through 145 Processing helix chain 'x' and resid 153 through 157 removed outlier: 4.064A pdb=" N LEU x 156 " --> pdb=" O ASN x 153 " (cutoff:3.500A) Processing helix chain 'x' and resid 164 through 175 Processing helix chain 'x' and resid 224 through 230 Processing helix chain 'x' and resid 275 through 280 removed outlier: 3.547A pdb=" N TYR x 278 " --> pdb=" O LYS x 275 " (cutoff:3.500A) Processing helix chain 'x' and resid 290 through 295 removed outlier: 3.646A pdb=" N GLN x 293 " --> pdb=" O LYS x 290 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS x 295 " --> pdb=" O TRP x 292 " (cutoff:3.500A) Processing helix chain 'x' and resid 301 through 309 Processing helix chain 'x' and resid 322 through 327 Processing helix chain 'x' and resid 341 through 361 removed outlier: 4.390A pdb=" N GLN x 345 " --> pdb=" O PHE x 341 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 76 Processing helix chain 'a' and resid 87 through 114 removed outlier: 3.672A pdb=" N ALA a 91 " --> pdb=" O ALA a 87 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 25 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.840A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 removed outlier: 3.551A pdb=" N GLN b 93 " --> pdb=" O ALA b 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 63 through 76 Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 131 Processing helix chain 'f' and resid 25 through 29 removed outlier: 3.611A pdb=" N ILE f 29 " --> pdb=" O ILE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 Processing helix chain 'f' and resid 82 through 94 removed outlier: 3.635A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 46 through 73 removed outlier: 3.625A 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 '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 'j' and resid 477 through 509 removed outlier: 3.929A pdb=" N THR j 481 " --> pdb=" O LEU j 477 " (cutoff:3.500A) Processing helix chain 'j' and resid 512 through 518 Processing helix chain 'j' and resid 539 through 543 Processing helix chain 'j' and resid 624 through 654 removed outlier: 4.176A pdb=" N ASP j 654 " --> pdb=" O LYS j 650 " (cutoff:3.500A) Processing helix chain 'j' and resid 775 through 806 Processing helix chain 'j' and resid 816 through 820 Processing helix chain 'j' and resid 893 through 904 Processing helix chain 'j' and resid 916 through 927 Processing helix chain 'j' and resid 927 through 934 Processing helix chain 'j' and resid 937 through 942 removed outlier: 3.860A pdb=" N GLY j 942 " --> pdb=" O SER j 938 " (cutoff:3.500A) Processing helix chain 'k' and resid 83 through 97 removed outlier: 4.393A pdb=" N GLN k 87 " --> pdb=" O GLN k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 202 through 214 removed outlier: 3.512A pdb=" N ALA k 213 " --> pdb=" O LEU k 209 " (cutoff:3.500A) Processing helix chain 'k' and resid 313 through 321 Processing helix chain 'k' and resid 334 through 347 Processing helix chain 'k' and resid 435 through 446 Processing sheet with id=AA1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.779A pdb=" N THR A 238 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N LYS A 88 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ILE A 236 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 178 Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.613A pdb=" N LYS A 344 " --> pdb=" O PHE B1130 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B1128 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.694A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL A 365 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N MET A 464 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL A 367 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.966A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA9, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.329A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS H 102 " --> pdb=" O TYR H 114 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER H 116 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL H 100 " --> pdb=" O SER H 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 589 through 591 removed outlier: 6.954A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB3, first strand: chain 'A' and resid 850 through 851 removed outlier: 6.738A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB5, first strand: chain 'A' and resid 1284 through 1295 removed outlier: 3.969A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A1118 " --> pdb=" O THR A1311 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1143 through 1144 Processing sheet with id=AB7, first strand: chain 'A' and resid 1226 through 1230 removed outlier: 4.334A pdb=" N LEU A1238 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A1244 " --> pdb=" O TRP A1193 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP A1193 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR A1156 " --> pdb=" O LYS I 42 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS I 42 " --> pdb=" O TYR A1156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1444 through 1448 Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 62 removed outlier: 4.939A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER B 113 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS B 160 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B 115 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC3, first strand: chain 'B' and resid 397 through 400 Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.950A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER B 243 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 537 through 538 removed outlier: 3.966A pdb=" N GLU B 644 " --> pdb=" O GLU B 634 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 644 through 645 current: chain 'B' and resid 740 through 741 Processing sheet with id=AC6, first strand: chain 'B' and resid 557 through 558 removed outlier: 5.658A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG B 572 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE B 619 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE B 574 " --> pdb=" O ILE B 619 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 792 through 796 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 853 through 862 current: chain 'B' and resid 947 through 956 removed outlier: 8.661A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 962 through 972 current: chain 'L' and resid 39 through 42 Processing sheet with id=AC8, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AC9, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.004A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 873 through 874 removed outlier: 7.426A pdb=" N LEU B 883 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.539A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD4, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD5, first strand: chain 'C' and resid 6 through 12 removed outlier: 6.588A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA C 12 " --> pdb=" O GLU C 16 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 119 through 122 removed outlier: 6.730A pdb=" N VAL C 97 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG C 156 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE C 50 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE C 158 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL C 48 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LYS C 160 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASP C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY C 162 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.671A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.474A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C 113 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 5 through 6 current: chain 'G' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 2 through 13 current: chain 'G' and resid 43 through 48 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 48 current: chain 'G' and resid 68 through 79 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE2, first strand: chain 'E' and resid 59 through 61 removed outlier: 6.469A pdb=" N TRP E 78 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE E 110 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU E 80 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 86 through 87 removed outlier: 3.522A pdb=" N VAL E 87 " --> pdb=" O ASN E 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.118A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.589A pdb=" N VAL G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER G 162 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA G 159 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY G 161 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N SER G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AE7, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.738A pdb=" N ARG I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AE9, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF1, first strand: chain 'M' and resid 16 through 21 removed outlier: 3.902A pdb=" N VAL M 34 " --> pdb=" O THR M 21 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 18 through 19 Processing sheet with id=AF3, first strand: chain 'V' and resid 81 through 86 removed outlier: 6.968A pdb=" N GLY V 56 " --> pdb=" O VAL V 84 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL V 86 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE V 54 " --> pdb=" O VAL V 86 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'W' and resid 337 through 339 Processing sheet with id=AF5, first strand: chain 'W' and resid 349 through 354 removed outlier: 4.663A pdb=" N GLU W 420 " --> pdb=" O TYR W 427 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'W' and resid 522 through 526 removed outlier: 7.778A pdb=" N ILE W 506 " --> pdb=" O VAL W 501 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL W 501 " --> pdb=" O ILE W 506 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER W 508 " --> pdb=" O SER W 499 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'W' and resid 572 through 576 removed outlier: 6.043A pdb=" N ILE W 565 " --> pdb=" O ILE W 554 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE W 554 " --> pdb=" O ILE W 565 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 601 through 603 removed outlier: 6.872A pdb=" N ASP W 621 " --> pdb=" O ILE W 613 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 650 through 651 removed outlier: 3.558A pdb=" N ALA W 650 " --> pdb=" O VAL W 658 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 697 through 701 removed outlier: 6.907A pdb=" N PHE W 683 " --> pdb=" O VAL W 679 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL W 679 " --> pdb=" O PHE W 683 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE W 685 " --> pdb=" O LEU W 677 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 787 through 791 removed outlier: 4.574A pdb=" N LYS W 787 " --> pdb=" O LEU W 782 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG W 779 " --> pdb=" O LYS W 771 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N THR W 755 " --> pdb=" O GLU W 799 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'm' and resid 396 through 397 Processing sheet with id=AG4, first strand: chain 'm' and resid 644 through 645 Processing sheet with id=AG5, first strand: chain 'm' and resid 790 through 796 removed outlier: 3.833A pdb=" N SER m 792 " --> pdb=" O PHE m 783 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU m 766 " --> pdb=" O GLY m 824 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'm' and resid 959 through 960 removed outlier: 6.876A pdb=" N VAL m 959 " --> pdb=" O TYR m1024 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'm' and resid 1167 through 1175 removed outlier: 6.711A pdb=" N SER m1181 " --> pdb=" O ARG m1173 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL m1175 " --> pdb=" O TYR m1179 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR m1179 " --> pdb=" O VAL m1175 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS m1230 " --> pdb=" O ALA m1189 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLN m1193 " --> pdb=" O LEU m1232 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N SER m1233 " --> pdb=" O ILE m1220 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE m1220 " --> pdb=" O SER m1233 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'm' and resid 1306 through 1310 removed outlier: 6.747A pdb=" N LEU m1328 " --> pdb=" O VAL m1324 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'm' and resid 1407 through 1412 Processing sheet with id=AH1, first strand: chain 'q' and resid 25 through 29 Processing sheet with id=AH2, first strand: chain 'r' and resid 228 through 232 removed outlier: 4.020A pdb=" N LEU r 229 " --> pdb=" O VAL r 246 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL r 246 " --> pdb=" O LEU r 229 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL r 248 " --> pdb=" O ALA r 275 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA r 275 " --> pdb=" O VAL r 248 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'r' and resid 259 through 260 Processing sheet with id=AH4, first strand: chain 'u' and resid 87 through 91 WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 87 through 91 current: chain 'u' and resid 178 through 182 removed outlier: 4.923A pdb=" N TYR u 178 " --> pdb=" O MET u 189 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 185 through 193 current: chain 'u' and resid 208 through 223 WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 208 through 223 current: chain 'v' and resid 263 through 268 removed outlier: 6.450A pdb=" N ILE v 264 " --> pdb=" O ASP v 302 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP v 302 " --> pdb=" O ILE v 264 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU v 266 " --> pdb=" O ILE v 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'v' and resid 295 through 309 current: chain 'v' and resid 327 through 333 Processing sheet with id=AH5, first strand: chain 'u' and resid 116 through 120 removed outlier: 4.464A pdb=" N TRP u 152 " --> pdb=" O ASN u 117 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU u 119 " --> pdb=" O TRP u 152 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N TYR u 154 " --> pdb=" O GLU u 119 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'v' and resid 29 through 30 Processing sheet with id=AH7, first strand: chain 'x' and resid 247 through 252 removed outlier: 5.935A pdb=" N ILE x 210 " --> pdb=" O VAL x 266 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE x 209 " --> pdb=" O VAL x 283 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE x 285 " --> pdb=" O ILE x 209 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL x 211 " --> pdb=" O ILE x 285 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N PHE x 312 " --> pdb=" O VAL x 283 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE x 285 " --> pdb=" O PHE x 312 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE x 314 " --> pdb=" O ILE x 285 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY x 311 " --> pdb=" O LYS x 331 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU x 333 " --> pdb=" O GLY x 311 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR x 313 " --> pdb=" O LEU x 333 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE x 335 " --> pdb=" O TYR x 313 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS x 315 " --> pdb=" O ILE x 335 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'a' and resid 83 through 84 removed outlier: 7.082A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AI1, first strand: chain 'b' and resid 96 through 98 removed outlier: 6.609A pdb=" N THR b 96 " --> pdb=" O THR g 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.592A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AI4, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.384A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AI6, first strand: chain 'j' and resid 525 through 526 removed outlier: 6.381A pdb=" N VAL j 525 " --> pdb=" O LEU j 604 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'j' and resid 548 through 550 Processing sheet with id=AI8, first strand: chain 'j' and resid 572 through 580 removed outlier: 3.535A pdb=" N ASN j 574 " --> pdb=" O ASN j 589 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG j 616 " --> pdb=" O PHE j 590 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU k 122 " --> pdb=" O GLU k 133 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU k 133 " --> pdb=" O LEU k 122 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N PHE k 124 " --> pdb=" O ALA k 131 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 129 through 135 current: chain 'k' and resid 149 through 154 removed outlier: 5.566A pdb=" N VAL k 172 " --> pdb=" O LEU k 154 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'j' and resid 707 through 711 removed outlier: 6.517A pdb=" N LEU j 689 " --> pdb=" O GLU j 672 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU j 672 " --> pdb=" O LEU j 689 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE j 691 " --> pdb=" O LYS j 670 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS j 670 " --> pdb=" O ILE j 691 " (cutoff:3.500A) removed outlier: 10.651A pdb=" N ASN j 673 " --> pdb=" O GLU j 754 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU j 754 " --> pdb=" O ASN j 673 " (cutoff:3.500A) removed outlier: 10.055A pdb=" N LYS j 745 " --> pdb=" O THR j 737 " (cutoff:3.500A) removed outlier: 11.283A pdb=" N THR j 737 " --> pdb=" O LYS j 745 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE j 747 " --> pdb=" O LEU j 735 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE j 730 " --> pdb=" O PHE j 720 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE j 720 " --> pdb=" O ILE j 730 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N HIS j 732 " --> pdb=" O LEU j 718 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU j 718 " --> pdb=" O HIS j 732 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N HIS j 734 " --> pdb=" O LYS j 716 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N GLU j 813 " --> pdb=" O LYS j 716 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU j 718 " --> pdb=" O GLU j 813 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'j' and resid 821 through 823 Processing sheet with id=AJ2, first strand: chain 'j' and resid 884 through 890 removed outlier: 5.221A pdb=" N PHE j 870 " --> pdb=" O THR j 888 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP j 871 " --> pdb=" O LEU j 860 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU j 860 " --> pdb=" O ASP j 871 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL j 873 " --> pdb=" O ALA j 858 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA j 858 " --> pdb=" O VAL j 873 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL j 875 " --> pdb=" O GLU j 856 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'k' and resid 44 through 47 removed outlier: 5.284A pdb=" N GLY k 18 " --> pdb=" O THR k 8 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL k 4 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 10.299A pdb=" N THR k 8 " --> pdb=" O PHE k 80 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N PHE k 80 " --> pdb=" O THR k 8 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N TRP k 63 " --> pdb=" O GLY k 79 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'k' and resid 254 through 258 removed outlier: 6.812A pdb=" N GLY k 235 " --> pdb=" O LEU k 229 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU k 229 " --> pdb=" O GLY k 235 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N PHE k 237 " --> pdb=" O ASP k 227 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP k 227 " --> pdb=" O PHE k 237 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL k 223 " --> pdb=" O MET k 241 " (cutoff:3.500A) removed outlier: 13.055A pdb=" N ASP k 227 " --> pdb=" O ASP k 301 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N ASP k 301 " --> pdb=" O ASP k 227 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU k 229 " --> pdb=" O GLN k 299 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL k 297 " --> pdb=" O LEU k 231 " (cutoff:3.500A) removed outlier: 9.864A pdb=" N ARG k 292 " --> pdb=" O PRO k 284 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG k 264 " --> pdb=" O GLN k 281 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASP k 283 " --> pdb=" O VAL k 262 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL k 262 " --> pdb=" O ASP k 283 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N ILE k 351 " --> pdb=" O LEU k 263 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE k 265 " --> pdb=" O ILE k 351 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'k' and resid 305 through 309 removed outlier: 5.419A pdb=" N LEU k 306 " --> pdb=" O THR k 331 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR k 331 " --> pdb=" O LEU k 306 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'k' and resid 391 through 394 removed outlier: 8.441A pdb=" N ASN k 366 " --> pdb=" O ILE k 431 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE k 431 " --> pdb=" O ASN k 366 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN k 430 " --> pdb=" O PHE k 415 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE k 415 " --> pdb=" O ASN k 430 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LYS k 451 " --> pdb=" O ILE k 399 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL k 401 " --> pdb=" O LYS k 451 " (cutoff:3.500A) 3633 hydrogen bonds defined for protein. 10323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 207 hydrogen bonds 414 hydrogen bond angles 0 basepair planarities 82 basepair parallelities 137 stacking parallelities Total time for adding SS restraints: 44.58 Time building geometry restraints manager: 17.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 14588 1.32 - 1.45: 20225 1.45 - 1.57: 44779 1.57 - 1.70: 364 1.70 - 1.82: 513 Bond restraints: 80469 Sorted by residual: bond pdb=" C1' DG N -10 " pdb=" N9 DG N -10 " ideal model delta sigma weight residual 1.460 1.380 0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1' DG N -7 " pdb=" N9 DG N -7 " ideal model delta sigma weight residual 1.460 1.381 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C1' DG N -5 " pdb=" N9 DG N -5 " ideal model delta sigma weight residual 1.460 1.385 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C1' DA N -13 " pdb=" N9 DA N -13 " ideal model delta sigma weight residual 1.460 1.385 0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C1' DA T 16 " pdb=" N9 DA T 16 " ideal model delta sigma weight residual 1.460 1.386 0.074 2.00e-02 2.50e+03 1.35e+01 ... (remaining 80464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 108572 3.32 - 6.64: 792 6.64 - 9.96: 7 9.96 - 13.28: 1 13.28 - 16.60: 1 Bond angle restraints: 109373 Sorted by residual: angle pdb=" N VAL A1001 " pdb=" CA VAL A1001 " pdb=" C VAL A1001 " ideal model delta sigma weight residual 112.96 107.29 5.67 1.00e+00 1.00e+00 3.21e+01 angle pdb=" O3' U P 10 " pdb=" P U P 11 " pdb=" OP1 U P 11 " ideal model delta sigma weight residual 108.00 124.60 -16.60 3.00e+00 1.11e-01 3.06e+01 angle pdb=" N VAL j 533 " pdb=" CA VAL j 533 " pdb=" C VAL j 533 " ideal model delta sigma weight residual 111.81 107.52 4.29 8.60e-01 1.35e+00 2.48e+01 angle pdb=" C3' DG N -45 " pdb=" O3' DG N -45 " pdb=" P DG N -44 " ideal model delta sigma weight residual 120.20 127.49 -7.29 1.50e+00 4.44e-01 2.36e+01 angle pdb=" OE1 GLN j 721 " pdb=" CD GLN j 721 " pdb=" NE2 GLN j 721 " ideal model delta sigma weight residual 122.60 117.97 4.63 1.00e+00 1.00e+00 2.15e+01 ... (remaining 109368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 46054 24.83 - 49.66: 2406 49.66 - 74.49: 395 74.49 - 99.32: 44 99.32 - 124.15: 2 Dihedral angle restraints: 48901 sinusoidal: 21598 harmonic: 27303 Sorted by residual: dihedral pdb=" CA ASP W 460 " pdb=" C ASP W 460 " pdb=" N LEU W 461 " pdb=" CA LEU W 461 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA TYR A 466 " pdb=" C TYR A 466 " pdb=" N SER A 467 " pdb=" CA SER A 467 " ideal model delta harmonic sigma weight residual 180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" O4' U P -5 " pdb=" C1' U P -5 " pdb=" N1 U P -5 " pdb=" C2 U P -5 " ideal model delta sinusoidal sigma weight residual -128.00 -58.57 -69.43 1 1.70e+01 3.46e-03 2.15e+01 ... (remaining 48898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 11503 0.103 - 0.206: 639 0.206 - 0.308: 22 0.308 - 0.411: 2 0.411 - 0.514: 1 Chirality restraints: 12167 Sorted by residual: chirality pdb=" P U P 11 " pdb=" OP1 U P 11 " pdb=" OP2 U P 11 " pdb=" O5' U P 11 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.61e+00 chirality pdb=" CA THR k 8 " pdb=" N THR k 8 " pdb=" C THR k 8 " pdb=" CB THR k 8 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA ASP k 72 " pdb=" N ASP k 72 " pdb=" C ASP k 72 " pdb=" CB ASP k 72 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 12164 not shown) Planarity restraints: 13560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP k 56 " 0.116 2.00e-02 2.50e+03 7.06e-02 1.25e+02 pdb=" CG TRP k 56 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP k 56 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP k 56 " -0.070 2.00e-02 2.50e+03 pdb=" NE1 TRP k 56 " -0.064 2.00e-02 2.50e+03 pdb=" CE2 TRP k 56 " -0.028 2.00e-02 2.50e+03 pdb=" CE3 TRP k 56 " -0.101 2.00e-02 2.50e+03 pdb=" CZ2 TRP k 56 " 0.072 2.00e-02 2.50e+03 pdb=" CZ3 TRP k 56 " -0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP k 56 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT N -62 " -0.146 2.00e-02 2.50e+03 6.33e-02 1.00e+02 pdb=" N1 DT N -62 " 0.060 2.00e-02 2.50e+03 pdb=" C2 DT N -62 " 0.036 2.00e-02 2.50e+03 pdb=" O2 DT N -62 " 0.049 2.00e-02 2.50e+03 pdb=" N3 DT N -62 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DT N -62 " -0.023 2.00e-02 2.50e+03 pdb=" O4 DT N -62 " -0.074 2.00e-02 2.50e+03 pdb=" C5 DT N -62 " 0.023 2.00e-02 2.50e+03 pdb=" C7 DT N -62 " 0.013 2.00e-02 2.50e+03 pdb=" C6 DT N -62 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC N -77 " -0.136 2.00e-02 2.50e+03 6.19e-02 8.62e+01 pdb=" N1 DC N -77 " 0.069 2.00e-02 2.50e+03 pdb=" C2 DC N -77 " 0.030 2.00e-02 2.50e+03 pdb=" O2 DC N -77 " 0.040 2.00e-02 2.50e+03 pdb=" N3 DC N -77 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DC N -77 " -0.018 2.00e-02 2.50e+03 pdb=" N4 DC N -77 " -0.062 2.00e-02 2.50e+03 pdb=" C5 DC N -77 " 0.025 2.00e-02 2.50e+03 pdb=" C6 DC N -77 " 0.061 2.00e-02 2.50e+03 ... (remaining 13557 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 468 2.55 - 3.14: 59451 3.14 - 3.72: 123051 3.72 - 4.31: 171583 4.31 - 4.90: 283953 Nonbonded interactions: 638506 Sorted by model distance: nonbonded pdb=" OP1 U P 11 " pdb="MG MG A1803 " model vdw 1.959 2.170 nonbonded pdb=" OD1 ASP A 484 " pdb="MG MG A1803 " model vdw 2.020 2.170 nonbonded pdb=" OG1 THR K 57 " pdb=" OE1 GLN K 76 " model vdw 2.170 3.040 nonbonded pdb=" O ILE u 145 " pdb=" OG1 THR u 149 " model vdw 2.174 3.040 nonbonded pdb=" OD2 ASP E 47 " pdb=" NE2 GLN E 53 " model vdw 2.189 3.120 ... (remaining 638501 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' selection = (chain 'e' and resid 60 through 134) } ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 2.140 Check model and map are aligned: 0.440 Set scattering table: 0.560 Process input model: 175.650 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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 : 0.006 0.092 80469 Z= 0.393 Angle : 0.737 16.604 109373 Z= 0.465 Chirality : 0.049 0.514 12167 Planarity : 0.006 0.248 13560 Dihedral : 14.729 124.148 31203 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.57 % Favored : 97.38 % Rotamer: Outliers : 0.12 % Allowed : 0.39 % Favored : 99.49 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.95 % Cis-general : 0.00 % 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: 1.23 (0.09), residues: 9224 helix: 1.92 (0.08), residues: 3960 sheet: 0.25 (0.14), residues: 1394 loop : -0.05 (0.10), residues: 3870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.116 0.003 TRP k 56 HIS 0.027 0.001 HIS j 692 PHE 0.069 0.002 PHE k 300 TYR 0.081 0.002 TYR k 60 ARG 0.022 0.001 ARG j 616 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18448 Ramachandran restraints generated. 9224 Oldfield, 0 Emsley, 9224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18448 Ramachandran restraints generated. 9224 Oldfield, 0 Emsley, 9224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3050 residues out of total 8321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 3040 time to evaluate : 6.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 12 ARG cc_start: 0.8262 (mtp180) cc_final: 0.7904 (mtm-85) REVERT: A 37 TYR cc_start: 0.8203 (m-80) cc_final: 0.7818 (m-80) REVERT: A 85 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7922 (mm-30) REVERT: A 132 LYS cc_start: 0.9246 (tptt) cc_final: 0.9015 (tptp) REVERT: A 235 MET cc_start: 0.8581 (mtm) cc_final: 0.8375 (mtp) REVERT: A 242 VAL cc_start: 0.9373 (t) cc_final: 0.9103 (p) REVERT: A 279 LYS cc_start: 0.9102 (ttpt) cc_final: 0.8837 (ttmm) REVERT: A 290 ILE cc_start: 0.9244 (mt) cc_final: 0.8836 (tp) REVERT: A 306 ASP cc_start: 0.8715 (t0) cc_final: 0.8394 (t0) REVERT: A 316 LEU cc_start: 0.9466 (mt) cc_final: 0.9190 (mp) REVERT: A 318 LYS cc_start: 0.8302 (mttm) cc_final: 0.8092 (ttmm) REVERT: A 379 GLU cc_start: 0.8988 (tt0) cc_final: 0.8278 (tt0) REVERT: A 405 TYR cc_start: 0.8831 (m-80) cc_final: 0.8594 (m-10) REVERT: A 413 ARG cc_start: 0.8565 (mtt180) cc_final: 0.8100 (mtt180) REVERT: A 455 SER cc_start: 0.9547 (m) cc_final: 0.9293 (t) REVERT: A 482 ASP cc_start: 0.8687 (p0) cc_final: 0.8475 (p0) REVERT: A 495 SER cc_start: 0.9302 (t) cc_final: 0.9013 (p) REVERT: A 501 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 539 ASP cc_start: 0.8665 (p0) cc_final: 0.8307 (p0) REVERT: A 540 THR cc_start: 0.9725 (m) cc_final: 0.9385 (p) REVERT: A 593 ASP cc_start: 0.7855 (m-30) cc_final: 0.7633 (m-30) REVERT: A 610 ASP cc_start: 0.8489 (t0) cc_final: 0.8146 (t70) REVERT: A 614 MET cc_start: 0.8367 (mmt) cc_final: 0.8133 (mmm) REVERT: A 660 HIS cc_start: 0.8992 (m-70) cc_final: 0.8354 (m-70) REVERT: A 735 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8523 (pp20) REVERT: A 738 LEU cc_start: 0.9171 (mt) cc_final: 0.8824 (mt) REVERT: A 747 MET cc_start: 0.9307 (mtm) cc_final: 0.8934 (mtm) REVERT: A 782 ASP cc_start: 0.7663 (m-30) cc_final: 0.7233 (m-30) REVERT: A 806 LEU cc_start: 0.9204 (tp) cc_final: 0.8958 (tp) REVERT: A 813 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8204 (mt-10) REVERT: A 835 THR cc_start: 0.9458 (m) cc_final: 0.9221 (t) REVERT: A 844 LYS cc_start: 0.9324 (mmmt) cc_final: 0.9118 (mmmt) REVERT: A 857 THR cc_start: 0.9578 (m) cc_final: 0.9333 (p) REVERT: A 909 ILE cc_start: 0.8676 (mm) cc_final: 0.8370 (mm) REVERT: A 975 LEU cc_start: 0.8648 (mt) cc_final: 0.8284 (mt) REVERT: A 1065 MET cc_start: 0.8887 (mmm) cc_final: 0.8661 (mmm) REVERT: A 1104 LYS cc_start: 0.8886 (tttt) cc_final: 0.8597 (ttpt) REVERT: A 1107 LEU cc_start: 0.9519 (mt) cc_final: 0.9048 (mt) REVERT: A 1112 ASN cc_start: 0.8579 (p0) cc_final: 0.8055 (p0) REVERT: A 1193 TRP cc_start: 0.8161 (m100) cc_final: 0.7321 (m100) REVERT: A 1211 MET cc_start: 0.7950 (mmm) cc_final: 0.7698 (mmp) REVERT: A 1226 LEU cc_start: 0.8421 (mt) cc_final: 0.8217 (tt) REVERT: A 1242 CYS cc_start: 0.7955 (t) cc_final: 0.6317 (t) REVERT: A 1274 ILE cc_start: 0.7808 (mm) cc_final: 0.6245 (mm) REVERT: A 1309 LEU cc_start: 0.9063 (mt) cc_final: 0.8774 (mt) REVERT: A 1316 LEU cc_start: 0.9125 (tp) cc_final: 0.8783 (tp) REVERT: A 1368 TYR cc_start: 0.8659 (t80) cc_final: 0.8037 (t80) REVERT: A 1403 CYS cc_start: 0.9030 (p) cc_final: 0.8788 (p) REVERT: A 1429 GLU cc_start: 0.7913 (mp0) cc_final: 0.7469 (mt-10) REVERT: A 1432 MET cc_start: 0.8120 (ptp) cc_final: 0.7639 (ptp) REVERT: A 1435 GLN cc_start: 0.8036 (mt0) cc_final: 0.7691 (mt0) REVERT: A 1450 GLU cc_start: 0.7929 (pm20) cc_final: 0.7683 (pm20) REVERT: B 14 THR cc_start: 0.9373 (m) cc_final: 0.9141 (p) REVERT: B 16 ASP cc_start: 0.9136 (m-30) cc_final: 0.8802 (m-30) REVERT: B 35 LEU cc_start: 0.9281 (mt) cc_final: 0.9079 (mt) REVERT: B 161 VAL cc_start: 0.9382 (t) cc_final: 0.9169 (p) REVERT: B 164 MET cc_start: 0.8794 (ttm) cc_final: 0.8166 (ttp) REVERT: B 177 GLU cc_start: 0.7778 (tp30) cc_final: 0.7474 (tp30) REVERT: B 184 LYS cc_start: 0.9216 (mmtp) cc_final: 0.8878 (mmtp) REVERT: B 199 SER cc_start: 0.8985 (t) cc_final: 0.8755 (p) REVERT: B 214 VAL cc_start: 0.9570 (t) cc_final: 0.9115 (p) REVERT: B 242 ILE cc_start: 0.9411 (mm) cc_final: 0.9163 (mt) REVERT: B 267 TYR cc_start: 0.7404 (m-80) cc_final: 0.7065 (m-10) REVERT: B 289 ILE cc_start: 0.9345 (mt) cc_final: 0.9087 (mt) REVERT: B 302 MET cc_start: 0.8758 (ptm) cc_final: 0.8557 (ptm) REVERT: B 307 LYS cc_start: 0.9431 (mmmm) cc_final: 0.8856 (mmtp) REVERT: B 318 ASP cc_start: 0.8254 (t0) cc_final: 0.7815 (t70) REVERT: B 320 GLU cc_start: 0.8751 (mp0) cc_final: 0.8517 (mp0) REVERT: B 347 ASP cc_start: 0.8387 (t0) cc_final: 0.7715 (t0) REVERT: B 348 ILE cc_start: 0.9209 (tt) cc_final: 0.8832 (tt) REVERT: B 459 TRP cc_start: 0.9069 (t-100) cc_final: 0.8693 (t-100) REVERT: B 473 SER cc_start: 0.9534 (t) cc_final: 0.9260 (p) REVERT: B 506 GLN cc_start: 0.8138 (mt0) cc_final: 0.7809 (mt0) REVERT: B 510 THR cc_start: 0.9617 (p) cc_final: 0.9373 (p) REVERT: B 536 SER cc_start: 0.9065 (m) cc_final: 0.8831 (m) REVERT: B 549 ASN cc_start: 0.9038 (m-40) cc_final: 0.8399 (m-40) REVERT: B 611 ASP cc_start: 0.8432 (t0) cc_final: 0.8078 (t0) REVERT: B 612 ILE cc_start: 0.8681 (mt) cc_final: 0.8449 (mt) REVERT: B 614 GLU cc_start: 0.7587 (mp0) cc_final: 0.7365 (mp0) REVERT: B 688 GLU cc_start: 0.8501 (pt0) cc_final: 0.8219 (pt0) REVERT: B 694 GLU cc_start: 0.8405 (tt0) cc_final: 0.8127 (tt0) REVERT: B 838 SER cc_start: 0.9040 (m) cc_final: 0.8607 (p) REVERT: B 841 MET cc_start: 0.8616 (ttm) cc_final: 0.8301 (ttm) REVERT: B 846 ILE cc_start: 0.9009 (mt) cc_final: 0.8331 (mt) REVERT: B 857 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.7826 (ttm-80) REVERT: B 883 LEU cc_start: 0.8865 (pt) cc_final: 0.8498 (pt) REVERT: B 904 ARG cc_start: 0.7910 (tmt-80) cc_final: 0.7513 (ttt-90) REVERT: B 942 ARG cc_start: 0.8645 (mtp85) cc_final: 0.8330 (mmm-85) REVERT: B 950 ASP cc_start: 0.7410 (t70) cc_final: 0.7115 (t70) REVERT: B 987 LYS cc_start: 0.9066 (pttt) cc_final: 0.8439 (ptpp) REVERT: B 1019 SER cc_start: 0.9560 (p) cc_final: 0.9300 (m) REVERT: B 1030 LEU cc_start: 0.9519 (tp) cc_final: 0.9148 (tt) REVERT: B 1108 ARG cc_start: 0.8237 (mtm-85) cc_final: 0.7907 (mtm180) REVERT: B 1137 CYS cc_start: 0.8446 (m) cc_final: 0.8202 (m) REVERT: B 1139 ILE cc_start: 0.9366 (mt) cc_final: 0.9145 (mt) REVERT: B 1181 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6930 (tm-30) REVERT: B 1211 ASN cc_start: 0.8855 (m-40) cc_final: 0.8611 (m-40) REVERT: C 16 GLU cc_start: 0.7630 (pt0) cc_final: 0.7385 (pt0) REVERT: C 32 LEU cc_start: 0.9534 (tp) cc_final: 0.8694 (tp) REVERT: C 48 VAL cc_start: 0.9339 (t) cc_final: 0.9093 (m) REVERT: C 100 LEU cc_start: 0.9062 (tt) cc_final: 0.8858 (tt) REVERT: C 112 ASP cc_start: 0.8200 (m-30) cc_final: 0.7802 (m-30) REVERT: C 146 LYS cc_start: 0.9090 (mttt) cc_final: 0.8812 (mtpp) REVERT: C 147 LEU cc_start: 0.9369 (mt) cc_final: 0.8939 (mt) REVERT: D 67 ARG cc_start: 0.9049 (ttm170) cc_final: 0.8465 (mmp80) REVERT: D 86 ASP cc_start: 0.7536 (m-30) cc_final: 0.6940 (t0) REVERT: D 88 GLU cc_start: 0.7968 (tt0) cc_final: 0.7757 (pp20) REVERT: D 108 TYR cc_start: 0.7339 (t80) cc_final: 0.6918 (t80) REVERT: D 119 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8772 (tp30) REVERT: D 125 ASP cc_start: 0.8383 (t0) cc_final: 0.8083 (m-30) REVERT: D 140 PHE cc_start: 0.8620 (t80) cc_final: 0.8225 (t80) REVERT: D 151 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6423 (pm20) REVERT: D 163 LEU cc_start: 0.7824 (mt) cc_final: 0.7617 (pp) REVERT: E 17 THR cc_start: 0.9489 (m) cc_final: 0.9052 (p) REVERT: E 21 MET cc_start: 0.8885 (ttm) cc_final: 0.8403 (tmm) REVERT: E 54 ARG cc_start: 0.8399 (mmt90) cc_final: 0.8110 (mtm-85) REVERT: E 55 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8147 (mmmt) REVERT: E 111 TYR cc_start: 0.8523 (p90) cc_final: 0.8057 (p90) REVERT: E 120 ASN cc_start: 0.9395 (m-40) cc_final: 0.8906 (m110) REVERT: E 122 MET cc_start: 0.6336 (ptm) cc_final: 0.5756 (ptm) REVERT: E 132 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7222 (mt-10) REVERT: E 151 LYS cc_start: 0.9011 (tptp) cc_final: 0.8753 (tppt) REVERT: E 172 SER cc_start: 0.9406 (p) cc_final: 0.8908 (t) REVERT: E 181 ASP cc_start: 0.8771 (t70) cc_final: 0.8184 (t0) REVERT: E 196 LYS cc_start: 0.9274 (tttt) cc_final: 0.9012 (tttp) REVERT: F 100 GLN cc_start: 0.8960 (mt0) cc_final: 0.8679 (mt0) REVERT: G 2 PHE cc_start: 0.8856 (m-80) cc_final: 0.8433 (m-80) REVERT: G 3 PHE cc_start: 0.8645 (m-80) cc_final: 0.7399 (m-80) REVERT: G 4 LEU cc_start: 0.8377 (mt) cc_final: 0.7855 (tp) REVERT: G 61 ILE cc_start: 0.9612 (mm) cc_final: 0.9370 (mm) REVERT: G 73 LYS cc_start: 0.8981 (mttt) cc_final: 0.8566 (tptt) REVERT: G 86 VAL cc_start: 0.8809 (t) cc_final: 0.8533 (m) REVERT: G 125 ASN cc_start: 0.6299 (t0) cc_final: 0.5930 (t0) REVERT: G 150 THR cc_start: 0.8802 (p) cc_final: 0.8548 (t) REVERT: H 52 ASP cc_start: 0.7935 (m-30) cc_final: 0.7659 (t0) REVERT: H 56 THR cc_start: 0.8978 (m) cc_final: 0.8666 (p) REVERT: I 12 ASN cc_start: 0.9075 (m110) cc_final: 0.8392 (m110) REVERT: I 90 GLN cc_start: 0.7887 (tp-100) cc_final: 0.7596 (pt0) REVERT: I 95 THR cc_start: 0.5760 (m) cc_final: 0.5246 (t) REVERT: I 99 LEU cc_start: 0.8194 (mt) cc_final: 0.7989 (mt) REVERT: I 101 TYR cc_start: 0.7180 (m-80) cc_final: 0.6912 (m-80) REVERT: I 108 LYS cc_start: 0.5523 (tttp) cc_final: 0.5126 (mtpp) REVERT: J 16 ASP cc_start: 0.7919 (p0) cc_final: 0.7479 (p0) REVERT: J 48 MET cc_start: 0.9411 (mmm) cc_final: 0.8796 (tpp) REVERT: K 36 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8458 (mm-30) REVERT: K 45 LEU cc_start: 0.9194 (tp) cc_final: 0.8938 (tp) REVERT: L 30 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8221 (mttt) REVERT: L 52 GLU cc_start: 0.8177 (pt0) cc_final: 0.7544 (pt0) REVERT: M 69 ILE cc_start: 0.8313 (mp) cc_final: 0.8056 (mp) REVERT: M 70 TYR cc_start: 0.8513 (t80) cc_final: 0.8101 (t80) REVERT: V 18 VAL cc_start: 0.8796 (t) cc_final: 0.8525 (t) REVERT: V 19 LEU cc_start: 0.8752 (mt) cc_final: 0.8501 (tp) REVERT: V 33 ASP cc_start: 0.7084 (t70) cc_final: 0.6847 (p0) REVERT: V 49 CYS cc_start: 0.6562 (m) cc_final: 0.6210 (p) REVERT: V 103 VAL cc_start: 0.6228 (t) cc_final: 0.5782 (p) REVERT: W 222 ASP cc_start: 0.8342 (m-30) cc_final: 0.7562 (p0) REVERT: W 226 ILE cc_start: 0.8440 (mt) cc_final: 0.7960 (mt) REVERT: W 230 LYS cc_start: 0.8564 (mmtm) cc_final: 0.8277 (tttt) REVERT: W 282 ILE cc_start: 0.7595 (mm) cc_final: 0.7346 (mm) REVERT: W 292 VAL cc_start: 0.8368 (t) cc_final: 0.8010 (p) REVERT: W 300 LEU cc_start: 0.9373 (mt) cc_final: 0.8961 (mt) REVERT: W 301 VAL cc_start: 0.8328 (t) cc_final: 0.8052 (t) REVERT: W 308 ASP cc_start: 0.8956 (m-30) cc_final: 0.8496 (m-30) REVERT: W 360 TYR cc_start: 0.5369 (m-80) cc_final: 0.3785 (m-10) REVERT: W 568 GLN cc_start: 0.5683 (mt0) cc_final: 0.5183 (pt0) REVERT: W 574 ILE cc_start: 0.7984 (mt) cc_final: 0.7168 (mt) REVERT: W 620 PHE cc_start: 0.8230 (m-80) cc_final: 0.7834 (m-80) REVERT: W 679 VAL cc_start: 0.7458 (t) cc_final: 0.6774 (t) REVERT: W 680 TYR cc_start: 0.8817 (t80) cc_final: 0.8495 (t80) REVERT: W 681 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7812 (mtt180) REVERT: W 682 ASN cc_start: 0.8336 (m-40) cc_final: 0.7913 (t0) REVERT: W 683 PHE cc_start: 0.8865 (m-80) cc_final: 0.8661 (m-10) REVERT: W 749 ASP cc_start: 0.3937 (m-30) cc_final: 0.3704 (m-30) REVERT: W 791 ILE cc_start: 0.8768 (tt) cc_final: 0.8562 (tt) REVERT: W 804 TRP cc_start: 0.7917 (m100) cc_final: 0.6822 (m100) REVERT: m 293 MET cc_start: 0.7109 (mmt) cc_final: 0.6554 (ttp) REVERT: m 298 ASP cc_start: 0.7276 (m-30) cc_final: 0.5174 (m-30) REVERT: m 344 ASP cc_start: 0.8771 (m-30) cc_final: 0.8515 (m-30) REVERT: m 361 GLU cc_start: 0.8632 (mp0) cc_final: 0.7932 (tp30) REVERT: m 381 VAL cc_start: 0.8176 (t) cc_final: 0.7975 (t) REVERT: m 415 TRP cc_start: 0.8100 (m100) cc_final: 0.7824 (m100) REVERT: m 462 GLU cc_start: 0.6389 (mt-10) cc_final: 0.5992 (mt-10) REVERT: m 511 MET cc_start: 0.2448 (tmm) cc_final: 0.2032 (ttm) REVERT: m 726 SER cc_start: 0.8508 (t) cc_final: 0.6967 (p) REVERT: m 727 ILE cc_start: 0.9091 (mt) cc_final: 0.8694 (pt) REVERT: m 730 ASP cc_start: 0.8939 (m-30) cc_final: 0.8710 (t0) REVERT: m 841 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8187 (mt-10) REVERT: m 884 TYR cc_start: 0.8222 (t80) cc_final: 0.8008 (t80) REVERT: m 918 TYR cc_start: 0.8919 (m-80) cc_final: 0.7842 (m-10) REVERT: m 978 CYS cc_start: 0.5999 (p) cc_final: 0.5641 (p) REVERT: m 1000 VAL cc_start: 0.6469 (t) cc_final: 0.6140 (t) REVERT: m 1005 LEU cc_start: 0.8908 (mt) cc_final: 0.8633 (mt) REVERT: m 1038 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7369 (pm20) REVERT: m 1173 ARG cc_start: 0.7376 (ttt180) cc_final: 0.6629 (ptt-90) REVERT: m 1232 LEU cc_start: 0.8160 (mt) cc_final: 0.7906 (mt) REVERT: n 259 VAL cc_start: 0.7973 (t) cc_final: 0.7269 (m) REVERT: n 260 MET cc_start: 0.8917 (mmt) cc_final: 0.8705 (ttm) REVERT: n 263 TYR cc_start: 0.9060 (m-80) cc_final: 0.8756 (m-80) REVERT: n 284 TRP cc_start: 0.8105 (m-10) cc_final: 0.6577 (m-10) REVERT: q 114 MET cc_start: 0.0661 (mmm) cc_final: 0.0369 (mtp) REVERT: q 232 LEU cc_start: 0.6786 (mt) cc_final: 0.6391 (mp) REVERT: q 464 TYR cc_start: 0.4068 (m-10) cc_final: 0.3857 (m-80) REVERT: q 678 TYR cc_start: 0.7950 (m-80) cc_final: 0.7542 (m-80) REVERT: q 713 PHE cc_start: 0.8640 (m-80) cc_final: 0.8388 (m-80) REVERT: q 716 LEU cc_start: 0.9505 (mt) cc_final: 0.9303 (mt) REVERT: q 720 PHE cc_start: 0.8923 (m-80) cc_final: 0.8458 (m-10) REVERT: q 766 MET cc_start: 0.8784 (tpt) cc_final: 0.8330 (tpp) REVERT: q 769 TYR cc_start: 0.7883 (m-80) cc_final: 0.7354 (m-10) REVERT: q 793 VAL cc_start: 0.8442 (t) cc_final: 0.7700 (t) REVERT: q 897 GLU cc_start: 0.9210 (tt0) cc_final: 0.9003 (mm-30) REVERT: q 928 MET cc_start: 0.7513 (mtt) cc_final: 0.7241 (tpp) REVERT: r 214 TYR cc_start: 0.8257 (m-80) cc_final: 0.7866 (m-80) REVERT: r 286 LEU cc_start: 0.7013 (mp) cc_final: 0.6781 (tt) REVERT: r 386 GLU cc_start: 0.8787 (tt0) cc_final: 0.8487 (mt-10) REVERT: u 136 LYS cc_start: 0.4214 (mttt) cc_final: 0.3501 (mmmt) REVERT: u 171 ILE cc_start: 0.5652 (mm) cc_final: 0.5446 (mt) REVERT: u 187 PHE cc_start: 0.6119 (m-80) cc_final: 0.5895 (m-10) REVERT: u 188 ASP cc_start: 0.7273 (m-30) cc_final: 0.6771 (p0) REVERT: v 249 THR cc_start: 0.6707 (p) cc_final: 0.6276 (t) REVERT: x 139 LEU cc_start: 0.5261 (mt) cc_final: 0.4906 (pp) REVERT: x 226 LYS cc_start: 0.8620 (tttt) cc_final: 0.8306 (ttmt) REVERT: x 230 GLN cc_start: 0.8764 (tt0) cc_final: 0.7942 (tt0) REVERT: x 231 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8434 (mt-10) REVERT: x 251 GLN cc_start: 0.7654 (mm110) cc_final: 0.7206 (mm-40) REVERT: x 271 LYS cc_start: 0.7376 (mttt) cc_final: 0.6997 (ptmm) REVERT: x 272 LEU cc_start: 0.8110 (mm) cc_final: 0.7150 (mm) REVERT: x 273 PHE cc_start: 0.8720 (m-80) cc_final: 0.8091 (m-80) REVERT: x 274 THR cc_start: 0.8016 (p) cc_final: 0.7671 (t) REVERT: x 296 ASN cc_start: 0.8091 (m-40) cc_final: 0.7550 (m-40) REVERT: x 301 ASP cc_start: 0.8002 (t70) cc_final: 0.7637 (p0) REVERT: x 316 TYR cc_start: 0.6308 (m-80) cc_final: 0.5731 (m-80) REVERT: x 328 TRP cc_start: 0.7422 (m-10) cc_final: 0.7098 (m-10) REVERT: x 330 VAL cc_start: 0.8514 (m) cc_final: 0.8157 (t) REVERT: x 336 ASP cc_start: 0.7881 (t0) cc_final: 0.5648 (t0) REVERT: j 717 HIS cc_start: 0.4821 (m-70) cc_final: 0.4595 (m-70) REVERT: j 791 LEU cc_start: 0.5032 (mt) cc_final: 0.4557 (mt) REVERT: j 888 THR cc_start: 0.3185 (OUTLIER) cc_final: 0.2894 (t) REVERT: k 268 LEU cc_start: 0.2072 (mt) cc_final: 0.0890 (pp) REVERT: k 369 LEU cc_start: 0.3360 (tp) cc_final: 0.2843 (tp) REVERT: k 388 LYS cc_start: -0.0295 (OUTLIER) cc_final: -0.1189 (ptmt) outliers start: 10 outliers final: 1 residues processed: 3048 average time/residue: 0.8326 time to fit residues: 4234.1961 Evaluate side-chains 2056 residues out of total 8321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 2053 time to evaluate : 6.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 459 ILE Chi-restraints excluded: chain j residue 888 THR Chi-restraints excluded: chain k residue 388 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 790 optimal weight: 1.9990 chunk 709 optimal weight: 50.0000 chunk 393 optimal weight: 6.9990 chunk 242 optimal weight: 4.9990 chunk 478 optimal weight: 20.0000 chunk 379 optimal weight: 4.9990 chunk 733 optimal weight: 2.9990 chunk 283 optimal weight: 4.9990 chunk 446 optimal weight: 6.9990 chunk 546 optimal weight: 9.9990 chunk 849 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 102 GLN B 474 GLN B 761 HIS ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 GLN ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1190 ASN C 25 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN H 44 ASN I 11 ASN I 46 HIS I 87 GLN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN V 100 GLN ** W 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 451 GLN W 502 ASN W 644 ASN ** W 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 235 GLN m 386 ASN m 425 HIS m 554 GLN ** m 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m1271 GLN ** m1407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 161 GLN n 210 ASN n 234 GLN n 272 ASN q 132 ASN q 147 ASN ** q 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 294 HIS ** q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 921 GLN r 232 ASN ** r 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 325 GLN u 172 GLN v 187 HIS v 212 HIS v 244 ASN ** x 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 310 ASN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 869 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.219334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140095 restraints weight = 186954.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.140099 restraints weight = 89415.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.142182 restraints weight = 60873.889| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 80469 Z= 0.312 Angle : 0.652 15.000 109373 Z= 0.346 Chirality : 0.044 0.266 12167 Planarity : 0.005 0.107 13560 Dihedral : 13.335 131.150 12260 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.52 % Favored : 97.45 % Rotamer: Outliers : 2.53 % Allowed : 11.27 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % Cis-general : 0.00 % 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: 1.19 (0.09), residues: 9224 helix: 1.81 (0.08), residues: 4005 sheet: 0.26 (0.14), residues: 1350 loop : -0.01 (0.10), residues: 3869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP q 338 HIS 0.008 0.001 HIS A 288 PHE 0.026 0.002 PHE j 526 TYR 0.021 0.002 TYR m 530 ARG 0.015 0.001 ARG G 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18448 Ramachandran restraints generated. 9224 Oldfield, 0 Emsley, 9224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18448 Ramachandran restraints generated. 9224 Oldfield, 0 Emsley, 9224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2311 residues out of total 8321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 2101 time to evaluate : 6.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7835 (tpt) cc_final: 0.7334 (tpp) REVERT: A 104 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8458 (mt-10) REVERT: A 128 ILE cc_start: 0.8916 (pt) cc_final: 0.8604 (tt) REVERT: A 228 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8472 (t0) REVERT: A 253 MET cc_start: 0.5781 (tmm) cc_final: 0.5465 (tmm) REVERT: A 306 ASP cc_start: 0.8882 (t0) cc_final: 0.8408 (t0) REVERT: A 318 LYS cc_start: 0.8393 (mttm) cc_final: 0.8036 (mtpt) REVERT: A 363 ASP cc_start: 0.8847 (p0) cc_final: 0.8559 (p0) REVERT: A 405 TYR cc_start: 0.9117 (m-80) cc_final: 0.8858 (m-10) REVERT: A 438 MET cc_start: 0.7812 (mmt) cc_final: 0.7554 (mmm) REVERT: A 441 ASP cc_start: 0.8688 (m-30) cc_final: 0.8411 (m-30) REVERT: A 453 LYS cc_start: 0.9383 (pttt) cc_final: 0.9166 (pttt) REVERT: A 455 SER cc_start: 0.9568 (m) cc_final: 0.9315 (t) REVERT: A 495 SER cc_start: 0.9240 (t) cc_final: 0.8857 (p) REVERT: A 539 ASP cc_start: 0.8762 (p0) cc_final: 0.8477 (p0) REVERT: A 540 THR cc_start: 0.9770 (m) cc_final: 0.9405 (p) REVERT: A 558 ASP cc_start: 0.8672 (p0) cc_final: 0.8281 (p0) REVERT: A 593 ASP cc_start: 0.8185 (m-30) cc_final: 0.7963 (m-30) REVERT: A 610 ASP cc_start: 0.8751 (t0) cc_final: 0.8438 (t70) REVERT: A 637 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7820 (mm-30) REVERT: A 660 HIS cc_start: 0.8758 (m-70) cc_final: 0.8332 (m-70) REVERT: A 738 LEU cc_start: 0.9013 (mt) cc_final: 0.8785 (mt) REVERT: A 747 MET cc_start: 0.9364 (mtm) cc_final: 0.8881 (mtm) REVERT: A 813 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8033 (mt-10) REVERT: A 844 LYS cc_start: 0.9446 (mmmt) cc_final: 0.9167 (mmmt) REVERT: A 880 GLU cc_start: 0.8168 (mp0) cc_final: 0.7940 (mp0) REVERT: A 940 ASP cc_start: 0.8152 (m-30) cc_final: 0.7818 (m-30) REVERT: A 964 ARG cc_start: 0.8849 (ttm110) cc_final: 0.8437 (ttm170) REVERT: A 987 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7708 (mt-10) REVERT: A 1222 PHE cc_start: 0.7716 (m-10) cc_final: 0.6959 (m-80) REVERT: A 1242 CYS cc_start: 0.8349 (t) cc_final: 0.6401 (t) REVERT: A 1316 LEU cc_start: 0.9170 (tp) cc_final: 0.8943 (tp) REVERT: A 1381 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7219 (mtm-85) REVERT: A 1403 CYS cc_start: 0.9315 (p) cc_final: 0.9005 (p) REVERT: A 1429 GLU cc_start: 0.8017 (mp0) cc_final: 0.7581 (mt-10) REVERT: B 177 GLU cc_start: 0.7820 (tp30) cc_final: 0.7543 (tp30) REVERT: B 214 VAL cc_start: 0.9408 (t) cc_final: 0.9184 (p) REVERT: B 259 ARG cc_start: 0.5810 (mmt180) cc_final: 0.5549 (mmt180) REVERT: B 267 TYR cc_start: 0.7728 (m-80) cc_final: 0.7342 (m-10) REVERT: B 289 ILE cc_start: 0.9273 (mt) cc_final: 0.9057 (mm) REVERT: B 307 LYS cc_start: 0.9367 (mmmm) cc_final: 0.9043 (mptt) REVERT: B 323 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9071 (mp) REVERT: B 363 PHE cc_start: 0.8089 (t80) cc_final: 0.7769 (t80) REVERT: B 396 LYS cc_start: 0.9240 (mptt) cc_final: 0.8934 (mmtm) REVERT: B 479 TYR cc_start: 0.8086 (t80) cc_final: 0.7662 (t80) REVERT: B 506 GLN cc_start: 0.8210 (mt0) cc_final: 0.7840 (mt0) REVERT: B 533 SER cc_start: 0.9047 (OUTLIER) cc_final: 0.8473 (p) REVERT: B 536 SER cc_start: 0.9242 (m) cc_final: 0.8935 (m) REVERT: B 549 ASN cc_start: 0.9113 (m-40) cc_final: 0.8855 (m-40) REVERT: B 585 ASP cc_start: 0.8732 (t0) cc_final: 0.8520 (t70) REVERT: B 611 ASP cc_start: 0.8578 (t0) cc_final: 0.8026 (t0) REVERT: B 612 ILE cc_start: 0.8818 (mt) cc_final: 0.8509 (tp) REVERT: B 693 GLU cc_start: 0.8217 (mm-30) cc_final: 0.8000 (mm-30) REVERT: B 699 MET cc_start: 0.8635 (tpt) cc_final: 0.8075 (tpt) REVERT: B 742 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8042 (mm-30) REVERT: B 810 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7420 (mm-30) REVERT: B 835 GLN cc_start: 0.7757 (mt0) cc_final: 0.7512 (mt0) REVERT: B 841 MET cc_start: 0.8240 (ttm) cc_final: 0.8013 (ttm) REVERT: B 846 ILE cc_start: 0.9521 (mt) cc_final: 0.9186 (mt) REVERT: B 857 ARG cc_start: 0.8922 (ttm-80) cc_final: 0.8194 (ttm-80) REVERT: B 904 ARG cc_start: 0.7814 (tmt-80) cc_final: 0.7594 (ttt-90) REVERT: B 909 ASP cc_start: 0.7997 (m-30) cc_final: 0.7782 (m-30) REVERT: B 950 ASP cc_start: 0.7581 (t70) cc_final: 0.7349 (t70) REVERT: B 995 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.8199 (mtm-85) REVERT: B 1019 SER cc_start: 0.9675 (p) cc_final: 0.9331 (m) REVERT: B 1070 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7941 (mt-10) REVERT: B 1108 ARG cc_start: 0.8326 (mtm-85) cc_final: 0.7918 (mtm-85) REVERT: B 1133 MET cc_start: 0.8838 (mtp) cc_final: 0.8486 (mtm) REVERT: B 1137 CYS cc_start: 0.8807 (m) cc_final: 0.8327 (m) REVERT: B 1219 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: C 42 THR cc_start: 0.9375 (p) cc_final: 0.9166 (t) REVERT: C 43 LEU cc_start: 0.9116 (tp) cc_final: 0.8586 (tp) REVERT: C 100 LEU cc_start: 0.9138 (tt) cc_final: 0.8932 (tt) REVERT: C 112 ASP cc_start: 0.8683 (m-30) cc_final: 0.8139 (m-30) REVERT: C 165 LYS cc_start: 0.9191 (mttt) cc_final: 0.8804 (mttt) REVERT: D 29 ARG cc_start: 0.7092 (mtm-85) cc_final: 0.6672 (mtm-85) REVERT: D 47 ASP cc_start: 0.7746 (m-30) cc_final: 0.7389 (p0) REVERT: D 88 GLU cc_start: 0.8018 (tt0) cc_final: 0.7467 (pp20) REVERT: D 108 TYR cc_start: 0.7537 (t80) cc_final: 0.7026 (t80) REVERT: D 125 ASP cc_start: 0.8638 (t0) cc_final: 0.8060 (m-30) REVERT: E 17 THR cc_start: 0.9538 (m) cc_final: 0.9096 (p) REVERT: E 77 LEU cc_start: 0.9338 (tp) cc_final: 0.9120 (tp) REVERT: E 83 ASP cc_start: 0.8157 (p0) cc_final: 0.7937 (p0) REVERT: E 120 ASN cc_start: 0.9221 (m-40) cc_final: 0.8771 (m110) REVERT: E 132 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7621 (mt-10) REVERT: E 185 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.7796 (mtm-85) REVERT: G 3 PHE cc_start: 0.8901 (m-80) cc_final: 0.8538 (m-80) REVERT: G 4 LEU cc_start: 0.8826 (mt) cc_final: 0.8284 (tp) REVERT: G 22 MET cc_start: 0.8624 (ttp) cc_final: 0.8419 (ttm) REVERT: G 65 SER cc_start: 0.9278 (p) cc_final: 0.8783 (t) REVERT: G 73 LYS cc_start: 0.9053 (mttt) cc_final: 0.8409 (tptt) REVERT: G 113 ARG cc_start: 0.7422 (mtm-85) cc_final: 0.7065 (mtm-85) REVERT: H 29 ILE cc_start: 0.9252 (pt) cc_final: 0.8873 (mm) REVERT: H 41 ASP cc_start: 0.8806 (m-30) cc_final: 0.8193 (m-30) REVERT: H 53 ASP cc_start: 0.8178 (m-30) cc_final: 0.7908 (m-30) REVERT: I 11 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.7868 (t0) REVERT: I 12 ASN cc_start: 0.9213 (m110) cc_final: 0.8692 (m-40) REVERT: I 30 ARG cc_start: 0.8334 (tpp80) cc_final: 0.8082 (tpp80) REVERT: I 36 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8568 (mm-30) REVERT: I 101 TYR cc_start: 0.7210 (m-80) cc_final: 0.6855 (m-80) REVERT: I 108 LYS cc_start: 0.5440 (tttp) cc_final: 0.5051 (mtpp) REVERT: J 16 ASP cc_start: 0.8093 (p0) cc_final: 0.7698 (p0) REVERT: J 26 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7812 (tm-30) REVERT: J 30 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8392 (tm-30) REVERT: J 48 MET cc_start: 0.9574 (mmm) cc_final: 0.9356 (tpp) REVERT: K 36 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8595 (mm-30) REVERT: K 47 ARG cc_start: 0.9480 (ttp80) cc_final: 0.9211 (tmm-80) REVERT: L 30 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8371 (mttt) REVERT: M 46 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7306 (tt) REVERT: M 47 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.6712 (pp) REVERT: M 70 TYR cc_start: 0.8224 (t80) cc_final: 0.8007 (t80) REVERT: V 49 CYS cc_start: 0.7269 (m) cc_final: 0.6842 (p) REVERT: W 222 ASP cc_start: 0.7711 (m-30) cc_final: 0.7039 (p0) REVERT: W 233 LEU cc_start: 0.9159 (mt) cc_final: 0.8614 (tp) REVERT: W 284 ASP cc_start: 0.7838 (t0) cc_final: 0.7606 (t0) REVERT: W 620 PHE cc_start: 0.8479 (m-80) cc_final: 0.8201 (m-80) REVERT: W 682 ASN cc_start: 0.8363 (m-40) cc_final: 0.7810 (t0) REVERT: W 683 PHE cc_start: 0.8995 (m-80) cc_final: 0.8669 (m-10) REVERT: W 779 ARG cc_start: 0.8582 (mmm-85) cc_final: 0.7818 (mtp85) REVERT: W 782 LEU cc_start: 0.8730 (mt) cc_final: 0.7752 (mt) REVERT: m 257 MET cc_start: 0.3614 (mpp) cc_final: 0.3322 (mpp) REVERT: m 290 LYS cc_start: 0.6781 (mptt) cc_final: 0.6554 (mptt) REVERT: m 344 ASP cc_start: 0.8412 (m-30) cc_final: 0.7981 (m-30) REVERT: m 347 GLN cc_start: 0.8232 (pt0) cc_final: 0.7845 (tm-30) REVERT: m 361 GLU cc_start: 0.8441 (mp0) cc_final: 0.7886 (tp30) REVERT: m 511 MET cc_start: 0.2811 (tmm) cc_final: 0.2294 (ttm) REVERT: m 620 GLU cc_start: 0.9435 (mt-10) cc_final: 0.9014 (mp0) REVERT: m 627 LEU cc_start: 0.7725 (mp) cc_final: 0.7487 (mt) REVERT: m 728 ARG cc_start: 0.9143 (tmm-80) cc_final: 0.8800 (tmm-80) REVERT: m 729 ARG cc_start: 0.8905 (mtm110) cc_final: 0.8619 (ptp-110) REVERT: m 784 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8089 (tmm) REVERT: m 882 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.8100 (mtm110) REVERT: m 943 ILE cc_start: 0.8800 (mm) cc_final: 0.8357 (mm) REVERT: m 955 ASN cc_start: 0.7656 (m-40) cc_final: 0.7435 (m110) REVERT: m 956 LEU cc_start: 0.8869 (tp) cc_final: 0.8560 (tt) REVERT: m 1019 MET cc_start: 0.7118 (ppp) cc_final: 0.6917 (ppp) REVERT: m 1046 ARG cc_start: 0.6551 (mtt90) cc_final: 0.5969 (mtt90) REVERT: n 167 MET cc_start: 0.8888 (ttt) cc_final: 0.8633 (ptm) REVERT: n 275 ARG cc_start: 0.9019 (mtt180) cc_final: 0.8759 (mtt180) REVERT: n 280 LEU cc_start: 0.9526 (mt) cc_final: 0.9286 (mt) REVERT: n 284 TRP cc_start: 0.7927 (m-10) cc_final: 0.7347 (m-90) REVERT: n 286 ARG cc_start: 0.7949 (tmt170) cc_final: 0.7599 (tpt170) REVERT: q 114 MET cc_start: 0.0616 (mmm) cc_final: 0.0358 (mtp) REVERT: q 293 LYS cc_start: 0.4427 (tmtt) cc_final: 0.2986 (ptpp) REVERT: q 406 MET cc_start: 0.1315 (OUTLIER) cc_final: 0.0896 (mmt) REVERT: q 553 TYR cc_start: 0.2521 (t80) cc_final: 0.2279 (t80) REVERT: q 678 TYR cc_start: 0.8014 (m-80) cc_final: 0.7585 (m-80) REVERT: q 700 PHE cc_start: 0.8708 (m-10) cc_final: 0.8464 (m-10) REVERT: q 714 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8522 (tp) REVERT: q 725 GLN cc_start: 0.8698 (mt0) cc_final: 0.8403 (mt0) REVERT: q 726 PHE cc_start: 0.8284 (m-80) cc_final: 0.7897 (m-10) REVERT: q 769 TYR cc_start: 0.7859 (m-80) cc_final: 0.7504 (m-10) REVERT: q 789 ARG cc_start: 0.6696 (ttm170) cc_final: 0.6377 (ttm170) REVERT: q 873 MET cc_start: 0.8587 (mmt) cc_final: 0.8378 (mmt) REVERT: q 928 MET cc_start: 0.7596 (mtt) cc_final: 0.7157 (tpp) REVERT: r 214 TYR cc_start: 0.8198 (m-80) cc_final: 0.7543 (m-80) REVERT: r 219 GLU cc_start: 0.5053 (OUTLIER) cc_final: 0.4704 (pm20) REVERT: r 282 MET cc_start: 0.5442 (ptp) cc_final: 0.4711 (pmm) REVERT: r 345 MET cc_start: 0.7771 (tpp) cc_final: 0.7476 (tpp) REVERT: r 386 GLU cc_start: 0.8785 (tt0) cc_final: 0.8505 (mt-10) REVERT: u 113 PHE cc_start: 0.8676 (p90) cc_final: 0.8432 (p90) REVERT: u 171 ILE cc_start: 0.6065 (mm) cc_final: 0.5851 (mt) REVERT: u 185 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7013 (mp0) REVERT: u 188 ASP cc_start: 0.7882 (m-30) cc_final: 0.6896 (p0) REVERT: u 209 LEU cc_start: 0.8919 (mt) cc_final: 0.8714 (mt) REVERT: u 210 MET cc_start: 0.3189 (tpt) cc_final: 0.2546 (tpt) REVERT: u 258 GLU cc_start: 0.8504 (mp0) cc_final: 0.8148 (mp0) REVERT: u 269 ASN cc_start: 0.8704 (m110) cc_final: 0.8356 (p0) REVERT: v 17 GLN cc_start: 0.7794 (mp10) cc_final: 0.7421 (mp10) REVERT: v 83 ASN cc_start: 0.4337 (m110) cc_final: 0.3666 (t0) REVERT: v 249 THR cc_start: 0.6279 (p) cc_final: 0.6056 (t) REVERT: v 252 PHE cc_start: 0.8043 (m-80) cc_final: 0.7730 (m-80) REVERT: v 314 PHE cc_start: 0.7189 (m-80) cc_final: 0.6693 (m-80) REVERT: x 230 GLN cc_start: 0.8985 (tt0) cc_final: 0.8426 (tt0) REVERT: x 231 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8250 (mt-10) REVERT: x 233 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7554 (pttt) REVERT: x 251 GLN cc_start: 0.7784 (mm110) cc_final: 0.7412 (mm-40) REVERT: x 271 LYS cc_start: 0.6872 (mttt) cc_final: 0.6493 (ptmm) REVERT: x 272 LEU cc_start: 0.7520 (mm) cc_final: 0.6976 (mm) REVERT: x 274 THR cc_start: 0.8118 (p) cc_final: 0.7820 (t) REVERT: x 301 ASP cc_start: 0.8062 (t70) cc_final: 0.7385 (p0) REVERT: x 312 PHE cc_start: 0.9049 (m-80) cc_final: 0.8813 (m-80) REVERT: x 328 TRP cc_start: 0.7570 (m-10) cc_final: 0.6918 (m-90) REVERT: x 330 VAL cc_start: 0.8490 (m) cc_final: 0.8061 (t) REVERT: x 336 ASP cc_start: 0.7252 (t0) cc_final: 0.6259 (t70) REVERT: x 345 GLN cc_start: 0.8960 (pp30) cc_final: 0.8731 (pp30) REVERT: x 348 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8521 (tt0) REVERT: j 595 MET cc_start: 0.1970 (tpt) cc_final: 0.1161 (mmm) REVERT: j 727 LEU cc_start: 0.4445 (mm) cc_final: 0.3813 (tt) REVERT: j 788 LYS cc_start: 0.3676 (mttt) cc_final: 0.3052 (mttt) REVERT: j 893 MET cc_start: 0.3356 (OUTLIER) cc_final: 0.0790 (mmt) REVERT: j 896 PHE cc_start: 0.2747 (t80) cc_final: 0.2447 (m-10) REVERT: j 915 LEU cc_start: 0.3215 (mt) cc_final: 0.2653 (tp) REVERT: k 268 LEU cc_start: 0.1671 (mt) cc_final: 0.0499 (pp) REVERT: k 377 TYR cc_start: 0.0540 (m-80) cc_final: 0.0079 (m-10) REVERT: k 388 LYS cc_start: 0.0369 (OUTLIER) cc_final: -0.0203 (ptmt) REVERT: k 437 LYS cc_start: 0.7141 (tttm) cc_final: 0.6659 (tptt) outliers start: 210 outliers final: 117 residues processed: 2197 average time/residue: 0.7639 time to fit residues: 2820.8328 Evaluate side-chains 1962 residues out of total 8321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 1830 time to evaluate : 6.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1381 ARG Chi-restraints excluded: chain A residue 1441 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 827 ILE Chi-restraints excluded: chain B residue 1099 VAL Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1176 LYS Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1219 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain V residue 65 HIS Chi-restraints excluded: chain V residue 100 GLN Chi-restraints excluded: chain W residue 238 ASP Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 392 ARG Chi-restraints excluded: chain W residue 459 ILE Chi-restraints excluded: chain W residue 505 THR Chi-restraints excluded: chain W residue 507 VAL Chi-restraints excluded: chain W residue 547 HIS Chi-restraints excluded: chain W residue 581 ILE Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain m residue 784 MET Chi-restraints excluded: chain m residue 911 ILE Chi-restraints excluded: chain m residue 921 LEU Chi-restraints excluded: chain m residue 925 MET Chi-restraints excluded: chain m residue 1151 PHE Chi-restraints excluded: chain m residue 1289 MET Chi-restraints excluded: chain n residue 188 LEU Chi-restraints excluded: chain n residue 203 LEU Chi-restraints excluded: chain n residue 213 LEU Chi-restraints excluded: chain n residue 244 LEU Chi-restraints excluded: chain n residue 256 LEU Chi-restraints excluded: chain q residue 376 CYS Chi-restraints excluded: chain q residue 406 MET Chi-restraints excluded: chain q residue 677 ILE Chi-restraints excluded: chain q residue 714 ILE Chi-restraints excluded: chain q residue 719 CYS Chi-restraints excluded: chain q residue 752 ILE Chi-restraints excluded: chain q residue 809 THR Chi-restraints excluded: chain r residue 219 GLU Chi-restraints excluded: chain r residue 267 ASN Chi-restraints excluded: chain r residue 351 SER Chi-restraints excluded: chain u residue 137 ASN Chi-restraints excluded: chain u residue 222 VAL Chi-restraints excluded: chain v residue 296 ILE Chi-restraints excluded: chain v residue 313 LEU Chi-restraints excluded: chain x residue 163 ASP Chi-restraints excluded: chain x residue 233 LYS Chi-restraints excluded: chain x residue 247 LEU Chi-restraints excluded: chain x residue 303 GLN Chi-restraints excluded: chain x residue 335 ILE Chi-restraints excluded: chain x residue 342 SER Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain e residue 112 ILE Chi-restraints excluded: chain j residue 682 SER Chi-restraints excluded: chain j residue 686 THR Chi-restraints excluded: chain j residue 865 PHE Chi-restraints excluded: chain j residue 874 PHE Chi-restraints excluded: chain j residue 893 MET Chi-restraints excluded: chain k residue 94 ARG Chi-restraints excluded: chain k residue 223 VAL Chi-restraints excluded: chain k residue 301 ASP Chi-restraints excluded: chain k residue 388 LYS Chi-restraints excluded: chain k residue 402 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 33 optimal weight: 4.9990 chunk 923 optimal weight: 20.0000 chunk 701 optimal weight: 20.0000 chunk 56 optimal weight: 0.7980 chunk 855 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 678 optimal weight: 20.0000 chunk 393 optimal weight: 9.9990 chunk 651 optimal weight: 20.0000 chunk 425 optimal weight: 30.0000 chunk 317 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 ASN ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1390 HIS A1430 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN H 44 ASN ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 816 ASN ** m 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m1407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 166 GLN n 176 ASN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 238 HIS q 294 HIS ** q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 926 ASN ** r 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 310 ASN ** x 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 706 HIS ** j 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.216420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138930 restraints weight = 186512.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137728 restraints weight = 93719.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.139708 restraints weight = 63273.787| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 80469 Z= 0.339 Angle : 0.647 13.454 109373 Z= 0.341 Chirality : 0.044 0.228 12167 Planarity : 0.005 0.123 13560 Dihedral : 13.394 129.516 12259 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.61 % Favored : 97.37 % Rotamer: Outliers : 3.33 % Allowed : 13.95 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.09), residues: 9224 helix: 1.70 (0.08), residues: 3988 sheet: 0.20 (0.14), residues: 1353 loop : -0.06 (0.10), residues: 3883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP m 385 HIS 0.008 0.001 HIS q 758 PHE 0.043 0.002 PHE n 238 TYR 0.024 0.002 TYR q 762 ARG 0.010 0.001 ARG W 327 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18448 Ramachandran restraints generated. 9224 Oldfield, 0 Emsley, 9224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18448 Ramachandran restraints generated. 9224 Oldfield, 0 Emsley, 9224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2136 residues out of total 8321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 276 poor density : 1860 time to evaluate : 6.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7956 (tpt) cc_final: 0.7515 (tpp) REVERT: A 104 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8509 (mt-10) REVERT: A 128 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8617 (tt) REVERT: A 177 LYS cc_start: 0.9006 (ttpp) cc_final: 0.8705 (ttpp) REVERT: A 228 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8362 (t0) REVERT: A 306 ASP cc_start: 0.8868 (t0) cc_final: 0.8191 (t0) REVERT: A 318 LYS cc_start: 0.8494 (mttm) cc_final: 0.8110 (mtpt) REVERT: A 329 ARG cc_start: 0.9132 (ttm170) cc_final: 0.8698 (ttm170) REVERT: A 363 ASP cc_start: 0.8860 (p0) cc_final: 0.8617 (p0) REVERT: A 438 MET cc_start: 0.7770 (mmt) cc_final: 0.7518 (mmm) REVERT: A 455 SER cc_start: 0.9624 (m) cc_final: 0.9420 (t) REVERT: A 495 SER cc_start: 0.9246 (t) cc_final: 0.8930 (p) REVERT: A 539 ASP cc_start: 0.8839 (p0) cc_final: 0.8577 (p0) REVERT: A 610 ASP cc_start: 0.8694 (t0) cc_final: 0.8342 (t70) REVERT: A 637 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7701 (mm-30) REVERT: A 660 HIS cc_start: 0.8896 (m-70) cc_final: 0.8396 (m-70) REVERT: A 747 MET cc_start: 0.9302 (mtm) cc_final: 0.8877 (mtm) REVERT: A 813 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7821 (mt-10) REVERT: A 844 LYS cc_start: 0.9406 (mmmt) cc_final: 0.9190 (tppt) REVERT: A 880 GLU cc_start: 0.8373 (mp0) cc_final: 0.8131 (mp0) REVERT: A 964 ARG cc_start: 0.8721 (ttm110) cc_final: 0.8347 (ttm110) REVERT: A 1076 GLU cc_start: 0.8454 (tp30) cc_final: 0.8229 (tp30) REVERT: A 1262 MET cc_start: 0.8070 (tpt) cc_final: 0.7804 (mmm) REVERT: A 1270 MET cc_start: 0.8560 (mmm) cc_final: 0.8187 (mmm) REVERT: A 1345 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8563 (mm-30) REVERT: A 1381 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7611 (mtm-85) REVERT: A 1429 GLU cc_start: 0.8100 (mp0) cc_final: 0.7691 (mt-10) REVERT: B 53 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8155 (tp30) REVERT: B 177 GLU cc_start: 0.7837 (tp30) cc_final: 0.7572 (tp30) REVERT: B 181 TYR cc_start: 0.9243 (m-80) cc_final: 0.9009 (m-80) REVERT: B 214 VAL cc_start: 0.9480 (t) cc_final: 0.9230 (p) REVERT: B 259 ARG cc_start: 0.5870 (mmt180) cc_final: 0.5492 (mmt180) REVERT: B 267 TYR cc_start: 0.7757 (m-80) cc_final: 0.7481 (m-10) REVERT: B 286 ASP cc_start: 0.9275 (m-30) cc_final: 0.8907 (m-30) REVERT: B 307 LYS cc_start: 0.9320 (mmmm) cc_final: 0.9101 (mptt) REVERT: B 339 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8204 (tm-30) REVERT: B 384 GLU cc_start: 0.8958 (mp0) cc_final: 0.8233 (mp0) REVERT: B 396 LYS cc_start: 0.9265 (mptt) cc_final: 0.8869 (mmtm) REVERT: B 479 TYR cc_start: 0.8111 (t80) cc_final: 0.7438 (t80) REVERT: B 549 ASN cc_start: 0.9075 (m-40) cc_final: 0.8834 (m-40) REVERT: B 556 MET cc_start: 0.9083 (tmm) cc_final: 0.8014 (tmm) REVERT: B 610 ARG cc_start: 0.8538 (ttt180) cc_final: 0.8095 (ttt180) REVERT: B 611 ASP cc_start: 0.8530 (t0) cc_final: 0.7908 (t0) REVERT: B 612 ILE cc_start: 0.8757 (mt) cc_final: 0.8319 (tp) REVERT: B 614 GLU cc_start: 0.7802 (mp0) cc_final: 0.7489 (mp0) REVERT: B 693 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7952 (mm-30) REVERT: B 769 TYR cc_start: 0.9049 (m-10) cc_final: 0.8837 (m-80) REVERT: B 810 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7289 (mm-30) REVERT: B 857 ARG cc_start: 0.8685 (ttm-80) cc_final: 0.8402 (ttm-80) REVERT: B 875 GLU cc_start: 0.8595 (pm20) cc_final: 0.8332 (pm20) REVERT: B 884 ARG cc_start: 0.7550 (mmm160) cc_final: 0.7306 (mmm160) REVERT: B 904 ARG cc_start: 0.7834 (tmt-80) cc_final: 0.7617 (ttt-90) REVERT: B 975 GLN cc_start: 0.9124 (pt0) cc_final: 0.8823 (pt0) REVERT: B 987 LYS cc_start: 0.9215 (pttt) cc_final: 0.8956 (ptpp) REVERT: B 995 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.8337 (mtm-85) REVERT: B 1019 SER cc_start: 0.9681 (p) cc_final: 0.9288 (m) REVERT: B 1045 THR cc_start: 0.9191 (m) cc_final: 0.8842 (p) REVERT: B 1070 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7735 (mt-10) REVERT: B 1137 CYS cc_start: 0.8771 (m) cc_final: 0.8328 (m) REVERT: B 1206 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7783 (mt-10) REVERT: C 39 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7400 (mm-30) REVERT: C 42 THR cc_start: 0.9493 (p) cc_final: 0.9255 (t) REVERT: C 43 LEU cc_start: 0.9325 (tp) cc_final: 0.8793 (tp) REVERT: C 100 LEU cc_start: 0.9127 (tt) cc_final: 0.8906 (tp) REVERT: C 165 LYS cc_start: 0.9163 (mttt) cc_final: 0.8847 (mttt) REVERT: C 221 TYR cc_start: 0.8664 (p90) cc_final: 0.8407 (p90) REVERT: D 47 ASP cc_start: 0.7782 (m-30) cc_final: 0.7158 (p0) REVERT: D 88 GLU cc_start: 0.8044 (tt0) cc_final: 0.7528 (pp20) REVERT: D 106 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9169 (tp) REVERT: D 112 PHE cc_start: 0.6791 (m-80) cc_final: 0.5983 (m-80) REVERT: D 125 ASP cc_start: 0.8671 (t0) cc_final: 0.8067 (m-30) REVERT: D 148 LEU cc_start: 0.7426 (mt) cc_final: 0.6880 (mt) REVERT: E 59 PHE cc_start: 0.9042 (p90) cc_final: 0.8780 (p90) REVERT: E 77 LEU cc_start: 0.9453 (tp) cc_final: 0.9200 (tp) REVERT: E 83 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8111 (p0) REVERT: E 111 TYR cc_start: 0.8256 (p90) cc_final: 0.7695 (p90) REVERT: E 120 ASN cc_start: 0.9249 (m-40) cc_final: 0.8783 (m110) REVERT: E 132 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7213 (mt-10) REVERT: E 179 ARG cc_start: 0.8546 (ttt90) cc_final: 0.8247 (ttm-80) REVERT: F 116 ASP cc_start: 0.8972 (t70) cc_final: 0.8679 (t70) REVERT: F 123 LYS cc_start: 0.9138 (ttmt) cc_final: 0.8851 (ttpt) REVERT: G 3 PHE cc_start: 0.8913 (m-80) cc_final: 0.8620 (m-80) REVERT: G 65 SER cc_start: 0.9507 (p) cc_final: 0.8987 (t) REVERT: G 73 LYS cc_start: 0.9058 (mttt) cc_final: 0.8268 (tptt) REVERT: G 86 VAL cc_start: 0.9281 (t) cc_final: 0.9052 (p) REVERT: G 131 MET cc_start: 0.8608 (ppp) cc_final: 0.8401 (ppp) REVERT: G 171 ILE cc_start: 0.4999 (OUTLIER) cc_final: 0.4558 (pt) REVERT: H 29 ILE cc_start: 0.9256 (pt) cc_final: 0.8880 (mm) REVERT: H 41 ASP cc_start: 0.8827 (m-30) cc_final: 0.8240 (m-30) REVERT: H 56 THR cc_start: 0.9026 (m) cc_final: 0.8569 (p) REVERT: I 12 ASN cc_start: 0.8775 (m-40) cc_final: 0.8170 (m-40) REVERT: I 36 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8521 (mm-30) REVERT: I 45 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.8121 (ttm-80) REVERT: I 96 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7461 (t0) REVERT: I 101 TYR cc_start: 0.7273 (m-80) cc_final: 0.6407 (m-80) REVERT: I 108 LYS cc_start: 0.5586 (tttp) cc_final: 0.5263 (mtpp) REVERT: J 30 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8218 (tm-30) REVERT: K 47 ARG cc_start: 0.9463 (ttp80) cc_final: 0.9200 (tmm-80) REVERT: L 30 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8374 (mttt) REVERT: L 64 LYS cc_start: 0.9318 (mmmt) cc_final: 0.8959 (mmtm) REVERT: V 57 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8170 (pt) REVERT: W 222 ASP cc_start: 0.7867 (m-30) cc_final: 0.7138 (p0) REVERT: W 237 LYS cc_start: 0.9193 (mmtt) cc_final: 0.8889 (mmtt) REVERT: W 269 LYS cc_start: 0.9118 (mmtm) cc_final: 0.8711 (mmtm) REVERT: W 779 ARG cc_start: 0.8383 (mmm-85) cc_final: 0.8169 (mmm-85) REVERT: W 782 LEU cc_start: 0.8592 (mt) cc_final: 0.7585 (mt) REVERT: m 296 ASP cc_start: 0.8941 (OUTLIER) cc_final: 0.8661 (p0) REVERT: m 344 ASP cc_start: 0.8386 (m-30) cc_final: 0.8021 (m-30) REVERT: m 347 GLN cc_start: 0.7748 (pt0) cc_final: 0.7236 (tm-30) REVERT: m 385 TRP cc_start: 0.8444 (t-100) cc_final: 0.8128 (t-100) REVERT: m 389 ARG cc_start: 0.8121 (mtp-110) cc_final: 0.7899 (mmm-85) REVERT: m 511 MET cc_start: 0.2833 (tmm) cc_final: 0.2391 (ttm) REVERT: m 620 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9026 (mp0) REVERT: m 661 GLN cc_start: 0.7687 (pt0) cc_final: 0.7427 (pp30) REVERT: m 728 ARG cc_start: 0.9258 (tmm-80) cc_final: 0.8750 (tmm-80) REVERT: m 784 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8183 (tmm) REVERT: m 931 HIS cc_start: 0.8371 (OUTLIER) cc_final: 0.8126 (t-170) REVERT: m 933 HIS cc_start: 0.8868 (m-70) cc_final: 0.8657 (m-70) REVERT: m 999 LEU cc_start: 0.7539 (tp) cc_final: 0.7261 (tp) REVERT: m 1019 MET cc_start: 0.7109 (ppp) cc_final: 0.6822 (ppp) REVERT: m 1076 MET cc_start: 0.5497 (mmp) cc_final: 0.5279 (mmm) REVERT: n 167 MET cc_start: 0.8973 (ttt) cc_final: 0.8671 (ttt) REVERT: n 275 ARG cc_start: 0.8651 (mtt180) cc_final: 0.8376 (mtt180) REVERT: n 286 ARG cc_start: 0.7948 (tmt170) cc_final: 0.7638 (tpt170) REVERT: q 114 MET cc_start: 0.0608 (mmm) cc_final: 0.0266 (mtp) REVERT: q 678 TYR cc_start: 0.8087 (m-80) cc_final: 0.7732 (m-80) REVERT: q 700 PHE cc_start: 0.8882 (m-10) cc_final: 0.8493 (m-10) REVERT: q 726 PHE cc_start: 0.8109 (m-80) cc_final: 0.7666 (m-10) REVERT: q 769 TYR cc_start: 0.7646 (m-80) cc_final: 0.7395 (m-10) REVERT: q 789 ARG cc_start: 0.6324 (ttm170) cc_final: 0.6002 (ttm170) REVERT: q 873 MET cc_start: 0.8554 (mmt) cc_final: 0.8350 (mmt) REVERT: q 928 MET cc_start: 0.7542 (mtt) cc_final: 0.7289 (tpp) REVERT: r 214 TYR cc_start: 0.8178 (m-80) cc_final: 0.7647 (m-80) REVERT: r 386 GLU cc_start: 0.8808 (tt0) cc_final: 0.8511 (mt-10) REVERT: u 185 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7033 (mp0) REVERT: u 188 ASP cc_start: 0.7915 (m-30) cc_final: 0.7000 (p0) REVERT: u 210 MET cc_start: 0.3345 (tpt) cc_final: 0.2731 (tpt) REVERT: v 135 SER cc_start: 0.7665 (p) cc_final: 0.6941 (t) REVERT: v 252 PHE cc_start: 0.8083 (m-80) cc_final: 0.7789 (m-80) REVERT: v 339 LEU cc_start: 0.4881 (mt) cc_final: 0.4610 (mt) REVERT: x 230 GLN cc_start: 0.9093 (tt0) cc_final: 0.8598 (tt0) REVERT: x 251 GLN cc_start: 0.7872 (mm110) cc_final: 0.7514 (mm-40) REVERT: x 271 LYS cc_start: 0.7087 (mttt) cc_final: 0.6629 (ptmm) REVERT: x 272 LEU cc_start: 0.7723 (mm) cc_final: 0.7210 (mm) REVERT: x 274 THR cc_start: 0.7944 (p) cc_final: 0.7684 (t) REVERT: x 301 ASP cc_start: 0.7985 (t70) cc_final: 0.7221 (p0) REVERT: x 310 ASN cc_start: 0.9040 (m110) cc_final: 0.8813 (m110) REVERT: x 315 LYS cc_start: 0.6991 (ptmm) cc_final: 0.6503 (pptt) REVERT: x 330 VAL cc_start: 0.8370 (m) cc_final: 0.7887 (t) REVERT: x 334 ASP cc_start: 0.8043 (m-30) cc_final: 0.7401 (m-30) REVERT: x 336 ASP cc_start: 0.7748 (t0) cc_final: 0.6903 (t70) REVERT: x 348 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8510 (tt0) REVERT: h 56 MET cc_start: -0.4035 (mmt) cc_final: -0.4720 (mmt) REVERT: j 504 GLN cc_start: 0.1213 (tp40) cc_final: 0.0966 (tt0) REVERT: j 595 MET cc_start: 0.2564 (tpt) cc_final: 0.1902 (mmm) REVERT: j 727 LEU cc_start: 0.4292 (mm) cc_final: 0.3688 (tt) REVERT: j 915 LEU cc_start: 0.3249 (mt) cc_final: 0.2696 (tp) REVERT: k 253 TYR cc_start: 0.5926 (m-80) cc_final: 0.5699 (t80) REVERT: k 268 LEU cc_start: 0.1220 (mt) cc_final: -0.0060 (pp) REVERT: k 377 TYR cc_start: 0.0569 (m-80) cc_final: 0.0040 (m-10) REVERT: k 388 LYS cc_start: 0.0983 (OUTLIER) cc_final: -0.1108 (ptmt) REVERT: k 437 LYS cc_start: 0.7094 (tttm) cc_final: 0.6683 (tptt) outliers start: 276 outliers final: 188 residues processed: 1989 average time/residue: 0.7439 time to fit residues: 2499.0344 Evaluate side-chains 1917 residues out of total 8321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 1717 time to evaluate : 6.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1376 ASP Chi-restraints excluded: chain A residue 1381 ARG Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1407 GLU Chi-restraints excluded: chain A residue 1441 THR Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 827 ILE Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1036 SER Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1099 VAL Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1176 LYS Chi-restraints excluded: chain B residue 1186 LYS Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 96 ASN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain V residue 65 HIS Chi-restraints excluded: chain W residue 238 ASP Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 391 GLN Chi-restraints excluded: chain W residue 392 ARG Chi-restraints excluded: chain W residue 459 ILE Chi-restraints excluded: chain W residue 505 THR Chi-restraints excluded: chain W residue 507 VAL Chi-restraints excluded: chain W residue 543 ILE Chi-restraints excluded: chain W residue 544 HIS Chi-restraints excluded: chain W residue 547 HIS Chi-restraints excluded: chain W residue 626 ASP Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain m residue 296 ASP Chi-restraints excluded: chain m residue 363 PHE Chi-restraints excluded: chain m residue 459 THR Chi-restraints excluded: chain m residue 635 TYR Chi-restraints excluded: chain m residue 784 MET Chi-restraints excluded: chain m residue 790 VAL Chi-restraints excluded: chain m residue 911 ILE Chi-restraints excluded: chain m residue 921 LEU Chi-restraints excluded: chain m residue 925 MET Chi-restraints excluded: chain m residue 931 HIS Chi-restraints excluded: chain m residue 978 CYS Chi-restraints excluded: chain m residue 998 ASN Chi-restraints excluded: chain m residue 1151 PHE Chi-restraints excluded: chain m residue 1168 ILE Chi-restraints excluded: chain m residue 1289 MET Chi-restraints excluded: chain n residue 188 LEU Chi-restraints excluded: chain n residue 191 LEU Chi-restraints excluded: chain n residue 203 LEU Chi-restraints excluded: chain n residue 213 LEU Chi-restraints excluded: chain n residue 256 LEU Chi-restraints excluded: chain n residue 273 LEU Chi-restraints excluded: chain q residue 232 LEU Chi-restraints excluded: chain q residue 337 PHE Chi-restraints excluded: chain q residue 376 CYS Chi-restraints excluded: chain q residue 555 SER Chi-restraints excluded: chain q residue 719 CYS Chi-restraints excluded: chain q residue 725 GLN Chi-restraints excluded: chain q residue 777 GLU Chi-restraints excluded: chain q residue 809 THR Chi-restraints excluded: chain q residue 924 GLU Chi-restraints excluded: chain r residue 216 TYR Chi-restraints excluded: chain r residue 267 ASN Chi-restraints excluded: chain r residue 334 LEU Chi-restraints excluded: chain r residue 401 SER Chi-restraints excluded: chain u residue 137 ASN Chi-restraints excluded: chain u residue 222 VAL Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 167 GLU Chi-restraints excluded: chain v residue 296 ILE Chi-restraints excluded: chain v residue 313 LEU Chi-restraints excluded: chain x residue 163 ASP Chi-restraints excluded: chain x residue 219 LEU Chi-restraints excluded: chain x residue 233 LYS Chi-restraints excluded: chain x residue 283 VAL Chi-restraints excluded: chain x residue 294 PHE Chi-restraints excluded: chain x residue 303 GLN Chi-restraints excluded: chain x residue 335 ILE Chi-restraints excluded: chain x residue 342 SER Chi-restraints excluded: chain e residue 112 ILE Chi-restraints excluded: chain j residue 613 GLU Chi-restraints excluded: chain j residue 682 SER Chi-restraints excluded: chain j residue 686 THR Chi-restraints excluded: chain j residue 690 PHE Chi-restraints excluded: chain j residue 865 PHE Chi-restraints excluded: chain j residue 874 PHE Chi-restraints excluded: chain k residue 6 PHE Chi-restraints excluded: chain k residue 65 LEU Chi-restraints excluded: chain k residue 94 ARG Chi-restraints excluded: chain k residue 223 VAL Chi-restraints excluded: chain k residue 301 ASP Chi-restraints excluded: chain k residue 385 PHE Chi-restraints excluded: chain k residue 388 LYS Chi-restraints excluded: chain k residue 400 SER Chi-restraints excluded: chain k residue 402 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 455 optimal weight: 4.9990 chunk 625 optimal weight: 9.9990 chunk 694 optimal weight: 10.0000 chunk 918 optimal weight: 0.7980 chunk 738 optimal weight: 20.0000 chunk 342 optimal weight: 20.0000 chunk 675 optimal weight: 10.0000 chunk 237 optimal weight: 0.9980 chunk 841 optimal weight: 50.0000 chunk 780 optimal weight: 50.0000 chunk 809 optimal weight: 30.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 144 GLN E 31 GLN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 ASN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 HIS ** W 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 451 GLN W 753 ASN ** W 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 473 ASN ** m 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 899 GLN m 931 HIS ** m 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 935 ASN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 294 HIS ** q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 896 GLN q 926 ASN ** r 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 100 GLN ** u 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 340 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.214456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132514 restraints weight = 187593.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.135690 restraints weight = 79297.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135593 restraints weight = 50678.258| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 80469 Z= 0.365 Angle : 0.641 11.407 109373 Z= 0.339 Chirality : 0.044 0.262 12167 Planarity : 0.005 0.085 13560 Dihedral : 13.462 132.701 12259 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.92 % Favored : 97.06 % Rotamer: Outliers : 3.65 % Allowed : 15.13 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % Cis-general : 0.00 % 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: 0.87 (0.09), residues: 9224 helix: 1.56 (0.08), residues: 4008 sheet: -0.01 (0.14), residues: 1374 loop : -0.15 (0.10), residues: 3842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP q 338 HIS 0.007 0.001 HIS j 706 PHE 0.036 0.002 PHE q 393 TYR 0.021 0.002 TYR m 685 ARG 0.008 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18448 Ramachandran restraints generated. 9224 Oldfield, 0 Emsley, 9224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18448 Ramachandran restraints generated. 9224 Oldfield, 0 Emsley, 9224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2091 residues out of total 8321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 303 poor density : 1788 time to evaluate : 6.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8254 (pt) REVERT: A 176 ARG cc_start: 0.7830 (mtm110) cc_final: 0.7039 (ptt-90) REVERT: A 228 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8423 (t0) REVERT: A 306 ASP cc_start: 0.8912 (t0) cc_final: 0.8160 (t0) REVERT: A 318 LYS cc_start: 0.8503 (mttm) cc_final: 0.7899 (ttmt) REVERT: A 437 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8887 (tp) REVERT: A 441 ASP cc_start: 0.8675 (m-30) cc_final: 0.8446 (m-30) REVERT: A 495 SER cc_start: 0.9286 (t) cc_final: 0.8982 (p) REVERT: A 610 ASP cc_start: 0.8689 (t0) cc_final: 0.8414 (t70) REVERT: A 659 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9281 (tp) REVERT: A 660 HIS cc_start: 0.8823 (m-70) cc_final: 0.8406 (m-70) REVERT: A 705 LEU cc_start: 0.9318 (mp) cc_final: 0.9036 (tt) REVERT: A 747 MET cc_start: 0.9283 (mtm) cc_final: 0.8803 (mtm) REVERT: A 813 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7798 (mt-10) REVERT: A 964 ARG cc_start: 0.8914 (ttm110) cc_final: 0.8548 (ttm110) REVERT: A 1076 GLU cc_start: 0.8611 (tp30) cc_final: 0.8333 (tp30) REVERT: A 1128 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8656 (pp) REVERT: A 1211 MET cc_start: 0.7734 (mmm) cc_final: 0.7323 (ttm) REVERT: A 1345 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8572 (mm-30) REVERT: A 1381 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7548 (mtm-85) REVERT: B 53 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8097 (mm-30) REVERT: B 89 MET cc_start: 0.7720 (tpt) cc_final: 0.7419 (tpt) REVERT: B 267 TYR cc_start: 0.7868 (m-80) cc_final: 0.7609 (m-10) REVERT: B 300 TRP cc_start: 0.8088 (p-90) cc_final: 0.7679 (p-90) REVERT: B 301 GLN cc_start: 0.8983 (mp10) cc_final: 0.8671 (mp10) REVERT: B 302 MET cc_start: 0.8444 (ptm) cc_final: 0.8164 (ptt) REVERT: B 304 GLU cc_start: 0.8279 (mp0) cc_final: 0.7852 (mp0) REVERT: B 307 LYS cc_start: 0.9373 (mmmm) cc_final: 0.9023 (mptt) REVERT: B 384 GLU cc_start: 0.8868 (mp0) cc_final: 0.8659 (mm-30) REVERT: B 396 LYS cc_start: 0.9257 (mptt) cc_final: 0.8861 (mmtm) REVERT: B 462 GLN cc_start: 0.8975 (tp-100) cc_final: 0.8700 (tp40) REVERT: B 545 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8484 (mp0) REVERT: B 610 ARG cc_start: 0.8532 (ttt180) cc_final: 0.8146 (ttt180) REVERT: B 611 ASP cc_start: 0.8435 (t0) cc_final: 0.7876 (t0) REVERT: B 612 ILE cc_start: 0.8902 (mt) cc_final: 0.8625 (tp) REVERT: B 693 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7951 (mm-30) REVERT: B 810 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7276 (mm-30) REVERT: B 857 ARG cc_start: 0.8689 (ttm-80) cc_final: 0.8384 (ttm-80) REVERT: B 873 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7754 (mm-30) REVERT: B 875 GLU cc_start: 0.8718 (pm20) cc_final: 0.8464 (pm20) REVERT: B 904 ARG cc_start: 0.7977 (tmt-80) cc_final: 0.7639 (ttt-90) REVERT: B 987 LYS cc_start: 0.9231 (pttt) cc_final: 0.8943 (ptpp) REVERT: B 1019 SER cc_start: 0.9666 (p) cc_final: 0.9292 (m) REVERT: B 1045 THR cc_start: 0.9159 (m) cc_final: 0.8833 (p) REVERT: B 1070 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7748 (mt-10) REVERT: B 1082 MET cc_start: 0.9040 (mmm) cc_final: 0.8332 (tpt) REVERT: B 1133 MET cc_start: 0.8746 (mtp) cc_final: 0.8315 (mtm) REVERT: B 1137 CYS cc_start: 0.8815 (m) cc_final: 0.8372 (m) REVERT: B 1156 ASP cc_start: 0.8412 (p0) cc_final: 0.8073 (p0) REVERT: C 32 LEU cc_start: 0.9715 (tp) cc_final: 0.9341 (tt) REVERT: C 36 MET cc_start: 0.7995 (mtm) cc_final: 0.7668 (mtm) REVERT: C 165 LYS cc_start: 0.9105 (mttt) cc_final: 0.8886 (mttt) REVERT: C 166 GLU cc_start: 0.8122 (tp30) cc_final: 0.7732 (tp30) REVERT: C 206 TYR cc_start: 0.8352 (m-80) cc_final: 0.8036 (m-80) REVERT: C 235 THR cc_start: 0.9394 (p) cc_final: 0.9190 (p) REVERT: D 47 ASP cc_start: 0.7465 (m-30) cc_final: 0.7051 (p0) REVERT: D 88 GLU cc_start: 0.7900 (tt0) cc_final: 0.7438 (pp20) REVERT: D 104 LYS cc_start: 0.9484 (mmtt) cc_final: 0.9125 (mtpp) REVERT: D 106 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9057 (pp) REVERT: D 108 TYR cc_start: 0.7611 (t80) cc_final: 0.6925 (t80) REVERT: D 125 ASP cc_start: 0.8621 (t0) cc_final: 0.8015 (m-30) REVERT: D 144 GLN cc_start: 0.9026 (tp-100) cc_final: 0.8733 (tp40) REVERT: D 148 LEU cc_start: 0.7250 (mt) cc_final: 0.7019 (mt) REVERT: E 59 PHE cc_start: 0.9068 (p90) cc_final: 0.8834 (p90) REVERT: E 77 LEU cc_start: 0.9413 (tp) cc_final: 0.9207 (tp) REVERT: E 111 TYR cc_start: 0.8433 (p90) cc_final: 0.8097 (p90) REVERT: E 120 ASN cc_start: 0.9309 (m-40) cc_final: 0.8832 (m110) REVERT: E 132 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7321 (mt-10) REVERT: E 137 SER cc_start: 0.9319 (m) cc_final: 0.9116 (p) REVERT: E 190 LYS cc_start: 0.9218 (mmmt) cc_final: 0.9015 (mmmm) REVERT: F 116 ASP cc_start: 0.9006 (t70) cc_final: 0.8764 (t70) REVERT: F 123 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8774 (ttpt) REVERT: G 65 SER cc_start: 0.9573 (p) cc_final: 0.9078 (t) REVERT: G 73 LYS cc_start: 0.9118 (mttt) cc_final: 0.8335 (mmmt) REVERT: G 85 GLU cc_start: 0.8754 (tp30) cc_final: 0.8386 (tp30) REVERT: G 131 MET cc_start: 0.8840 (ppp) cc_final: 0.8604 (ppp) REVERT: G 135 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6569 (tm-30) REVERT: H 29 ILE cc_start: 0.9343 (pt) cc_final: 0.8952 (mm) REVERT: H 41 ASP cc_start: 0.8858 (m-30) cc_final: 0.8284 (m-30) REVERT: I 12 ASN cc_start: 0.8920 (m-40) cc_final: 0.8302 (m-40) REVERT: I 45 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.8102 (ttm-80) REVERT: I 101 TYR cc_start: 0.7466 (m-80) cc_final: 0.6892 (m-80) REVERT: I 108 LYS cc_start: 0.5697 (tttp) cc_final: 0.5354 (mtpp) REVERT: J 16 ASP cc_start: 0.7988 (p0) cc_final: 0.7696 (p0) REVERT: K 6 ARG cc_start: 0.9044 (mmm-85) cc_final: 0.8785 (mmm160) REVERT: K 47 ARG cc_start: 0.9464 (ttp80) cc_final: 0.9164 (tmm-80) REVERT: L 30 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8320 (mttt) REVERT: L 52 GLU cc_start: 0.8535 (pt0) cc_final: 0.8045 (pt0) REVERT: L 64 LYS cc_start: 0.9261 (mmmt) cc_final: 0.8966 (mmmt) REVERT: V 25 MET cc_start: 0.7615 (tpp) cc_final: 0.7260 (tpp) REVERT: V 57 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8182 (pt) REVERT: W 237 LYS cc_start: 0.9266 (mmtt) cc_final: 0.8960 (mmtt) REVERT: W 269 LYS cc_start: 0.9059 (mmtm) cc_final: 0.8614 (mmtt) REVERT: W 300 LEU cc_start: 0.9285 (mt) cc_final: 0.8662 (mp) REVERT: W 641 LEU cc_start: 0.7082 (mt) cc_final: 0.6471 (mm) REVERT: W 680 TYR cc_start: 0.9243 (t80) cc_final: 0.8082 (t80) REVERT: W 681 ARG cc_start: 0.8240 (ttm110) cc_final: 0.7681 (mmp80) REVERT: W 779 ARG cc_start: 0.8837 (mmm-85) cc_final: 0.8619 (mmm-85) REVERT: W 782 LEU cc_start: 0.8671 (mt) cc_final: 0.7758 (mt) REVERT: m 296 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8692 (p0) REVERT: m 309 ARG cc_start: 0.7426 (mmt90) cc_final: 0.6866 (mmt90) REVERT: m 344 ASP cc_start: 0.8370 (m-30) cc_final: 0.7963 (m-30) REVERT: m 347 GLN cc_start: 0.7707 (pt0) cc_final: 0.7235 (tm-30) REVERT: m 385 TRP cc_start: 0.8492 (t-100) cc_final: 0.8170 (t-100) REVERT: m 389 ARG cc_start: 0.8236 (mtp-110) cc_final: 0.7923 (mmm-85) REVERT: m 511 MET cc_start: 0.3244 (tmm) cc_final: 0.2768 (ttm) REVERT: m 728 ARG cc_start: 0.9203 (tmm-80) cc_final: 0.8726 (tmm-80) REVERT: m 784 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8351 (ppp) REVERT: m 812 TYR cc_start: 0.7109 (m-10) cc_final: 0.6814 (m-80) REVERT: m 931 HIS cc_start: 0.8797 (OUTLIER) cc_final: 0.8437 (t-90) REVERT: m 933 HIS cc_start: 0.9002 (m-70) cc_final: 0.8755 (m-70) REVERT: m 999 LEU cc_start: 0.7309 (tp) cc_final: 0.7042 (tt) REVERT: m 1019 MET cc_start: 0.7039 (ppp) cc_final: 0.6739 (ppp) REVERT: m 1076 MET cc_start: 0.5421 (mmp) cc_final: 0.5119 (mmm) REVERT: m 1083 MET cc_start: 0.6869 (tpp) cc_final: 0.6643 (tpp) REVERT: n 167 MET cc_start: 0.8784 (ttt) cc_final: 0.8419 (ttt) REVERT: n 286 ARG cc_start: 0.7961 (tmt170) cc_final: 0.7656 (tpt170) REVERT: q 114 MET cc_start: 0.0497 (mmm) cc_final: 0.0142 (mtp) REVERT: q 293 LYS cc_start: 0.4061 (tmtt) cc_final: 0.2450 (mtmm) REVERT: q 466 MET cc_start: 0.1208 (mtt) cc_final: 0.0726 (mmm) REVERT: q 668 LYS cc_start: 0.3275 (tttt) cc_final: 0.2900 (tptt) REVERT: q 678 TYR cc_start: 0.7896 (m-80) cc_final: 0.7595 (m-80) REVERT: q 700 PHE cc_start: 0.8935 (m-10) cc_final: 0.8591 (m-10) REVERT: q 769 TYR cc_start: 0.7633 (m-80) cc_final: 0.7354 (m-10) REVERT: q 789 ARG cc_start: 0.6363 (ttm170) cc_final: 0.5994 (ttm170) REVERT: q 873 MET cc_start: 0.8626 (mmt) cc_final: 0.8376 (mmt) REVERT: r 214 TYR cc_start: 0.8142 (m-80) cc_final: 0.7492 (m-80) REVERT: r 386 GLU cc_start: 0.8767 (tt0) cc_final: 0.8457 (mt-10) REVERT: u 108 VAL cc_start: 0.5961 (m) cc_final: 0.5752 (m) REVERT: u 185 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7071 (mp0) REVERT: u 188 ASP cc_start: 0.8099 (m-30) cc_final: 0.7106 (p0) REVERT: u 210 MET cc_start: 0.3335 (tpt) cc_final: 0.2772 (tpt) REVERT: v 126 PHE cc_start: 0.9053 (p90) cc_final: 0.8828 (p90) REVERT: v 135 SER cc_start: 0.7799 (p) cc_final: 0.7165 (t) REVERT: v 314 PHE cc_start: 0.6525 (OUTLIER) cc_final: 0.5923 (t80) REVERT: x 230 GLN cc_start: 0.9219 (tt0) cc_final: 0.8825 (tt0) REVERT: x 251 GLN cc_start: 0.7914 (mm110) cc_final: 0.7644 (mm-40) REVERT: x 271 LYS cc_start: 0.7058 (mttt) cc_final: 0.6624 (ptmm) REVERT: x 274 THR cc_start: 0.8114 (p) cc_final: 0.7770 (t) REVERT: x 301 ASP cc_start: 0.8036 (t70) cc_final: 0.7155 (p0) REVERT: x 315 LYS cc_start: 0.7430 (ptmm) cc_final: 0.6363 (pptt) REVERT: x 348 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8570 (tt0) REVERT: j 504 GLN cc_start: 0.1353 (tp40) cc_final: 0.1054 (tt0) REVERT: j 595 MET cc_start: 0.2862 (tpt) cc_final: 0.1986 (mmm) REVERT: j 893 MET cc_start: 0.2216 (ptp) cc_final: 0.2015 (ptt) REVERT: k 253 TYR cc_start: 0.5756 (OUTLIER) cc_final: 0.5530 (t80) REVERT: k 268 LEU cc_start: 0.1279 (mt) cc_final: -0.0011 (pp) REVERT: k 377 TYR cc_start: 0.0379 (m-80) cc_final: 0.0052 (m-10) REVERT: k 437 LYS cc_start: 0.6907 (tttm) cc_final: 0.6519 (tptt) outliers start: 303 outliers final: 214 residues processed: 1937 average time/residue: 0.7747 time to fit residues: 2542.3016 Evaluate side-chains 1906 residues out of total 8321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 1679 time to evaluate : 6.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1376 ASP Chi-restraints excluded: chain A residue 1381 ARG Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1407 GLU Chi-restraints excluded: chain A residue 1424 CYS Chi-restraints excluded: chain A residue 1441 THR Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 827 ILE Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1099 VAL Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1176 LYS Chi-restraints excluded: chain B residue 1186 LYS Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 96 ASN Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain V residue 65 HIS Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 238 ASP Chi-restraints excluded: chain W residue 292 VAL Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 308 ASP Chi-restraints excluded: chain W residue 392 ARG Chi-restraints excluded: chain W residue 459 ILE Chi-restraints excluded: chain W residue 505 THR Chi-restraints excluded: chain W residue 507 VAL Chi-restraints excluded: chain W residue 543 ILE Chi-restraints excluded: chain W residue 544 HIS Chi-restraints excluded: chain W residue 626 ASP Chi-restraints excluded: chain W residue 697 VAL Chi-restraints excluded: chain W residue 749 ASP Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain m residue 296 ASP Chi-restraints excluded: chain m residue 363 PHE Chi-restraints excluded: chain m residue 459 THR Chi-restraints excluded: chain m residue 635 TYR Chi-restraints excluded: chain m residue 784 MET Chi-restraints excluded: chain m residue 790 VAL Chi-restraints excluded: chain m residue 848 LEU Chi-restraints excluded: chain m residue 921 LEU Chi-restraints excluded: chain m residue 925 MET Chi-restraints excluded: chain m residue 931 HIS Chi-restraints excluded: chain m residue 956 LEU Chi-restraints excluded: chain m residue 1151 PHE Chi-restraints excluded: chain m residue 1168 ILE Chi-restraints excluded: chain m residue 1289 MET Chi-restraints excluded: chain m residue 1332 ILE Chi-restraints excluded: chain n residue 188 LEU Chi-restraints excluded: chain n residue 191 LEU Chi-restraints excluded: chain n residue 203 LEU Chi-restraints excluded: chain n residue 213 LEU Chi-restraints excluded: chain q residue 322 LEU Chi-restraints excluded: chain q residue 337 PHE Chi-restraints excluded: chain q residue 376 CYS Chi-restraints excluded: chain q residue 555 SER Chi-restraints excluded: chain q residue 809 THR Chi-restraints excluded: chain q residue 924 GLU Chi-restraints excluded: chain r residue 216 TYR Chi-restraints excluded: chain r residue 267 ASN Chi-restraints excluded: chain r residue 323 TYR Chi-restraints excluded: chain r residue 401 SER Chi-restraints excluded: chain u residue 137 ASN Chi-restraints excluded: chain u residue 197 ASN Chi-restraints excluded: chain u residue 209 LEU Chi-restraints excluded: chain u residue 222 VAL Chi-restraints excluded: chain u residue 251 VAL Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 167 GLU Chi-restraints excluded: chain v residue 204 THR Chi-restraints excluded: chain v residue 247 ILE Chi-restraints excluded: chain v residue 296 ILE Chi-restraints excluded: chain v residue 314 PHE Chi-restraints excluded: chain x residue 163 ASP Chi-restraints excluded: chain x residue 219 LEU Chi-restraints excluded: chain x residue 233 LYS Chi-restraints excluded: chain x residue 263 LEU Chi-restraints excluded: chain x residue 283 VAL Chi-restraints excluded: chain x residue 294 PHE Chi-restraints excluded: chain x residue 303 GLN Chi-restraints excluded: chain x residue 335 ILE Chi-restraints excluded: chain x residue 342 SER Chi-restraints excluded: chain b residue 84 MET Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain e residue 112 ILE Chi-restraints excluded: chain j residue 613 GLU Chi-restraints excluded: chain j residue 686 THR Chi-restraints excluded: chain j residue 690 PHE Chi-restraints excluded: chain j residue 874 PHE Chi-restraints excluded: chain k residue 6 PHE Chi-restraints excluded: chain k residue 65 LEU Chi-restraints excluded: chain k residue 94 ARG Chi-restraints excluded: chain k residue 223 VAL Chi-restraints excluded: chain k residue 253 TYR Chi-restraints excluded: chain k residue 301 ASP Chi-restraints excluded: chain k residue 385 PHE Chi-restraints excluded: chain k residue 391 VAL Chi-restraints excluded: chain k residue 400 SER Chi-restraints excluded: chain k residue 402 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 602 optimal weight: 10.0000 chunk 544 optimal weight: 4.9990 chunk 551 optimal weight: 0.6980 chunk 343 optimal weight: 4.9990 chunk 576 optimal weight: 40.0000 chunk 726 optimal weight: 9.9990 chunk 290 optimal weight: 30.0000 chunk 188 optimal weight: 1.9990 chunk 773 optimal weight: 20.0000 chunk 868 optimal weight: 40.0000 chunk 338 optimal weight: 8.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 140 GLN A 214 HIS ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN B 102 GLN B 317 GLN B 549 ASN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN E 178 GLN I 31 ASN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 451 GLN ** W 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 272 ASN q 294 HIS ** q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 926 ASN ** r 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 269 ASN ** v 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 224 ASN ** x 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 GLN k 143 ASN k 299 GLN k 340 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.215550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.138504 restraints weight = 180119.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.142035 restraints weight = 77419.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.142088 restraints weight = 53830.441| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4730 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: