Starting phenix.real_space_refine on Tue Aug 26 16:10:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5fj9_3179/08_2025/5fj9_3179.cif Found real_map, /net/cci-nas-00/data/ceres_data/5fj9_3179/08_2025/5fj9_3179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5fj9_3179/08_2025/5fj9_3179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5fj9_3179/08_2025/5fj9_3179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5fj9_3179/08_2025/5fj9_3179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5fj9_3179/08_2025/5fj9_3179.map" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 213 5.16 5 C 24513 2.51 5 N 6659 2.21 5 O 7289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38680 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 11071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1412, 11071 Classifications: {'peptide': 1412} Link IDs: {'PTRANS': 65, 'TRANS': 1346} Chain breaks: 4 Chain: "B" Number of atoms: 8788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8788 Classifications: {'peptide': 1114} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 1070} Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 977 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 2 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1544 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 12, 'TRANS': 178} Chain breaks: 2 Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 1 Chain: "I" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 728 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain breaks: 1 Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 1 Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Chain: "O" Number of atoms: 4247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4247 Classifications: {'peptide': 528} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 510} Chain breaks: 2 Chain: "P" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 820 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 95} Chain breaks: 2 Chain: "Q" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 271 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 5, 'TRANS': 29} Chain: "Q" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 175 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'TRANS': 34} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'UNK:plan-1': 35} Unresolved non-hydrogen planarities: 35 Chain: "A" 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: "B" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 492 SG CYS A 67 74.196 63.300 83.366 1.00194.09 S ATOM 510 SG CYS A 70 76.689 64.349 80.653 1.00175.43 S ATOM 557 SG CYS A 77 77.513 64.650 84.469 1.00111.18 S ATOM 795 SG CYS A 107 60.636 108.929 99.134 1.00134.69 S ATOM 818 SG CYS A 110 58.789 108.589 96.809 1.00148.86 S ATOM 1184 SG CYS A 154 59.509 111.753 99.520 1.00185.01 S ATOM 1208 SG CYS A 157 57.704 111.283 97.166 1.00225.22 S ATOM 19455 SG CYS B1098 76.703 82.956 77.548 1.00123.67 S ATOM 19521 SG CYS B1107 77.391 79.219 77.436 1.00126.15 S ATOM 19541 SG CYS B1110 75.562 80.853 74.593 1.00169.23 S ATOM 28624 SG CYS I 5 68.110 108.676 168.041 1.00191.21 S ATOM 28643 SG CYS I 8 66.821 105.202 166.850 1.00180.32 S ATOM 28771 SG CYS I 26 67.210 106.924 163.968 1.00205.23 S ATOM 29367 SG CYS J 7 133.114 37.466 124.739 1.00 72.76 S ATOM 29390 SG CYS J 10 136.250 40.167 125.397 1.00 79.78 S ATOM 29670 SG CYS J 45 135.898 40.123 127.291 1.00 94.36 S ATOM 29676 SG CYS J 46 134.844 36.773 127.834 1.00 96.31 S ATOM 30704 SG CYS L 31 89.894 20.345 124.446 1.00174.91 S ATOM 30724 SG CYS L 34 89.435 21.740 127.979 1.00166.10 S ATOM 30828 SG CYS L 48 86.742 22.012 125.543 1.00217.49 S ATOM 30851 SG CYS L 51 87.567 18.929 126.867 1.00194.60 S Time building chain proxies: 7.15, per 1000 atoms: 0.18 Number of scatterers: 38680 At special positions: 0 Unit cell: (189.7, 160.432, 211.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 213 16.00 O 7289 8.00 N 6659 7.00 C 24513 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.98 Conformation dependent library (CDL) restraints added in 2.1 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 77 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 67 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 70 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 110 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 157 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 154 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1107 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1110 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1098 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 8 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 26 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 5 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 46 " pdb=" ZN L2000 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 51 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 48 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 34 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 31 " Number of angles added : 21 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9224 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 55 sheets defined 37.0% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.763A pdb=" N GLN A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 133 through 151 removed outlier: 3.696A pdb=" N ARG A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 203 removed outlier: 3.956A pdb=" N ILE A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 removed outlier: 4.168A pdb=" N HIS A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 4.462A pdb=" N GLU A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A 213 " --> pdb=" O PRO A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 283 through 301 removed outlier: 3.631A pdb=" N LEU A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRP A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 4.319A pdb=" N MET A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A 320 " --> pdb=" O TRP A 316 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 369 removed outlier: 4.751A pdb=" N SER A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.758A pdb=" N GLN A 417 " --> pdb=" O ARG A 413 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.199A pdb=" N ASN A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 456' Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.514A pdb=" N ILE A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 removed outlier: 3.518A pdb=" N LEU A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.575A pdb=" N GLN A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 removed outlier: 3.574A pdb=" N PHE A 610 " --> pdb=" O GLY A 606 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 612 " --> pdb=" O GLN A 608 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 686 removed outlier: 4.171A pdb=" N ILE A 681 " --> pdb=" O VAL A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.567A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 718 Processing helix chain 'A' and resid 722 through 733 removed outlier: 3.566A pdb=" N LYS A 726 " --> pdb=" O ASP A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 748 removed outlier: 3.799A pdb=" N LEU A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASN A 746 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS A 747 " --> pdb=" O THR A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 784 removed outlier: 3.534A pdb=" N VAL A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS A 781 " --> pdb=" O VAL A 777 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 782 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 783 " --> pdb=" O ASP A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 797 Processing helix chain 'A' and resid 802 through 811 Processing helix chain 'A' and resid 857 through 860 Processing helix chain 'A' and resid 861 through 894 removed outlier: 3.514A pdb=" N SER A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 875 " --> pdb=" O GLY A 871 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER A 886 " --> pdb=" O THR A 882 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 892 " --> pdb=" O ARG A 888 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 893 " --> pdb=" O LEU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 934 through 946 removed outlier: 3.866A pdb=" N ILE A 945 " --> pdb=" O HIS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 963 Processing helix chain 'A' and resid 963 through 975 removed outlier: 4.013A pdb=" N LEU A 967 " --> pdb=" O ALA A 963 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 968 " --> pdb=" O ASN A 964 " (cutoff:3.500A) Proline residue: A 969 - end of helix removed outlier: 4.205A pdb=" N ARG A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 975 " --> pdb=" O GLU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 992 removed outlier: 3.759A pdb=" N LYS A 991 " --> pdb=" O GLU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1025 removed outlier: 3.521A pdb=" N TYR A1005 " --> pdb=" O GLU A1001 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A1012 " --> pdb=" O LEU A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1048 removed outlier: 4.152A pdb=" N THR A1047 " --> pdb=" O PRO A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1060 removed outlier: 3.619A pdb=" N THR A1054 " --> pdb=" O ASP A1050 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A1056 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1081 removed outlier: 3.558A pdb=" N LEU A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1099 removed outlier: 3.883A pdb=" N ALA A1094 " --> pdb=" O GLY A1090 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A1099 " --> pdb=" O GLN A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1132 removed outlier: 3.650A pdb=" N ILE A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1161 removed outlier: 3.772A pdb=" N LYS A1158 " --> pdb=" O ALA A1154 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL A1161 " --> pdb=" O VAL A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1170 Processing helix chain 'A' and resid 1189 through 1196 removed outlier: 4.533A pdb=" N ILE A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1217 removed outlier: 3.504A pdb=" N ILE A1217 " --> pdb=" O SER A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1267 removed outlier: 3.765A pdb=" N TYR A1258 " --> pdb=" O ASN A1254 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A1265 " --> pdb=" O GLN A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1306 Processing helix chain 'A' and resid 1318 through 1323 removed outlier: 3.913A pdb=" N VAL A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1344 Processing helix chain 'A' and resid 1351 through 1364 removed outlier: 4.247A pdb=" N ILE A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN A1356 " --> pdb=" O PRO A1352 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A1357 " --> pdb=" O ARG A1353 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A1358 " --> pdb=" O HIS A1354 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET A1362 " --> pdb=" O LEU A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1390 removed outlier: 3.632A pdb=" N LEU A1386 " --> pdb=" O SER A1382 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1402 removed outlier: 4.437A pdb=" N LEU A1396 " --> pdb=" O THR A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1418 removed outlier: 3.989A pdb=" N ILE A1416 " --> pdb=" O SER A1412 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A1417 " --> pdb=" O GLU A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1426 removed outlier: 3.511A pdb=" N GLY A1426 " --> pdb=" O ILE A1423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1423 through 1426' Processing helix chain 'A' and resid 1447 through 1457 removed outlier: 4.231A pdb=" N LEU A1451 " --> pdb=" O LEU A1447 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A1452 " --> pdb=" O PHE A1448 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASN A1453 " --> pdb=" O GLU A1449 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A1454 " --> pdb=" O SER A1450 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA A1456 " --> pdb=" O SER A1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 46 removed outlier: 4.011A pdb=" N ASP B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TRP B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 39 through 46' Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.752A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 80 removed outlier: 3.740A pdb=" N ASP B 70 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.583A pdb=" N LYS B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 278 through 294 removed outlier: 4.342A pdb=" N ILE B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 removed outlier: 3.867A pdb=" N ILE B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 332 Processing helix chain 'B' and resid 342 through 362 removed outlier: 3.597A pdb=" N ARG B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN B 362 " --> pdb=" O MET B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 408 removed outlier: 4.142A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 398 " --> pdb=" O LYS B 394 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 426 removed outlier: 3.600A pdb=" N VAL B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 440 Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.914A pdb=" N ALA B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 467 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 493 Processing helix chain 'B' and resid 529 through 536 Processing helix chain 'B' and resid 567 through 581 removed outlier: 3.577A pdb=" N PHE B 571 " --> pdb=" O PHE B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 632 removed outlier: 3.576A pdb=" N ARG B 628 " --> pdb=" O ASP B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.803A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 657 removed outlier: 3.784A pdb=" N ASP B 656 " --> pdb=" O ASN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.769A pdb=" N ILE B 666 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.687A pdb=" N ILE B 680 " --> pdb=" O PRO B 677 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 681 " --> pdb=" O PHE B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 removed outlier: 3.803A pdb=" N LEU B 687 " --> pdb=" O VAL B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 706 removed outlier: 3.505A pdb=" N GLN B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 704 " --> pdb=" O THR B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 715 through 720 removed outlier: 4.272A pdb=" N PHE B 718 " --> pdb=" O TYR B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 744 removed outlier: 3.800A pdb=" N GLU B 742 " --> pdb=" O THR B 738 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 743 " --> pdb=" O LYS B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 953 removed outlier: 4.743A pdb=" N SER B 951 " --> pdb=" O HIS B 947 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 952 " --> pdb=" O GLY B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 970 removed outlier: 3.515A pdb=" N GLU B 960 " --> pdb=" O GLY B 956 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 961 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 993 removed outlier: 3.568A pdb=" N SER B 988 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP B 993 " --> pdb=" O LYS B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1073 removed outlier: 4.492A pdb=" N CYS B1069 " --> pdb=" O MET B1065 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1083 Processing helix chain 'B' and resid 1122 through 1135 removed outlier: 3.536A pdb=" N LYS B1126 " --> pdb=" O PRO B1122 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 40 removed outlier: 3.891A pdb=" N LYS C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 73 removed outlier: 3.501A pdb=" N SER C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 104 removed outlier: 3.513A pdb=" N LEU C 103 " --> pdb=" O HIS C 99 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 104 " --> pdb=" O ARG C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 242 through 251 removed outlier: 3.542A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.717A pdb=" N LEU C 280 " --> pdb=" O ARG C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 288 removed outlier: 4.049A pdb=" N LYS C 288 " --> pdb=" O GLU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 removed outlier: 3.579A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS C 331 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 27 removed outlier: 3.616A pdb=" N LYS D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 72 removed outlier: 3.772A pdb=" N ASN D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN D 64 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN D 69 " --> pdb=" O TYR D 65 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE D 72 " --> pdb=" O ILE D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 removed outlier: 4.301A pdb=" N ALA D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 113 removed outlier: 3.745A pdb=" N LEU D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER D 112 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 138 removed outlier: 3.720A pdb=" N SER D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE D 137 " --> pdb=" O HIS D 133 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 132 through 138' Processing helix chain 'D' and resid 150 through 158 Processing helix chain 'E' and resid 1 through 25 removed outlier: 3.795A pdb=" N ASP E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.719A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 removed outlier: 3.811A pdb=" N PHE E 42 " --> pdb=" O PRO E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 66 through 72 removed outlier: 3.633A pdb=" N PHE E 72 " --> pdb=" O SER E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 104 removed outlier: 4.256A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 165 Processing helix chain 'F' and resid 86 through 103 removed outlier: 3.529A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 127 removed outlier: 4.218A pdb=" N ILE F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.592A pdb=" N GLN G 17 " --> pdb=" O PRO G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'G' and resid 162 through 173 removed outlier: 3.726A pdb=" N LEU G 168 " --> pdb=" O LYS G 164 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 removed outlier: 3.872A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 38 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.861A pdb=" N ARG J 47 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.929A pdb=" N GLY K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.577A pdb=" N ALA K 116 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU K 127 " --> pdb=" O ASP K 123 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N CYS K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP K 129 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL K 130 " --> pdb=" O ASP K 126 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS K 138 " --> pdb=" O LYS K 134 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS K 140 " --> pdb=" O THR K 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 139 removed outlier: 3.719A pdb=" N ALA M 136 " --> pdb=" O ASN M 132 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER M 138 " --> pdb=" O ASP M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 196 removed outlier: 3.899A pdb=" N ASP M 187 " --> pdb=" O PHE M 183 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA M 189 " --> pdb=" O TYR M 185 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU M 196 " --> pdb=" O THR M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 241 removed outlier: 3.733A pdb=" N VAL M 236 " --> pdb=" O LEU M 232 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU M 239 " --> pdb=" O LYS M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 260 removed outlier: 4.603A pdb=" N LYS M 256 " --> pdb=" O PHE M 252 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR M 258 " --> pdb=" O GLN M 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 274 through 297 removed outlier: 3.729A pdb=" N ALA N 278 " --> pdb=" O LYS N 274 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU N 279 " --> pdb=" O GLU N 275 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA N 285 " --> pdb=" O GLU N 281 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU N 291 " --> pdb=" O HIS N 287 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET N 297 " --> pdb=" O LYS N 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 367 through 369 No H-bonds generated for 'chain 'N' and resid 367 through 369' Processing helix chain 'O' and resid 46 through 57 removed outlier: 3.967A pdb=" N LYS O 50 " --> pdb=" O LEU O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 71 removed outlier: 3.620A pdb=" N ILE O 65 " --> pdb=" O ALA O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 84 removed outlier: 4.167A pdb=" N VAL O 80 " --> pdb=" O VAL O 76 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU O 81 " --> pdb=" O ARG O 77 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS O 82 " --> pdb=" O GLU O 78 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE O 83 " --> pdb=" O LEU O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 101 removed outlier: 3.642A pdb=" N THR O 93 " --> pdb=" O ASP O 89 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL O 96 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 131 Processing helix chain 'O' and resid 133 through 143 Processing helix chain 'O' and resid 151 through 167 removed outlier: 3.882A pdb=" N ALA O 157 " --> pdb=" O LYS O 153 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU O 158 " --> pdb=" O GLN O 154 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER O 165 " --> pdb=" O GLN O 161 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU O 166 " --> pdb=" O ASN O 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 178 removed outlier: 3.540A pdb=" N SER O 177 " --> pdb=" O ASP O 173 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL O 178 " --> pdb=" O TYR O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 196 removed outlier: 3.698A pdb=" N GLU O 196 " --> pdb=" O VAL O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 219 Processing helix chain 'O' and resid 234 through 258 removed outlier: 4.102A pdb=" N ARG O 238 " --> pdb=" O ASP O 234 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER O 239 " --> pdb=" O LEU O 235 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS O 251 " --> pdb=" O THR O 247 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE O 252 " --> pdb=" O ASP O 248 " (cutoff:3.500A) Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 284 through 304 removed outlier: 3.556A pdb=" N ARG O 291 " --> pdb=" O PHE O 287 " (cutoff:3.500A) Processing helix chain 'O' and resid 305 through 320 removed outlier: 3.646A pdb=" N ALA O 315 " --> pdb=" O VAL O 311 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU O 318 " --> pdb=" O ILE O 314 " (cutoff:3.500A) Processing helix chain 'O' and resid 324 through 328 Processing helix chain 'O' and resid 341 through 360 removed outlier: 3.993A pdb=" N GLU O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL O 352 " --> pdb=" O GLU O 348 " (cutoff:3.500A) Proline residue: O 357 - end of helix Processing helix chain 'O' and resid 453 through 459 removed outlier: 3.525A pdb=" N LEU O 457 " --> pdb=" O ILE O 453 " (cutoff:3.500A) Processing helix chain 'O' and resid 482 through 500 removed outlier: 4.589A pdb=" N VAL O 486 " --> pdb=" O LYS O 482 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL O 491 " --> pdb=" O LEU O 487 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 514 removed outlier: 3.714A pdb=" N MET O 505 " --> pdb=" O GLY O 501 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG O 506 " --> pdb=" O PRO O 502 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU O 507 " --> pdb=" O SER O 503 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER O 508 " --> pdb=" O ALA O 504 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG O 509 " --> pdb=" O MET O 505 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG O 512 " --> pdb=" O SER O 508 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN O 514 " --> pdb=" O CYS O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 526 removed outlier: 3.585A pdb=" N ILE O 522 " --> pdb=" O SER O 518 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER O 524 " --> pdb=" O LYS O 520 " (cutoff:3.500A) Processing helix chain 'O' and resid 529 through 541 Processing helix chain 'O' and resid 571 through 576 removed outlier: 3.821A pdb=" N PHE O 576 " --> pdb=" O HIS O 572 " (cutoff:3.500A) Processing helix chain 'O' and resid 578 through 610 removed outlier: 4.470A pdb=" N GLU O 582 " --> pdb=" O ARG O 578 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP O 583 " --> pdb=" O GLN O 579 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN O 584 " --> pdb=" O ASN O 580 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET O 585 " --> pdb=" O LEU O 581 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN O 587 " --> pdb=" O TRP O 583 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR O 601 " --> pdb=" O GLN O 597 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LEU O 602 " --> pdb=" O GLU O 598 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS O 605 " --> pdb=" O THR O 601 " (cutoff:3.500A) Processing helix chain 'O' and resid 620 through 651 removed outlier: 4.177A pdb=" N LEU O 624 " --> pdb=" O LEU O 620 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN O 625 " --> pdb=" O PRO O 621 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN O 626 " --> pdb=" O SER O 622 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU O 627 " --> pdb=" O GLU O 623 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN O 631 " --> pdb=" O LEU O 627 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU O 644 " --> pdb=" O ARG O 640 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL O 650 " --> pdb=" O SER O 646 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE O 651 " --> pdb=" O LEU O 647 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 228 removed outlier: 3.980A pdb=" N ALA P 228 " --> pdb=" O PHE P 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 240 Processing helix chain 'P' and resid 241 through 247 removed outlier: 3.510A pdb=" N GLU P 245 " --> pdb=" O ARG P 241 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU P 247 " --> pdb=" O LEU P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 271 removed outlier: 3.705A pdb=" N LEU P 269 " --> pdb=" O LEU P 265 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 68 Processing helix chain 'Q' and resid 1079 through 1086 removed outlier: 3.741A pdb=" N UNK Q1085 " --> pdb=" O UNK Q1081 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1090 through 1095 removed outlier: 3.793A pdb=" N UNK Q1094 " --> pdb=" O UNK Q1090 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 11 through 19 removed outlier: 5.444A pdb=" N ILE A 13 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU B1144 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLY A 15 " --> pdb=" O ARG B1142 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG B1142 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 19 " --> pdb=" O ALA B1138 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 30 through 33 removed outlier: 7.636A pdb=" N HIS A 83 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLU A 33 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 82 " --> pdb=" O ALA A 263 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 106 through 107 removed outlier: 3.626A pdb=" N ALA A 112 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 179 through 180 removed outlier: 3.765A pdb=" N ASP A 220 " --> pdb=" O HIS A 180 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'A' and resid 381 through 382 removed outlier: 3.539A pdb=" N SER A 382 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 500 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 499 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 379 " --> pdb=" O MET A 517 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 405 through 406 removed outlier: 6.749A pdb=" N VAL A 461 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU A 433 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLU A 463 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 431 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AH, first strand: chain 'A' and resid 597 through 598 removed outlier: 3.613A pdb=" N VAL H 96 " --> pdb=" O MET A 598 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA H 28 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU H 38 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY H 127 " --> pdb=" O ILE H 112 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE H 112 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU H 111 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU H 106 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR H 102 " --> pdb=" O TYR H 115 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'A' and resid 627 through 628 Processing sheet with id=AJ, first strand: chain 'A' and resid 897 through 898 removed outlier: 7.667A pdb=" N VAL A 904 " --> pdb=" O VAL A 912 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 912 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 4.274A pdb=" N ARG A1280 " --> pdb=" O GLU A1296 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A1293 " --> pdb=" O ALA A1143 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A1143 " --> pdb=" O LEU A1293 " (cutoff:3.500A) Processing sheet with id=AL, first strand: chain 'A' and resid 1223 through 1224 removed outlier: 3.570A pdb=" N ALA A1231 " --> pdb=" O ASN A1223 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A1186 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A1232 " --> pdb=" O ILE A1184 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A1178 " --> pdb=" O LEU A1181 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG A1187 " --> pdb=" O TYR A1172 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR A1172 " --> pdb=" O ARG A1187 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A1173 " --> pdb=" O TYR I 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR I 41 " --> pdb=" O VAL A1173 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU I 39 " --> pdb=" O ASP A1175 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A1177 " --> pdb=" O GLY I 37 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY I 37 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AM, first strand: chain 'A' and resid 1428 through 1432 Processing sheet with id=BA, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.695A pdb=" N LEU B 93 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR B 95 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU B 134 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 97 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N MET B 143 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing sheet with id=BB, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.695A pdb=" N LEU B 93 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR B 95 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU B 134 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 97 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE B 129 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 149 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing sheet with id=BC, first strand: chain 'B' and resid 143 through 144 removed outlier: 3.568A pdb=" N MET B 143 " --> pdb=" O TYR B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=BC Processing sheet with id=BD, first strand: chain 'B' and resid 185 through 186 Processing sheet with id=BE, first strand: chain 'B' and resid 375 through 378 removed outlier: 3.992A pdb=" N GLN B 197 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL B 196 " --> pdb=" O ARG B 472 " (cutoff:3.500A) Processing sheet with id=BF, first strand: chain 'B' and resid 206 through 209 removed outlier: 5.088A pdb=" N ILE B 215 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 234 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN B 217 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N TYR B 232 " --> pdb=" O LYS B 243 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LYS B 243 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE B 234 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TYR B 241 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS B 236 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 251 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=BG, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=BH, first strand: chain 'B' and resid 619 through 620 Processing sheet with id=BI, first strand: chain 'B' and resid 646 through 649 removed outlier: 3.737A pdb=" N ARG B 610 " --> pdb=" O LEU B 649 " (cutoff:3.500A) Processing sheet with id=BJ, first strand: chain 'B' and resid 672 through 673 removed outlier: 6.847A pdb=" N VAL B 615 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing sheet with id=BK, first strand: chain 'B' and resid 560 through 561 removed outlier: 4.030A pdb=" N ALA B 598 " --> pdb=" O ASN B 593 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA B 602 " --> pdb=" O SER B 589 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 589 " --> pdb=" O ALA B 602 " (cutoff:3.500A) Processing sheet with id=BL, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.802A pdb=" N CYS B 785 " --> pdb=" O ARG B 904 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG B 904 " --> pdb=" O CYS B 785 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU B 895 " --> pdb=" O MET B 886 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET B 886 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS B 897 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL B 884 " --> pdb=" O LYS B 897 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 882 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET B 886 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU L 56 " --> pdb=" O MET B 886 " (cutoff:3.500A) Processing sheet with id=BM, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.802A pdb=" N CYS B 785 " --> pdb=" O ARG B 904 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG B 904 " --> pdb=" O CYS B 785 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU B 895 " --> pdb=" O MET B 886 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET B 886 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS B 897 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL B 884 " --> pdb=" O LYS B 897 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP B 882 " --> pdb=" O LEU B 899 " (cutoff:3.500A) Processing sheet with id=BN, first strand: chain 'B' and resid 736 through 737 removed outlier: 3.826A pdb=" N THR B 977 " --> pdb=" O GLY B 980 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 980 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing sheet with id=BO, first strand: chain 'B' and resid 753 through 755 removed outlier: 3.660A pdb=" N GLY B 920 " --> pdb=" O PHE B 912 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU B 773 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE B 925 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing sheet with id=BP, first strand: chain 'B' and resid 943 through 944 removed outlier: 4.337A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=BQ, first strand: chain 'B' and resid 846 through 847 Processing sheet with id=BR, first strand: chain 'B' and resid 1101 through 1102 removed outlier: 4.307A pdb=" N ASP B1093 " --> pdb=" O GLY B1102 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET B1119 " --> pdb=" O VAL B1092 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.527A pdb=" N ARG C 293 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N LEU C 291 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N ILE C 235 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N ARG C 293 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N ILE C 233 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 9.535A pdb=" N ARG C 295 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N HIS C 297 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU C 229 " --> pdb=" O HIS C 297 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 299 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR C 227 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ASN C 301 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ALA C 225 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU C 303 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.527A pdb=" N ARG C 293 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 54 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 302 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 52 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLU C 41 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE C 57 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ASN C 43 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'C' and resid 222 through 235 removed outlier: 8.688A pdb=" N VAL C 222 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N VAL C 302 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 11.629A pdb=" N THR C 224 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N PHE C 300 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 12.001A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 10.565A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 9.524A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 294 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN C 234 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing sheet with id=CD, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.389A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C 83 " --> pdb=" O PHE L 67 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=CE, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.520A pdb=" N VAL C 162 " --> pdb=" O ALA C 194 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA C 194 " --> pdb=" O VAL C 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=CE Processing sheet with id=DA, first strand: chain 'D' and resid 3 through 5 removed outlier: 6.929A pdb=" N LYS G 6 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N ASN G 69 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N LEU G 52 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR G 71 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP G 50 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ARG G 73 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE G 48 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY G 43 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE G 39 " --> pdb=" O GLY G 43 " (cutoff:3.500A) Processing sheet with id=EA, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.919A pdb=" N ALA E 62 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE E 109 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL E 111 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE E 110 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing sheet with id=EB, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.001A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG E 212 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=GA, first strand: chain 'G' and resid 99 through 100 Processing sheet with id=GB, first strand: chain 'G' and resid 96 through 97 Processing sheet with id=GC, first strand: chain 'G' and resid 120 through 121 Processing sheet with id=GD, first strand: chain 'G' and resid 152 through 155 removed outlier: 3.989A pdb=" N ALA G 195 " --> pdb=" O VAL G 154 " (cutoff:3.500A) Processing sheet with id=IA, first strand: chain 'I' and resid 12 through 16 removed outlier: 3.781A pdb=" N LEU I 13 " --> pdb=" O ALA I 25 " (cutoff:3.500A) Processing sheet with id=IB, first strand: chain 'I' and resid 65 through 66 removed outlier: 4.036A pdb=" N LEU I 85 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR I 95 " --> pdb=" O LEU I 85 " (cutoff:3.500A) Processing sheet with id=KA, first strand: chain 'K' and resid 48 through 49 Processing sheet with id=MA, first strand: chain 'M' and resid 86 through 90 removed outlier: 3.697A pdb=" N TYR M 90 " --> pdb=" O ASP N 393 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP N 393 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA N 396 " --> pdb=" O GLU N 407 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU N 407 " --> pdb=" O ALA N 396 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER N 398 " --> pdb=" O SER N 405 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N SER N 405 " --> pdb=" O SER N 398 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA N 400 " --> pdb=" O ALA N 403 " (cutoff:3.500A) Processing sheet with id=MB, first strand: chain 'M' and resid 120 through 123 Processing sheet with id=MC, first strand: chain 'M' and resid 152 through 153 Processing sheet with id=MD, first strand: chain 'M' and resid 167 through 172 Processing sheet with id=NA, first strand: chain 'N' and resid 364 through 365 Processing sheet with id=OA, first strand: chain 'O' and resid 74 through 75 Processing sheet with id=OB, first strand: chain 'O' and resid 201 through 202 Processing sheet with id=OC, first strand: chain 'O' and resid 470 through 472 Processing sheet with id=PA, first strand: chain 'P' and resid 254 through 256 removed outlier: 3.514A pdb=" N CYS P 260 " --> pdb=" O VAL P 256 " (cutoff:3.500A) 1222 hydrogen bonds defined for protein. 3405 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.94 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12578 1.34 - 1.46: 8149 1.46 - 1.59: 18292 1.59 - 1.71: 0 1.71 - 1.83: 344 Bond restraints: 39363 Sorted by residual: bond pdb=" CG HIS P 307 " pdb=" CD2 HIS P 307 " ideal model delta sigma weight residual 1.354 1.394 -0.040 1.10e-02 8.26e+03 1.32e+01 bond pdb=" CA VAL N 378 " pdb=" CB VAL N 378 " ideal model delta sigma weight residual 1.540 1.581 -0.041 1.36e-02 5.41e+03 9.00e+00 bond pdb=" CG HIS P 307 " pdb=" ND1 HIS P 307 " ideal model delta sigma weight residual 1.378 1.346 0.032 1.10e-02 8.26e+03 8.62e+00 bond pdb=" CA ILE C 239 " pdb=" CB ILE C 239 " ideal model delta sigma weight residual 1.540 1.578 -0.038 1.36e-02 5.41e+03 7.94e+00 bond pdb=" CA VAL A 975 " pdb=" CB VAL A 975 " ideal model delta sigma weight residual 1.540 1.577 -0.037 1.36e-02 5.41e+03 7.44e+00 ... (remaining 39358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 50556 2.55 - 5.11: 2270 5.11 - 7.66: 283 7.66 - 10.21: 41 10.21 - 12.76: 3 Bond angle restraints: 53153 Sorted by residual: angle pdb=" C PRO A 858 " pdb=" N PRO A 859 " pdb=" CA PRO A 859 " ideal model delta sigma weight residual 119.84 109.64 10.20 1.25e+00 6.40e-01 6.66e+01 angle pdb=" CA GLU P 310 " pdb=" C GLU P 310 " pdb=" N VAL P 311 " ideal model delta sigma weight residual 119.63 113.08 6.55 8.10e-01 1.52e+00 6.53e+01 angle pdb=" C ILE Q 39 " pdb=" N PRO Q 40 " pdb=" CA PRO Q 40 " ideal model delta sigma weight residual 120.31 127.74 -7.43 9.80e-01 1.04e+00 5.75e+01 angle pdb=" C LYS B 479 " pdb=" CA LYS B 479 " pdb=" CB LYS B 479 " ideal model delta sigma weight residual 116.63 108.10 8.53 1.16e+00 7.43e-01 5.41e+01 angle pdb=" C LEU A 955 " pdb=" N PRO A 956 " pdb=" CA PRO A 956 " ideal model delta sigma weight residual 118.85 126.87 -8.02 1.09e+00 8.42e-01 5.41e+01 ... (remaining 53148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 22062 16.68 - 33.37: 1704 33.37 - 50.05: 321 50.05 - 66.73: 80 66.73 - 83.41: 13 Dihedral angle restraints: 24180 sinusoidal: 9941 harmonic: 14239 Sorted by residual: dihedral pdb=" CA GLY B 839 " pdb=" C GLY B 839 " pdb=" N GLN B 840 " pdb=" CA GLN B 840 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ILE E 127 " pdb=" C ILE E 127 " pdb=" N PRO E 128 " pdb=" CA PRO E 128 " ideal model delta harmonic sigma weight residual -180.00 -150.76 -29.24 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ARG O 145 " pdb=" C ARG O 145 " pdb=" N VAL O 146 " pdb=" CA VAL O 146 " ideal model delta harmonic sigma weight residual 180.00 -150.83 -29.17 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 24177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 5069 0.064 - 0.128: 874 0.128 - 0.191: 69 0.191 - 0.255: 3 0.255 - 0.319: 1 Chirality restraints: 6016 Sorted by residual: chirality pdb=" CA HIS P 307 " pdb=" N HIS P 307 " pdb=" C HIS P 307 " pdb=" CB HIS P 307 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA VAL B 87 " pdb=" N VAL B 87 " pdb=" C VAL B 87 " pdb=" CB VAL B 87 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE O 548 " pdb=" N ILE O 548 " pdb=" C ILE O 548 " pdb=" CB ILE O 548 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 6013 not shown) Planarity restraints: 6843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 599 " 0.065 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO A 600 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO A 600 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 600 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR P 236 " -0.058 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO P 237 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO P 237 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO P 237 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP O 328 " 0.049 5.00e-02 4.00e+02 7.41e-02 8.77e+00 pdb=" N PRO O 329 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO O 329 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO O 329 " 0.045 5.00e-02 4.00e+02 ... (remaining 6840 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 387 2.59 - 3.16: 33368 3.16 - 3.74: 56393 3.74 - 4.32: 75490 4.32 - 4.90: 120751 Nonbonded interactions: 286389 Sorted by model distance: nonbonded pdb=" OD1 ASN A 109 " pdb="ZN ZN A2001 " model vdw 2.008 2.230 nonbonded pdb=" OE2 GLU O 493 " pdb=" NH1 ARG O 512 " model vdw 2.158 3.120 nonbonded pdb=" O ASP K 85 " pdb=" OG1 THR K 107 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR O 477 " pdb=" OH TYR O 480 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP A 829 " pdb=" ND2 ASN A 838 " model vdw 2.201 3.120 ... (remaining 286384 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 40.910 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 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 0.519 39386 Z= 0.387 Angle : 1.306 63.230 53174 Z= 0.819 Chirality : 0.045 0.319 6016 Planarity : 0.005 0.100 6843 Dihedral : 12.449 83.413 14956 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 1.13 % Allowed : 16.05 % Favored : 82.82 % Rotamer: Outliers : 4.04 % Allowed : 9.84 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.61 (0.09), residues: 4779 helix: -3.68 (0.09), residues: 1416 sheet: -1.63 (0.19), residues: 533 loop : -3.13 (0.10), residues: 2830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 364 TYR 0.018 0.001 TYR B 296 PHE 0.034 0.001 PHE O 47 TRP 0.029 0.001 TRP D 29 HIS 0.006 0.001 HIS A1318 Details of bonding type rmsd covalent geometry : bond 0.00436 (39363) covalent geometry : angle 1.20541 (53153) hydrogen bonds : bond 0.30691 ( 1198) hydrogen bonds : angle 10.34928 ( 3405) metal coordination : bond 0.13468 ( 22) metal coordination : angle 25.36142 ( 21) Misc. bond : bond 0.41243 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1782 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 1609 time to evaluate : 1.389 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: A 26 ILE cc_start: 0.8691 (mt) cc_final: 0.8343 (tp) REVERT: A 58 MET cc_start: 0.7409 (ttm) cc_final: 0.7205 (ttm) REVERT: A 91 PHE cc_start: 0.6878 (t80) cc_final: 0.6150 (t80) REVERT: A 161 ASN cc_start: 0.5797 (p0) cc_final: 0.4273 (m-40) REVERT: A 221 ASP cc_start: 0.6785 (p0) cc_final: 0.6531 (m-30) REVERT: A 222 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7523 (mp) REVERT: A 273 MET cc_start: 0.6823 (ptp) cc_final: 0.6544 (mmt) REVERT: A 313 MET cc_start: 0.7780 (mmt) cc_final: 0.7507 (tmm) REVERT: A 368 LEU cc_start: 0.7785 (tt) cc_final: 0.7518 (mt) REVERT: A 373 VAL cc_start: 0.8842 (t) cc_final: 0.8384 (m) REVERT: A 394 VAL cc_start: 0.9208 (t) cc_final: 0.8802 (p) REVERT: A 474 PHE cc_start: 0.8836 (t80) cc_final: 0.8604 (t80) REVERT: A 668 VAL cc_start: 0.9116 (t) cc_final: 0.8882 (t) REVERT: A 682 LEU cc_start: 0.8719 (tp) cc_final: 0.8415 (tp) REVERT: A 712 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8917 (mp) REVERT: A 714 ILE cc_start: 0.8861 (mm) cc_final: 0.8586 (mm) REVERT: A 739 ASP cc_start: 0.9453 (t0) cc_final: 0.9202 (m-30) REVERT: A 857 SER cc_start: 0.9023 (t) cc_final: 0.8311 (m) REVERT: A 885 MET cc_start: 0.7443 (ttt) cc_final: 0.6975 (tmm) REVERT: A 924 LEU cc_start: 0.8838 (tt) cc_final: 0.8593 (tt) REVERT: A 925 GLU cc_start: 0.8264 (pt0) cc_final: 0.8052 (pm20) REVERT: A 938 SER cc_start: 0.9548 (m) cc_final: 0.9049 (p) REVERT: A 940 ASP cc_start: 0.8804 (m-30) cc_final: 0.8445 (t0) REVERT: A 977 TYR cc_start: 0.8210 (m-10) cc_final: 0.7162 (m-80) REVERT: A 1019 LEU cc_start: 0.9398 (tp) cc_final: 0.9101 (tt) REVERT: A 1075 LEU cc_start: 0.8944 (pp) cc_final: 0.8562 (mt) REVERT: A 1185 GLN cc_start: 0.5290 (tt0) cc_final: 0.4718 (tt0) REVERT: A 1233 ASN cc_start: 0.8047 (m-40) cc_final: 0.7000 (t0) REVERT: A 1294 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7820 (pp) REVERT: A 1328 ILE cc_start: 0.8207 (mt) cc_final: 0.7957 (mt) REVERT: B 204 ARG cc_start: 0.7957 (ttm110) cc_final: 0.7595 (mmt-90) REVERT: B 295 ILE cc_start: -0.3311 (OUTLIER) cc_final: -0.3843 (tt) REVERT: B 338 GLU cc_start: 0.5702 (tm-30) cc_final: 0.5299 (tt0) REVERT: B 469 MET cc_start: 0.8042 (ttp) cc_final: 0.7444 (tmm) REVERT: B 470 MET cc_start: 0.9061 (mtm) cc_final: 0.8540 (mtm) REVERT: B 490 GLN cc_start: 0.7930 (pm20) cc_final: 0.7250 (mp10) REVERT: B 530 LYS cc_start: 0.6905 (mtpp) cc_final: 0.6631 (ptpp) REVERT: B 545 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6383 (t0) REVERT: B 624 ASP cc_start: 0.8984 (t0) cc_final: 0.8618 (m-30) REVERT: B 661 LEU cc_start: 0.8735 (mt) cc_final: 0.8384 (mm) REVERT: B 695 GLN cc_start: 0.6581 (pt0) cc_final: 0.6367 (pt0) REVERT: B 705 MET cc_start: 0.7824 (mtm) cc_final: 0.7583 (ptm) REVERT: B 736 VAL cc_start: 0.9490 (m) cc_final: 0.9281 (p) REVERT: B 773 LEU cc_start: 0.9080 (mm) cc_final: 0.8812 (mt) REVERT: B 958 MET cc_start: 0.8138 (ttp) cc_final: 0.7564 (ttm) REVERT: B 1026 LYS cc_start: 0.8174 (tttm) cc_final: 0.7512 (tmtt) REVERT: B 1119 MET cc_start: 0.7311 (ptm) cc_final: 0.6436 (ptp) REVERT: C 69 ARG cc_start: 0.8901 (mtp85) cc_final: 0.8254 (ttm170) REVERT: C 94 ASP cc_start: 0.8684 (p0) cc_final: 0.8477 (p0) REVERT: C 145 ASP cc_start: 0.6996 (m-30) cc_final: 0.6604 (m-30) REVERT: D 4 LEU cc_start: 0.8602 (mp) cc_final: 0.8340 (tt) REVERT: D 8 ASN cc_start: 0.6951 (t0) cc_final: 0.6317 (t0) REVERT: D 61 ASN cc_start: 0.8050 (m-40) cc_final: 0.7794 (m-40) REVERT: D 98 MET cc_start: 0.6781 (mtm) cc_final: 0.5918 (ptm) REVERT: D 108 THR cc_start: 0.8535 (p) cc_final: 0.8305 (p) REVERT: D 130 ASN cc_start: 0.8326 (t0) cc_final: 0.7849 (m-40) REVERT: E 22 MET cc_start: 0.8808 (ttt) cc_final: 0.8427 (tpt) REVERT: E 41 ASP cc_start: 0.7629 (m-30) cc_final: 0.6955 (p0) REVERT: E 121 MET cc_start: 0.8861 (mmp) cc_final: 0.8342 (mmm) REVERT: E 127 ILE cc_start: 0.9013 (mm) cc_final: 0.8687 (pt) REVERT: E 174 GLN cc_start: 0.8429 (pt0) cc_final: 0.8140 (pt0) REVERT: E 191 LYS cc_start: 0.8931 (mptt) cc_final: 0.8668 (mmtp) REVERT: F 103 MET cc_start: 0.9038 (mtt) cc_final: 0.8771 (tpp) REVERT: F 109 VAL cc_start: 0.8855 (p) cc_final: 0.8209 (p) REVERT: F 115 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7743 (p) REVERT: F 119 ARG cc_start: 0.9037 (mtm180) cc_final: 0.8518 (mtt-85) REVERT: F 145 ASP cc_start: 0.8283 (m-30) cc_final: 0.8006 (m-30) REVERT: G 9 ASP cc_start: 0.7281 (t0) cc_final: 0.6108 (p0) REVERT: G 10 LEU cc_start: 0.8967 (tt) cc_final: 0.8728 (tp) REVERT: G 11 VAL cc_start: 0.9203 (t) cc_final: 0.8987 (p) REVERT: G 51 LEU cc_start: 0.8645 (tp) cc_final: 0.8310 (tp) REVERT: G 72 PHE cc_start: 0.8277 (p90) cc_final: 0.7781 (p90) REVERT: G 80 PHE cc_start: 0.6742 (p90) cc_final: 0.6395 (p90) REVERT: G 99 VAL cc_start: 0.7838 (m) cc_final: 0.7394 (p) REVERT: G 113 ASN cc_start: 0.6598 (OUTLIER) cc_final: 0.6304 (m-40) REVERT: G 114 MET cc_start: 0.5781 (mmt) cc_final: 0.5561 (mmp) REVERT: G 148 PHE cc_start: 0.7947 (p90) cc_final: 0.7293 (p90) REVERT: G 164 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7961 (tptp) REVERT: H 27 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7471 (tm-30) REVERT: H 56 THR cc_start: 0.8368 (m) cc_final: 0.7408 (p) REVERT: H 93 TYR cc_start: 0.8932 (m-80) cc_final: 0.8336 (m-80) REVERT: H 116 TYR cc_start: 0.8186 (m-10) cc_final: 0.7953 (m-10) REVERT: H 126 GLU cc_start: 0.7253 (pt0) cc_final: 0.6655 (tm-30) REVERT: H 136 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8088 (mtpt) REVERT: I 12 LEU cc_start: 0.7567 (mt) cc_final: 0.7041 (mt) REVERT: J 21 TYR cc_start: 0.8888 (t80) cc_final: 0.8576 (t80) REVERT: J 28 ASP cc_start: 0.8939 (t0) cc_final: 0.8688 (t0) REVERT: J 59 LYS cc_start: 0.9235 (mmtt) cc_final: 0.8697 (mmmt) REVERT: J 66 LEU cc_start: 0.6403 (tt) cc_final: 0.6182 (pt) REVERT: K 49 LEU cc_start: 0.9237 (tt) cc_final: 0.8554 (tt) REVERT: K 56 GLU cc_start: 0.6078 (tm-30) cc_final: 0.5601 (tm-30) REVERT: K 81 MET cc_start: 0.8740 (tpp) cc_final: 0.8489 (tpp) REVERT: K 114 VAL cc_start: 0.7963 (m) cc_final: 0.7461 (p) REVERT: K 115 ASP cc_start: 0.8989 (m-30) cc_final: 0.8505 (m-30) REVERT: L 30 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8564 (mm) REVERT: L 56 LEU cc_start: 0.7927 (pp) cc_final: 0.7105 (pt) REVERT: L 57 LEU cc_start: 0.8854 (mp) cc_final: 0.8634 (mp) REVERT: M 90 TYR cc_start: 0.7137 (p90) cc_final: 0.5980 (p90) REVERT: M 159 TYR cc_start: 0.8524 (m-10) cc_final: 0.8137 (m-80) REVERT: M 166 MET cc_start: 0.8516 (mmp) cc_final: 0.7583 (ttm) REVERT: M 170 LEU cc_start: 0.8892 (tt) cc_final: 0.8655 (mp) REVERT: M 184 LYS cc_start: 0.9183 (mmtt) cc_final: 0.8871 (mmmt) REVERT: M 245 LEU cc_start: 0.7633 (mt) cc_final: 0.6600 (tp) REVERT: N 312 ARG cc_start: 0.8299 (mmt180) cc_final: 0.7598 (ptp-170) REVERT: N 389 THR cc_start: 0.4973 (t) cc_final: 0.4393 (t) REVERT: O 74 LEU cc_start: 0.7741 (tp) cc_final: 0.7400 (tp) REVERT: O 89 ASP cc_start: 0.8612 (m-30) cc_final: 0.8033 (m-30) REVERT: O 98 LEU cc_start: 0.8768 (mt) cc_final: 0.8466 (mt) REVERT: O 103 CYS cc_start: 0.6981 (m) cc_final: 0.6488 (m) REVERT: O 128 HIS cc_start: 0.8309 (t70) cc_final: 0.7932 (t70) REVERT: O 205 LYS cc_start: 0.8053 (tptp) cc_final: 0.7754 (tttm) REVERT: O 287 PHE cc_start: 0.6684 (t80) cc_final: 0.6206 (t80) REVERT: O 295 GLN cc_start: 0.8688 (mt0) cc_final: 0.8468 (mm-40) REVERT: O 312 TYR cc_start: 0.8496 (t80) cc_final: 0.8221 (t80) REVERT: O 316 LEU cc_start: 0.8814 (mp) cc_final: 0.8566 (tt) REVERT: O 476 TYR cc_start: 0.6567 (p90) cc_final: 0.6189 (p90) REVERT: O 505 MET cc_start: 0.9223 (mtm) cc_final: 0.9011 (mtp) REVERT: O 576 PHE cc_start: 0.6573 (p90) cc_final: 0.5600 (p90) REVERT: O 593 GLU cc_start: 0.8641 (mm-30) cc_final: 0.7819 (mm-30) REVERT: O 603 LEU cc_start: 0.9042 (mt) cc_final: 0.8680 (pp) REVERT: P 175 ILE cc_start: 0.7219 (OUTLIER) cc_final: 0.6731 (pt) REVERT: P 224 PHE cc_start: 0.6663 (m-10) cc_final: 0.6438 (m-80) REVERT: P 240 ILE cc_start: 0.1773 (OUTLIER) cc_final: 0.1304 (mt) REVERT: P 313 TYR cc_start: 0.6851 (t80) cc_final: 0.6642 (t80) REVERT: Q 50 LYS cc_start: 0.8871 (mttt) cc_final: 0.8560 (mttp) REVERT: Q 51 GLU cc_start: 0.9376 (mt-10) cc_final: 0.9168 (mt-10) outliers start: 173 outliers final: 26 residues processed: 1721 average time/residue: 0.2435 time to fit residues: 659.0397 Evaluate side-chains 853 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 817 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.0270 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 7.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN A 518 ASN A 533 ASN A 540 ASN A 815 GLN A 838 ASN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 ASN B 175 ASN B 550 HIS ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN B 774 ASN B 880 HIS B 970 ASN ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 99 HIS E 153 HIS G 28 HIS G 143 ASN J 53 HIS K 70 HIS M 104 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 ASN O 39 GLN O 143 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 ASN O 544 ASN O 587 ASN P 176 ASN P 219 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.102127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.084239 restraints weight = 162581.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.085956 restraints weight = 115265.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.087472 restraints weight = 77943.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.087511 restraints weight = 62714.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.087613 restraints weight = 58986.683| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 39386 Z= 0.252 Angle : 1.033 59.306 53174 Z= 0.497 Chirality : 0.050 0.257 6016 Planarity : 0.007 0.099 6843 Dihedral : 6.829 62.461 5284 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.80 % Allowed : 12.05 % Favored : 87.15 % Rotamer: Outliers : 0.37 % Allowed : 5.81 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.47 (0.11), residues: 4779 helix: -1.93 (0.12), residues: 1500 sheet: -1.31 (0.19), residues: 625 loop : -2.87 (0.11), residues: 2654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG G 147 TYR 0.035 0.002 TYR B 296 PHE 0.027 0.002 PHE F 143 TRP 0.053 0.004 TRP P 317 HIS 0.009 0.002 HIS D 27 Details of bonding type rmsd covalent geometry : bond 0.00550 (39363) covalent geometry : angle 0.92840 (53153) hydrogen bonds : bond 0.06479 ( 1198) hydrogen bonds : angle 6.69753 ( 3405) metal coordination : bond 0.01483 ( 22) metal coordination : angle 22.76953 ( 21) Misc. bond : bond 0.06140 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 968 time to evaluate : 1.412 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: A 26 ILE cc_start: 0.9146 (mt) cc_final: 0.8846 (tp) REVERT: A 91 PHE cc_start: 0.7445 (t80) cc_final: 0.6674 (t80) REVERT: A 120 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8640 (ptpt) REVERT: A 273 MET cc_start: 0.7079 (ptp) cc_final: 0.6598 (mmt) REVERT: A 313 MET cc_start: 0.8094 (mmt) cc_final: 0.7703 (tmm) REVERT: A 394 VAL cc_start: 0.9430 (t) cc_final: 0.9125 (p) REVERT: A 540 ASN cc_start: 0.8466 (m-40) cc_final: 0.8228 (t0) REVERT: A 603 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.8006 (pt) REVERT: A 857 SER cc_start: 0.9130 (t) cc_final: 0.8454 (m) REVERT: A 885 MET cc_start: 0.7549 (ttt) cc_final: 0.7099 (tmm) REVERT: A 926 MET cc_start: 0.8812 (ttp) cc_final: 0.8354 (mmm) REVERT: A 1163 LYS cc_start: 0.7087 (mppt) cc_final: 0.6289 (mmtt) REVERT: A 1260 MET cc_start: 0.6636 (tpt) cc_final: 0.6171 (tpp) REVERT: A 1263 LEU cc_start: 0.9071 (mt) cc_final: 0.8773 (mt) REVERT: A 1269 ASP cc_start: 0.7161 (m-30) cc_final: 0.6933 (m-30) REVERT: A 1321 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8118 (tt0) REVERT: B 204 ARG cc_start: 0.7764 (ttm110) cc_final: 0.7472 (mmt-90) REVERT: B 375 LYS cc_start: 0.8880 (mptt) cc_final: 0.8348 (mmtt) REVERT: B 449 MET cc_start: 0.5209 (tpp) cc_final: 0.4709 (tpp) REVERT: B 469 MET cc_start: 0.8225 (ttp) cc_final: 0.7502 (tmm) REVERT: B 470 MET cc_start: 0.8968 (mtm) cc_final: 0.8679 (mtp) REVERT: B 527 GLU cc_start: 0.7829 (mp0) cc_final: 0.6714 (mp0) REVERT: B 533 CYS cc_start: 0.9092 (m) cc_final: 0.8713 (p) REVERT: B 670 MET cc_start: 0.8413 (mtt) cc_final: 0.7827 (mtt) REVERT: B 885 MET cc_start: 0.7769 (tpp) cc_final: 0.7501 (tpp) REVERT: B 958 MET cc_start: 0.9101 (ttp) cc_final: 0.8883 (ttm) REVERT: B 1008 ILE cc_start: 0.9117 (pt) cc_final: 0.8755 (mt) REVERT: B 1115 ASN cc_start: 0.8188 (t0) cc_final: 0.7948 (t0) REVERT: B 1119 MET cc_start: 0.8146 (ptm) cc_final: 0.7628 (ptp) REVERT: C 63 ILE cc_start: 0.9134 (pt) cc_final: 0.8717 (mm) REVERT: C 69 ARG cc_start: 0.9158 (mtp85) cc_final: 0.8533 (ttm170) REVERT: C 71 MET cc_start: 0.8969 (mtp) cc_final: 0.8628 (mtp) REVERT: C 145 ASP cc_start: 0.6943 (m-30) cc_final: 0.6567 (m-30) REVERT: C 174 ARG cc_start: 0.8182 (mtt180) cc_final: 0.7468 (ptp-170) REVERT: D 4 LEU cc_start: 0.8568 (mp) cc_final: 0.8009 (pp) REVERT: D 98 MET cc_start: 0.6950 (mtm) cc_final: 0.5511 (ptm) REVERT: D 108 THR cc_start: 0.7665 (p) cc_final: 0.7392 (p) REVERT: E 22 MET cc_start: 0.8667 (ttt) cc_final: 0.8017 (ttt) REVERT: E 28 TYR cc_start: 0.6298 (m-10) cc_final: 0.6079 (m-10) REVERT: E 82 PHE cc_start: 0.6809 (t80) cc_final: 0.6601 (t80) REVERT: E 121 MET cc_start: 0.8699 (mmp) cc_final: 0.8276 (mmm) REVERT: E 191 LYS cc_start: 0.8609 (mptt) cc_final: 0.8233 (mmtp) REVERT: F 104 ASN cc_start: 0.8780 (t0) cc_final: 0.8498 (t0) REVERT: F 145 ASP cc_start: 0.8246 (m-30) cc_final: 0.7862 (m-30) REVERT: G 53 THR cc_start: 0.7884 (p) cc_final: 0.7678 (p) REVERT: G 65 SER cc_start: 0.9237 (m) cc_final: 0.9011 (p) REVERT: G 130 TRP cc_start: 0.6685 (m-10) cc_final: 0.6458 (m100) REVERT: G 148 PHE cc_start: 0.7699 (p90) cc_final: 0.7284 (p90) REVERT: G 205 MET cc_start: 0.2993 (mtp) cc_final: 0.2403 (mtp) REVERT: H 14 GLU cc_start: 0.7896 (pm20) cc_final: 0.7158 (pm20) REVERT: H 56 THR cc_start: 0.8462 (m) cc_final: 0.8021 (p) REVERT: H 98 TYR cc_start: 0.8637 (t80) cc_final: 0.8330 (t80) REVERT: H 126 GLU cc_start: 0.7002 (pt0) cc_final: 0.6566 (tm-30) REVERT: J 39 LEU cc_start: 0.9092 (mt) cc_final: 0.8634 (pp) REVERT: K 56 GLU cc_start: 0.5829 (tm-30) cc_final: 0.5110 (tp30) REVERT: K 99 ASN cc_start: 0.8493 (t0) cc_final: 0.7759 (p0) REVERT: K 114 VAL cc_start: 0.8833 (m) cc_final: 0.8450 (p) REVERT: L 55 ILE cc_start: 0.7703 (pt) cc_final: 0.7464 (mm) REVERT: L 56 LEU cc_start: 0.7948 (pp) cc_final: 0.7333 (pp) REVERT: M 121 ILE cc_start: 0.8294 (mm) cc_final: 0.8040 (tp) REVERT: M 166 MET cc_start: 0.8286 (mmp) cc_final: 0.7718 (ttt) REVERT: M 185 TYR cc_start: 0.7498 (m-80) cc_final: 0.7280 (m-80) REVERT: M 194 LYS cc_start: 0.4724 (pttp) cc_final: 0.4480 (pttp) REVERT: N 297 MET cc_start: 0.5593 (mmt) cc_final: 0.5070 (mpp) REVERT: N 312 ARG cc_start: 0.8101 (mmt180) cc_final: 0.7583 (ptp-170) REVERT: N 382 ILE cc_start: 0.8067 (pt) cc_final: 0.7275 (tp) REVERT: N 387 GLU cc_start: 0.3001 (pp20) cc_final: 0.2634 (pp20) REVERT: O 86 MET cc_start: 0.7369 (tpt) cc_final: 0.6861 (tpp) REVERT: O 87 ASP cc_start: 0.7226 (t0) cc_final: 0.6834 (m-30) REVERT: O 89 ASP cc_start: 0.8294 (m-30) cc_final: 0.7871 (m-30) REVERT: O 128 HIS cc_start: 0.8075 (t70) cc_final: 0.7739 (t70) REVERT: O 295 GLN cc_start: 0.8876 (mt0) cc_final: 0.8453 (mm-40) REVERT: O 361 PHE cc_start: 0.5460 (m-10) cc_final: 0.5228 (m-10) REVERT: O 514 ASN cc_start: 0.7836 (t0) cc_final: 0.7018 (p0) REVERT: O 540 LEU cc_start: 0.7909 (tp) cc_final: 0.7646 (pp) REVERT: O 577 MET cc_start: 0.7110 (mmt) cc_final: 0.6833 (mmt) REVERT: O 653 MET cc_start: 0.4415 (mtp) cc_final: 0.4006 (mtp) REVERT: P 224 PHE cc_start: 0.6610 (m-10) cc_final: 0.6307 (m-80) REVERT: Q 51 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9084 (mt-10) REVERT: Q 60 ASN cc_start: 0.9081 (t0) cc_final: 0.8607 (m-40) outliers start: 16 outliers final: 3 residues processed: 979 average time/residue: 0.2202 time to fit residues: 350.8193 Evaluate side-chains 626 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 622 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 462 optimal weight: 9.9990 chunk 333 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 470 optimal weight: 0.0970 chunk 219 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 432 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 338 optimal weight: 5.9990 overall best weight: 4.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 944 ASN A1095 GLN A1385 GLN B 175 ASN ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 ASN B 550 HIS ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 ASN B 865 GLN B 902 GLN B1025 GLN ** B1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN G 143 ASN I 64 GLN J 53 HIS K 70 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 298 ASN O 162 ASN O 254 ASN O 549 GLN P 239 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.096663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.077666 restraints weight = 165172.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.079439 restraints weight = 106785.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.080652 restraints weight = 77320.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.081317 restraints weight = 61297.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.081901 restraints weight = 53089.774| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 39386 Z= 0.246 Angle : 0.992 49.463 53174 Z= 0.476 Chirality : 0.050 0.234 6016 Planarity : 0.007 0.112 6843 Dihedral : 6.821 59.382 5284 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.92 % Allowed : 12.85 % Favored : 86.23 % Rotamer: Outliers : 0.23 % Allowed : 7.25 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.10 (0.11), residues: 4779 helix: -1.28 (0.12), residues: 1513 sheet: -1.20 (0.20), residues: 598 loop : -2.84 (0.11), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG O 567 TYR 0.028 0.002 TYR P 261 PHE 0.041 0.002 PHE E 16 TRP 0.051 0.003 TRP P 183 HIS 0.013 0.002 HIS B 144 Details of bonding type rmsd covalent geometry : bond 0.00543 (39363) covalent geometry : angle 0.89898 (53153) hydrogen bonds : bond 0.05572 ( 1198) hydrogen bonds : angle 6.24294 ( 3405) metal coordination : bond 0.02132 ( 22) metal coordination : angle 21.12300 ( 21) Misc. bond : bond 0.03058 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 816 time to evaluate : 1.230 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: A 21 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7303 (tt) REVERT: A 91 PHE cc_start: 0.7169 (t80) cc_final: 0.6453 (t80) REVERT: A 273 MET cc_start: 0.7185 (ptp) cc_final: 0.6638 (mmt) REVERT: A 313 MET cc_start: 0.8286 (mmt) cc_final: 0.8002 (tmm) REVERT: A 394 VAL cc_start: 0.9330 (t) cc_final: 0.9025 (p) REVERT: A 463 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6532 (mm-30) REVERT: A 502 GLU cc_start: 0.7741 (pm20) cc_final: 0.7423 (mp0) REVERT: A 661 SER cc_start: 0.8693 (p) cc_final: 0.7703 (m) REVERT: A 759 GLU cc_start: 0.8237 (pt0) cc_final: 0.7752 (pp20) REVERT: A 794 MET cc_start: 0.8741 (mtm) cc_final: 0.8497 (mtm) REVERT: A 809 MET cc_start: 0.8378 (mmm) cc_final: 0.8077 (mmm) REVERT: A 835 PHE cc_start: 0.9111 (m-10) cc_final: 0.8795 (m-10) REVERT: A 857 SER cc_start: 0.9157 (t) cc_final: 0.8499 (m) REVERT: A 885 MET cc_start: 0.7641 (ttt) cc_final: 0.7341 (tmm) REVERT: A 926 MET cc_start: 0.8920 (ttp) cc_final: 0.8294 (ttm) REVERT: A 929 ASN cc_start: 0.7822 (m110) cc_final: 0.7610 (m110) REVERT: A 1163 LYS cc_start: 0.7081 (mppt) cc_final: 0.6350 (mmtt) REVERT: A 1260 MET cc_start: 0.6864 (tpt) cc_final: 0.6444 (tpp) REVERT: A 1263 LEU cc_start: 0.9161 (mt) cc_final: 0.8911 (mt) REVERT: A 1275 LEU cc_start: 0.7582 (tp) cc_final: 0.7348 (tt) REVERT: A 1358 LEU cc_start: 0.8197 (mp) cc_final: 0.7487 (tp) REVERT: B 204 ARG cc_start: 0.8075 (ttm110) cc_final: 0.7506 (mmt-90) REVERT: B 370 ASP cc_start: 0.7824 (t0) cc_final: 0.7575 (t0) REVERT: B 375 LYS cc_start: 0.9059 (mptt) cc_final: 0.8508 (mmtt) REVERT: B 449 MET cc_start: 0.5144 (tpp) cc_final: 0.4498 (tpp) REVERT: B 469 MET cc_start: 0.8549 (ttp) cc_final: 0.7540 (tmm) REVERT: B 470 MET cc_start: 0.8991 (mtm) cc_final: 0.8350 (mtp) REVERT: B 609 CYS cc_start: 0.7394 (m) cc_final: 0.6802 (m) REVERT: B 628 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7851 (ttp80) REVERT: B 722 ASP cc_start: 0.7978 (t0) cc_final: 0.7727 (t70) REVERT: B 885 MET cc_start: 0.7739 (tpp) cc_final: 0.7415 (tpt) REVERT: B 958 MET cc_start: 0.9099 (ttp) cc_final: 0.8816 (ttm) REVERT: B 1060 LEU cc_start: 0.8242 (mt) cc_final: 0.7922 (mt) REVERT: B 1115 ASN cc_start: 0.8452 (t0) cc_final: 0.8076 (t0) REVERT: C 63 ILE cc_start: 0.9248 (pt) cc_final: 0.8944 (mm) REVERT: C 69 ARG cc_start: 0.9372 (mtp85) cc_final: 0.7516 (ttp-170) REVERT: C 145 ASP cc_start: 0.7123 (m-30) cc_final: 0.6711 (m-30) REVERT: C 174 ARG cc_start: 0.8011 (mtt180) cc_final: 0.7471 (ptp-170) REVERT: D 4 LEU cc_start: 0.8513 (mp) cc_final: 0.7976 (tt) REVERT: D 98 MET cc_start: 0.6941 (mtm) cc_final: 0.5330 (ptm) REVERT: D 150 ILE cc_start: 0.8088 (mt) cc_final: 0.7598 (mm) REVERT: E 22 MET cc_start: 0.8961 (ttt) cc_final: 0.8222 (ttt) REVERT: E 57 MET cc_start: 0.8843 (tpt) cc_final: 0.8476 (tpp) REVERT: E 121 MET cc_start: 0.8704 (mmp) cc_final: 0.8375 (mmm) REVERT: F 104 ASN cc_start: 0.9042 (t0) cc_final: 0.8603 (t0) REVERT: F 145 ASP cc_start: 0.8289 (m-30) cc_final: 0.7792 (m-30) REVERT: G 147 ARG cc_start: 0.7261 (tpm170) cc_final: 0.6540 (mmm160) REVERT: G 205 MET cc_start: 0.3145 (mtp) cc_final: 0.2562 (mtp) REVERT: H 14 GLU cc_start: 0.8047 (pm20) cc_final: 0.7409 (pm20) REVERT: I 12 LEU cc_start: 0.6957 (mt) cc_final: 0.6576 (mt) REVERT: I 33 PHE cc_start: 0.7683 (t80) cc_final: 0.7289 (t80) REVERT: J 27 GLU cc_start: 0.7774 (pp20) cc_final: 0.7412 (pp20) REVERT: J 39 LEU cc_start: 0.9243 (mt) cc_final: 0.8846 (mt) REVERT: J 51 LEU cc_start: 0.9495 (tt) cc_final: 0.9246 (tp) REVERT: K 56 GLU cc_start: 0.6174 (tm-30) cc_final: 0.5493 (tm-30) REVERT: K 99 ASN cc_start: 0.8446 (t0) cc_final: 0.7851 (p0) REVERT: L 56 LEU cc_start: 0.7870 (pp) cc_final: 0.7655 (pp) REVERT: M 112 TYR cc_start: 0.5824 (t80) cc_final: 0.5539 (t80) REVERT: M 121 ILE cc_start: 0.8452 (mm) cc_final: 0.8026 (tp) REVERT: M 159 TYR cc_start: 0.8397 (m-80) cc_final: 0.7911 (m-80) REVERT: M 166 MET cc_start: 0.8171 (mmp) cc_final: 0.7742 (ttt) REVERT: M 180 LYS cc_start: 0.7834 (mmpt) cc_final: 0.7261 (pttt) REVERT: M 185 TYR cc_start: 0.7422 (m-80) cc_final: 0.6792 (m-80) REVERT: M 194 LYS cc_start: 0.4715 (pttp) cc_final: 0.4432 (pttm) REVERT: N 297 MET cc_start: 0.5502 (mmt) cc_final: 0.4886 (mpp) REVERT: N 312 ARG cc_start: 0.8235 (mmt180) cc_final: 0.7579 (ptp-170) REVERT: N 389 THR cc_start: 0.5502 (m) cc_final: 0.4912 (p) REVERT: O 86 MET cc_start: 0.7307 (tpt) cc_final: 0.6717 (tpp) REVERT: O 89 ASP cc_start: 0.8197 (m-30) cc_final: 0.7429 (m-30) REVERT: O 128 HIS cc_start: 0.7960 (t70) cc_final: 0.7547 (t70) REVERT: O 140 ILE cc_start: 0.8808 (mm) cc_final: 0.8167 (mm) REVERT: O 288 MET cc_start: 0.8828 (mpp) cc_final: 0.8385 (mmm) REVERT: O 295 GLN cc_start: 0.8825 (mt0) cc_final: 0.8426 (mm110) REVERT: O 514 ASN cc_start: 0.7842 (t0) cc_final: 0.7109 (p0) REVERT: O 653 MET cc_start: 0.4535 (mtp) cc_final: 0.4128 (mtp) REVERT: P 218 THR cc_start: 0.7193 (m) cc_final: 0.6925 (p) REVERT: P 221 ILE cc_start: 0.8974 (mm) cc_final: 0.8703 (mm) REVERT: P 224 PHE cc_start: 0.6416 (m-10) cc_final: 0.6077 (m-80) REVERT: P 261 TYR cc_start: 0.8012 (m-80) cc_final: 0.7449 (m-80) REVERT: Q 47 ILE cc_start: 0.4602 (mt) cc_final: 0.3594 (tt) REVERT: Q 51 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8818 (mt-10) REVERT: Q 60 ASN cc_start: 0.9121 (t0) cc_final: 0.8563 (m-40) REVERT: Q 66 LYS cc_start: 0.8998 (pttm) cc_final: 0.8590 (tptt) outliers start: 10 outliers final: 1 residues processed: 825 average time/residue: 0.2164 time to fit residues: 292.6271 Evaluate side-chains 577 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 575 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 450 optimal weight: 0.9980 chunk 366 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 113 optimal weight: 9.9990 chunk 240 optimal weight: 0.0670 chunk 421 optimal weight: 7.9990 chunk 270 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 101 optimal weight: 0.0000 overall best weight: 1.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN A 520 HIS ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 944 ASN ** A1419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 ASN B 902 GLN B1115 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 ASN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 298 ASN O 549 GLN P 239 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.099253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.080010 restraints weight = 161567.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.081810 restraints weight = 103628.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.082862 restraints weight = 74656.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.083914 restraints weight = 60093.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.084480 restraints weight = 50482.468| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 39386 Z= 0.153 Angle : 0.895 37.265 53174 Z= 0.420 Chirality : 0.048 0.341 6016 Planarity : 0.006 0.081 6843 Dihedral : 6.401 56.433 5284 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.92 % Allowed : 11.59 % Favored : 87.49 % Rotamer: Outliers : 0.07 % Allowed : 3.87 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (0.11), residues: 4779 helix: -0.92 (0.13), residues: 1512 sheet: -0.97 (0.20), residues: 606 loop : -2.70 (0.11), residues: 2661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 364 TYR 0.053 0.002 TYR O 480 PHE 0.031 0.002 PHE E 16 TRP 0.049 0.003 TRP P 183 HIS 0.016 0.001 HIS O 56 Details of bonding type rmsd covalent geometry : bond 0.00334 (39363) covalent geometry : angle 0.81059 (53153) hydrogen bonds : bond 0.04543 ( 1198) hydrogen bonds : angle 5.81464 ( 3405) metal coordination : bond 0.01454 ( 22) metal coordination : angle 19.08091 ( 21) Misc. bond : bond 0.00868 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 831 time to evaluate : 1.005 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: A 91 PHE cc_start: 0.7274 (t80) cc_final: 0.6519 (t80) REVERT: A 202 LYS cc_start: 0.8859 (mptt) cc_final: 0.8588 (mmtm) REVERT: A 245 ASP cc_start: 0.7601 (p0) cc_final: 0.7175 (p0) REVERT: A 247 THR cc_start: 0.8749 (p) cc_final: 0.8529 (p) REVERT: A 273 MET cc_start: 0.7179 (ptp) cc_final: 0.6713 (mmt) REVERT: A 396 ASP cc_start: 0.8405 (p0) cc_final: 0.7879 (t0) REVERT: A 463 GLU cc_start: 0.6756 (mm-30) cc_final: 0.6473 (mm-30) REVERT: A 577 THR cc_start: 0.9280 (m) cc_final: 0.9077 (m) REVERT: A 661 SER cc_start: 0.8602 (p) cc_final: 0.7787 (m) REVERT: A 794 MET cc_start: 0.8759 (mtm) cc_final: 0.8484 (mtm) REVERT: A 800 LYS cc_start: 0.9125 (mmmt) cc_final: 0.8764 (tppp) REVERT: A 835 PHE cc_start: 0.9046 (m-10) cc_final: 0.8699 (m-10) REVERT: A 857 SER cc_start: 0.9131 (t) cc_final: 0.8557 (m) REVERT: A 885 MET cc_start: 0.7656 (ttt) cc_final: 0.7398 (tmm) REVERT: A 929 ASN cc_start: 0.7834 (m110) cc_final: 0.7606 (m-40) REVERT: A 1163 LYS cc_start: 0.7074 (mppt) cc_final: 0.6385 (tptt) REVERT: A 1260 MET cc_start: 0.6701 (tpt) cc_final: 0.6485 (tpp) REVERT: A 1358 LEU cc_start: 0.8208 (mp) cc_final: 0.7792 (tp) REVERT: B 155 MET cc_start: 0.8818 (ttp) cc_final: 0.8612 (ttp) REVERT: B 210 ASP cc_start: 0.5330 (t0) cc_final: 0.5050 (m-30) REVERT: B 245 ASN cc_start: 0.8245 (p0) cc_final: 0.7946 (p0) REVERT: B 370 ASP cc_start: 0.7803 (t0) cc_final: 0.7437 (t0) REVERT: B 390 ASP cc_start: 0.8616 (t70) cc_final: 0.8327 (t0) REVERT: B 449 MET cc_start: 0.4863 (tpp) cc_final: 0.4317 (tpp) REVERT: B 469 MET cc_start: 0.8638 (ttt) cc_final: 0.7494 (tmm) REVERT: B 470 MET cc_start: 0.8926 (mtm) cc_final: 0.8465 (mtp) REVERT: B 628 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7747 (ttp80) REVERT: B 885 MET cc_start: 0.7646 (tpp) cc_final: 0.7446 (tpt) REVERT: B 944 MET cc_start: 0.8869 (ttp) cc_final: 0.8658 (ttp) REVERT: B 1060 LEU cc_start: 0.7849 (mt) cc_final: 0.7491 (mt) REVERT: B 1115 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.7980 (t0) REVERT: C 63 ILE cc_start: 0.9236 (pt) cc_final: 0.8929 (mm) REVERT: C 174 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7321 (ptp-170) REVERT: D 4 LEU cc_start: 0.8344 (mp) cc_final: 0.8086 (tt) REVERT: D 98 MET cc_start: 0.6466 (mtm) cc_final: 0.6054 (ptm) REVERT: D 108 THR cc_start: 0.7274 (p) cc_final: 0.7029 (p) REVERT: D 131 MET cc_start: 0.8160 (mpp) cc_final: 0.7657 (mpp) REVERT: E 22 MET cc_start: 0.8714 (ttt) cc_final: 0.8130 (ttt) REVERT: E 57 MET cc_start: 0.8866 (tpt) cc_final: 0.8555 (tpp) REVERT: E 104 ASN cc_start: 0.7582 (m110) cc_final: 0.6975 (t0) REVERT: E 121 MET cc_start: 0.8664 (mmp) cc_final: 0.8351 (mmm) REVERT: F 104 ASN cc_start: 0.8856 (t0) cc_final: 0.8326 (t0) REVERT: F 116 ASP cc_start: 0.8192 (p0) cc_final: 0.7738 (p0) REVERT: G 114 MET cc_start: 0.6153 (mtm) cc_final: 0.5543 (mmt) REVERT: G 147 ARG cc_start: 0.6762 (tpm170) cc_final: 0.6065 (mmm160) REVERT: G 148 PHE cc_start: 0.8018 (p90) cc_final: 0.7722 (p90) REVERT: G 205 MET cc_start: 0.3514 (mtp) cc_final: 0.2882 (mtp) REVERT: H 136 LYS cc_start: 0.8690 (tppt) cc_final: 0.7755 (mppt) REVERT: I 33 PHE cc_start: 0.7816 (t80) cc_final: 0.7265 (t80) REVERT: J 21 TYR cc_start: 0.9127 (t80) cc_final: 0.8902 (t80) REVERT: J 27 GLU cc_start: 0.7825 (pp20) cc_final: 0.7510 (pp20) REVERT: J 32 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6390 (mm-30) REVERT: J 39 LEU cc_start: 0.9149 (mt) cc_final: 0.8769 (mt) REVERT: K 56 GLU cc_start: 0.6345 (tm-30) cc_final: 0.5876 (tm-30) REVERT: K 99 ASN cc_start: 0.8355 (t0) cc_final: 0.7821 (p0) REVERT: L 56 LEU cc_start: 0.7890 (pp) cc_final: 0.7542 (pp) REVERT: L 58 LYS cc_start: 0.8400 (mmtt) cc_final: 0.8129 (mmmt) REVERT: L 67 PHE cc_start: 0.8639 (m-10) cc_final: 0.8345 (m-10) REVERT: M 74 PHE cc_start: 0.8147 (m-80) cc_final: 0.7715 (m-10) REVERT: M 90 TYR cc_start: 0.6917 (p90) cc_final: 0.6572 (p90) REVERT: M 117 HIS cc_start: 0.8372 (p90) cc_final: 0.7904 (p90) REVERT: M 166 MET cc_start: 0.8202 (mmp) cc_final: 0.7741 (ttt) REVERT: M 194 LYS cc_start: 0.4969 (pttp) cc_final: 0.4455 (mtmt) REVERT: N 312 ARG cc_start: 0.8205 (mmt180) cc_final: 0.7544 (ptp-170) REVERT: O 49 TYR cc_start: 0.8711 (m-80) cc_final: 0.8302 (m-80) REVERT: O 86 MET cc_start: 0.7401 (tpt) cc_final: 0.6814 (tpp) REVERT: O 89 ASP cc_start: 0.8059 (m-30) cc_final: 0.7226 (m-30) REVERT: O 128 HIS cc_start: 0.7852 (t70) cc_final: 0.7368 (t70) REVERT: O 136 ILE cc_start: 0.8557 (pt) cc_final: 0.7929 (pt) REVERT: O 139 GLU cc_start: 0.8800 (pp20) cc_final: 0.8385 (pp20) REVERT: O 295 GLN cc_start: 0.8763 (mt0) cc_final: 0.8424 (mm110) REVERT: O 514 ASN cc_start: 0.7704 (t0) cc_final: 0.7226 (p0) REVERT: O 582 GLU cc_start: 0.8405 (pm20) cc_final: 0.8038 (pm20) REVERT: P 175 ILE cc_start: 0.5891 (pt) cc_final: 0.5629 (pt) REVERT: P 221 ILE cc_start: 0.8901 (mm) cc_final: 0.8655 (mm) REVERT: P 224 PHE cc_start: 0.6380 (m-10) cc_final: 0.6075 (m-80) REVERT: P 261 TYR cc_start: 0.8208 (m-80) cc_final: 0.7761 (m-80) REVERT: Q 47 ILE cc_start: 0.4943 (mt) cc_final: 0.4033 (tt) REVERT: Q 51 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8860 (mt-10) outliers start: 3 outliers final: 0 residues processed: 832 average time/residue: 0.1950 time to fit residues: 269.3399 Evaluate side-chains 602 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 601 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 44 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 310 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 317 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 518 ASN A 566 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 944 ASN A1318 HIS A1340 ASN B 116 HIS ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 ASN ** B 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 147 HIS E 179 GLN G 143 ASN H 11 GLN H 35 GLN I 110 ASN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 298 ASN O 549 GLN P 219 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.092416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.073748 restraints weight = 168593.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075418 restraints weight = 107957.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076496 restraints weight = 78238.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.077217 restraints weight = 62045.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.077799 restraints weight = 53185.174| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.7374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 39386 Z= 0.281 Angle : 1.000 49.132 53174 Z= 0.483 Chirality : 0.051 0.265 6016 Planarity : 0.007 0.093 6843 Dihedral : 6.783 52.326 5284 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 1.09 % Allowed : 13.58 % Favored : 85.33 % Rotamer: Outliers : 0.09 % Allowed : 4.74 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.88 (0.11), residues: 4779 helix: -0.99 (0.12), residues: 1542 sheet: -1.15 (0.20), residues: 606 loop : -2.77 (0.11), residues: 2631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG O 567 TYR 0.026 0.003 TYR B 296 PHE 0.054 0.003 PHE E 16 TRP 0.051 0.004 TRP P 317 HIS 0.018 0.003 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00617 (39363) covalent geometry : angle 0.92051 (53153) hydrogen bonds : bond 0.05451 ( 1198) hydrogen bonds : angle 6.08809 ( 3405) metal coordination : bond 0.01743 ( 22) metal coordination : angle 19.69639 ( 21) Misc. bond : bond 0.03676 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 679 time to evaluate : 1.634 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: A 91 PHE cc_start: 0.8236 (t80) cc_final: 0.7856 (t80) REVERT: A 273 MET cc_start: 0.7392 (ptp) cc_final: 0.6828 (mmt) REVERT: A 661 SER cc_start: 0.8827 (p) cc_final: 0.8190 (m) REVERT: A 794 MET cc_start: 0.8782 (mtm) cc_final: 0.8566 (mtm) REVERT: A 835 PHE cc_start: 0.9086 (m-10) cc_final: 0.8209 (m-80) REVERT: A 885 MET cc_start: 0.8031 (ttt) cc_final: 0.7616 (tmm) REVERT: A 1097 ILE cc_start: 0.9250 (mt) cc_final: 0.8929 (tp) REVERT: A 1163 LYS cc_start: 0.6951 (mppt) cc_final: 0.6205 (mmtt) REVERT: A 1260 MET cc_start: 0.6947 (tpt) cc_final: 0.6568 (tpp) REVERT: A 1348 MET cc_start: 0.6850 (pmm) cc_final: 0.6479 (pmm) REVERT: A 1358 LEU cc_start: 0.8559 (mp) cc_final: 0.7853 (tt) REVERT: A 1421 MET cc_start: 0.8845 (tpt) cc_final: 0.8639 (tpt) REVERT: B 155 MET cc_start: 0.8982 (ttp) cc_final: 0.8735 (ttt) REVERT: B 375 LYS cc_start: 0.9055 (mmtt) cc_final: 0.8571 (mmtt) REVERT: B 449 MET cc_start: 0.4562 (tpp) cc_final: 0.3788 (tpp) REVERT: B 469 MET cc_start: 0.8672 (ttt) cc_final: 0.7382 (tmm) REVERT: B 470 MET cc_start: 0.8997 (mtm) cc_final: 0.7846 (mtp) REVERT: B 564 SER cc_start: 0.9187 (t) cc_final: 0.8711 (p) REVERT: B 987 MET cc_start: 0.9044 (mmm) cc_final: 0.8101 (mtt) REVERT: B 1026 LYS cc_start: 0.8422 (tttm) cc_final: 0.7735 (tttp) REVERT: B 1060 LEU cc_start: 0.8389 (mt) cc_final: 0.8141 (mt) REVERT: C 31 TRP cc_start: 0.8209 (t-100) cc_final: 0.7803 (t-100) REVERT: C 69 ARG cc_start: 0.9336 (mtp85) cc_final: 0.8318 (mtm-85) REVERT: C 148 LYS cc_start: 0.6047 (mmpt) cc_final: 0.5815 (mmmt) REVERT: C 174 ARG cc_start: 0.7907 (mtt180) cc_final: 0.7486 (ptp-170) REVERT: D 4 LEU cc_start: 0.8480 (mp) cc_final: 0.7971 (tt) REVERT: D 98 MET cc_start: 0.7043 (mtm) cc_final: 0.6119 (ptm) REVERT: D 108 THR cc_start: 0.7501 (p) cc_final: 0.7288 (p) REVERT: D 131 MET cc_start: 0.7982 (mpp) cc_final: 0.7619 (mpp) REVERT: E 22 MET cc_start: 0.9122 (ttt) cc_final: 0.8363 (ttt) REVERT: E 57 MET cc_start: 0.8921 (tpt) cc_final: 0.8472 (tpp) REVERT: E 121 MET cc_start: 0.8810 (mmp) cc_final: 0.8476 (mmm) REVERT: F 116 ASP cc_start: 0.8477 (p0) cc_final: 0.8129 (p0) REVERT: F 145 ASP cc_start: 0.8112 (m-30) cc_final: 0.7748 (m-30) REVERT: G 130 TRP cc_start: 0.6459 (m-10) cc_final: 0.6058 (m100) REVERT: G 147 ARG cc_start: 0.7273 (tpm170) cc_final: 0.7006 (mmm160) REVERT: G 155 PHE cc_start: 0.6528 (m-10) cc_final: 0.6172 (m-10) REVERT: G 205 MET cc_start: 0.3537 (mtp) cc_final: 0.2765 (mtp) REVERT: H 14 GLU cc_start: 0.8412 (pm20) cc_final: 0.8096 (pm20) REVERT: H 95 TYR cc_start: 0.7394 (t80) cc_final: 0.7098 (t80) REVERT: I 12 LEU cc_start: 0.7436 (mt) cc_final: 0.7041 (mt) REVERT: I 33 PHE cc_start: 0.8100 (t80) cc_final: 0.7333 (t80) REVERT: I 35 ILE cc_start: 0.4857 (tp) cc_final: 0.4282 (tp) REVERT: J 23 ASN cc_start: 0.8609 (t0) cc_final: 0.8359 (t0) REVERT: J 39 LEU cc_start: 0.9363 (mt) cc_final: 0.8890 (mt) REVERT: K 56 GLU cc_start: 0.6740 (tm-30) cc_final: 0.6474 (tp30) REVERT: K 99 ASN cc_start: 0.8409 (t0) cc_final: 0.7858 (p0) REVERT: L 56 LEU cc_start: 0.7945 (pp) cc_final: 0.7420 (pp) REVERT: M 166 MET cc_start: 0.8277 (mmp) cc_final: 0.7801 (ttt) REVERT: M 194 LYS cc_start: 0.5130 (pttp) cc_final: 0.4803 (pttm) REVERT: N 312 ARG cc_start: 0.8300 (mmt180) cc_final: 0.7655 (ptp-170) REVERT: N 389 THR cc_start: 0.5749 (m) cc_final: 0.5238 (p) REVERT: O 77 ARG cc_start: 0.8642 (ttm-80) cc_final: 0.8142 (ttp-110) REVERT: O 86 MET cc_start: 0.7192 (tpt) cc_final: 0.6721 (tpp) REVERT: O 87 ASP cc_start: 0.7226 (t0) cc_final: 0.6779 (m-30) REVERT: O 89 ASP cc_start: 0.8290 (m-30) cc_final: 0.7382 (m-30) REVERT: O 128 HIS cc_start: 0.7738 (t70) cc_final: 0.7260 (t70) REVERT: O 139 GLU cc_start: 0.9001 (pp20) cc_final: 0.8688 (pp20) REVERT: O 326 ILE cc_start: 0.8833 (mm) cc_final: 0.8582 (mm) REVERT: O 514 ASN cc_start: 0.8149 (t0) cc_final: 0.7545 (p0) REVERT: O 529 LYS cc_start: 0.8952 (ptpt) cc_final: 0.8196 (tttm) REVERT: P 175 ILE cc_start: 0.6194 (pt) cc_final: 0.5541 (pt) REVERT: P 224 PHE cc_start: 0.6160 (m-10) cc_final: 0.5770 (m-80) REVERT: Q 60 ASN cc_start: 0.9095 (t0) cc_final: 0.8492 (m110) outliers start: 4 outliers final: 1 residues processed: 683 average time/residue: 0.2424 time to fit residues: 273.9166 Evaluate side-chains 513 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 512 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 3 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 456 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 201 optimal weight: 0.0060 chunk 288 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 435 optimal weight: 9.9990 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 944 ASN ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1385 GLN ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 550 HIS ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 HIS G 143 ASN I 110 ASN K 95 HIS M 104 HIS ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 298 ASN ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.094865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.077523 restraints weight = 162922.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.078599 restraints weight = 116269.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.079434 restraints weight = 81393.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.079518 restraints weight = 75546.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.079691 restraints weight = 69319.318| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.7552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 39386 Z= 0.160 Angle : 0.895 39.978 53174 Z= 0.421 Chirality : 0.048 0.266 6016 Planarity : 0.006 0.082 6843 Dihedral : 6.402 59.643 5284 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 1.09 % Allowed : 11.66 % Favored : 87.26 % Rotamer: Outliers : 0.02 % Allowed : 2.43 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.63 (0.11), residues: 4779 helix: -0.67 (0.13), residues: 1528 sheet: -1.05 (0.21), residues: 577 loop : -2.68 (0.11), residues: 2674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 567 TYR 0.024 0.002 TYR A 679 PHE 0.021 0.002 PHE O 651 TRP 0.040 0.002 TRP P 183 HIS 0.014 0.001 HIS O 56 Details of bonding type rmsd covalent geometry : bond 0.00354 (39363) covalent geometry : angle 0.81331 (53153) hydrogen bonds : bond 0.04524 ( 1198) hydrogen bonds : angle 5.74269 ( 3405) metal coordination : bond 0.01292 ( 22) metal coordination : angle 18.84406 ( 21) Misc. bond : bond 0.01606 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 712 time to evaluate : 1.636 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: A 91 PHE cc_start: 0.8077 (t80) cc_final: 0.7830 (t80) REVERT: A 273 MET cc_start: 0.7774 (ptp) cc_final: 0.6887 (mmt) REVERT: A 274 MET cc_start: 0.6360 (ppp) cc_final: 0.6126 (ppp) REVERT: A 396 ASP cc_start: 0.8333 (p0) cc_final: 0.8077 (t70) REVERT: A 463 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6570 (mm-30) REVERT: A 577 THR cc_start: 0.9292 (m) cc_final: 0.9058 (m) REVERT: A 598 MET cc_start: 0.6883 (mmm) cc_final: 0.6583 (tpt) REVERT: A 644 GLU cc_start: 0.8945 (pm20) cc_final: 0.8156 (pm20) REVERT: A 661 SER cc_start: 0.8732 (p) cc_final: 0.8106 (m) REVERT: A 674 LYS cc_start: 0.8398 (mmmt) cc_final: 0.8041 (mmmt) REVERT: A 794 MET cc_start: 0.8813 (mtm) cc_final: 0.8295 (mtm) REVERT: A 800 LYS cc_start: 0.9139 (mmmt) cc_final: 0.8780 (tppp) REVERT: A 809 MET cc_start: 0.8277 (mmm) cc_final: 0.7962 (mmm) REVERT: A 835 PHE cc_start: 0.9039 (m-10) cc_final: 0.8144 (m-80) REVERT: A 885 MET cc_start: 0.8136 (ttt) cc_final: 0.7581 (tmm) REVERT: A 974 LEU cc_start: 0.8890 (pp) cc_final: 0.8681 (pp) REVERT: A 1097 ILE cc_start: 0.9341 (mt) cc_final: 0.9070 (tp) REVERT: A 1163 LYS cc_start: 0.6932 (mppt) cc_final: 0.6105 (mmtt) REVERT: A 1260 MET cc_start: 0.6794 (tpt) cc_final: 0.6438 (tpp) REVERT: A 1348 MET cc_start: 0.6632 (pmm) cc_final: 0.6295 (pmm) REVERT: A 1358 LEU cc_start: 0.8463 (mp) cc_final: 0.7719 (tt) REVERT: A 1421 MET cc_start: 0.8836 (tpt) cc_final: 0.8624 (tpt) REVERT: B 155 MET cc_start: 0.8747 (ttp) cc_final: 0.8507 (ttt) REVERT: B 361 TYR cc_start: 0.9492 (t80) cc_final: 0.9283 (t80) REVERT: B 370 ASP cc_start: 0.8071 (t0) cc_final: 0.7807 (t0) REVERT: B 375 LYS cc_start: 0.8978 (mmtt) cc_final: 0.8544 (mmtt) REVERT: B 449 MET cc_start: 0.4711 (tpp) cc_final: 0.4130 (tpp) REVERT: B 469 MET cc_start: 0.8572 (ttt) cc_final: 0.7313 (tmm) REVERT: B 470 MET cc_start: 0.8934 (mtm) cc_final: 0.8129 (mtp) REVERT: B 481 ARG cc_start: 0.3399 (mpt180) cc_final: 0.1608 (ppt170) REVERT: B 490 GLN cc_start: 0.7963 (pm20) cc_final: 0.7410 (pm20) REVERT: B 564 SER cc_start: 0.9224 (t) cc_final: 0.8782 (p) REVERT: B 907 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7918 (tt0) REVERT: B 944 MET cc_start: 0.9120 (ttp) cc_final: 0.8885 (ttm) REVERT: B 1026 LYS cc_start: 0.8046 (tttm) cc_final: 0.7437 (tttp) REVERT: B 1060 LEU cc_start: 0.8240 (mt) cc_final: 0.7990 (mt) REVERT: C 31 TRP cc_start: 0.7971 (t-100) cc_final: 0.7724 (t-100) REVERT: C 70 ILE cc_start: 0.9514 (tp) cc_final: 0.9277 (tp) REVERT: C 112 MET cc_start: 0.9374 (pmm) cc_final: 0.9143 (pmm) REVERT: C 174 ARG cc_start: 0.7848 (mtt180) cc_final: 0.7380 (ptp-170) REVERT: C 248 GLN cc_start: 0.9502 (pt0) cc_final: 0.8655 (pp30) REVERT: D 4 LEU cc_start: 0.8399 (mp) cc_final: 0.7916 (tt) REVERT: D 98 MET cc_start: 0.6836 (mtm) cc_final: 0.6608 (ptm) REVERT: D 108 THR cc_start: 0.7439 (p) cc_final: 0.7129 (p) REVERT: D 131 MET cc_start: 0.7816 (mpp) cc_final: 0.7588 (mpp) REVERT: E 22 MET cc_start: 0.8867 (ttt) cc_final: 0.8651 (ttp) REVERT: E 57 MET cc_start: 0.8817 (tpt) cc_final: 0.8436 (tpp) REVERT: E 104 ASN cc_start: 0.7632 (m110) cc_final: 0.6965 (t0) REVERT: E 121 MET cc_start: 0.8809 (mmp) cc_final: 0.8216 (mpp) REVERT: F 145 ASP cc_start: 0.7993 (m-30) cc_final: 0.7630 (m-30) REVERT: G 147 ARG cc_start: 0.7084 (tpm170) cc_final: 0.6788 (mmm160) REVERT: G 148 PHE cc_start: 0.7963 (p90) cc_final: 0.7727 (p90) REVERT: G 205 MET cc_start: 0.3372 (mtp) cc_final: 0.2615 (mtp) REVERT: H 14 GLU cc_start: 0.8383 (pm20) cc_final: 0.7935 (pm20) REVERT: H 136 LYS cc_start: 0.8632 (tppt) cc_final: 0.7245 (mppt) REVERT: I 12 LEU cc_start: 0.7368 (mt) cc_final: 0.6931 (mt) REVERT: J 32 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6402 (mm-30) REVERT: J 39 LEU cc_start: 0.9226 (mt) cc_final: 0.8818 (mt) REVERT: K 56 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6489 (tm-30) REVERT: K 99 ASN cc_start: 0.8373 (t0) cc_final: 0.7810 (p0) REVERT: M 158 GLN cc_start: 0.8371 (mt0) cc_final: 0.8021 (mt0) REVERT: M 166 MET cc_start: 0.8253 (mmp) cc_final: 0.7578 (ttt) REVERT: N 312 ARG cc_start: 0.8251 (mmt180) cc_final: 0.7625 (ptp-170) REVERT: O 77 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.8145 (ttp-110) REVERT: O 87 ASP cc_start: 0.7156 (t0) cc_final: 0.6817 (m-30) REVERT: O 128 HIS cc_start: 0.7406 (t70) cc_final: 0.6892 (t70) REVERT: O 139 GLU cc_start: 0.8929 (pp20) cc_final: 0.8557 (pp20) REVERT: O 140 ILE cc_start: 0.8753 (mm) cc_final: 0.8483 (mm) REVERT: O 505 MET cc_start: 0.8873 (mmp) cc_final: 0.8503 (mmm) REVERT: O 514 ASN cc_start: 0.8048 (t0) cc_final: 0.7606 (p0) REVERT: O 582 GLU cc_start: 0.8423 (pm20) cc_final: 0.8029 (pm20) REVERT: O 629 MET cc_start: 0.8393 (ppp) cc_final: 0.8018 (ppp) REVERT: P 224 PHE cc_start: 0.6346 (m-10) cc_final: 0.5882 (m-80) REVERT: P 261 TYR cc_start: 0.8459 (m-80) cc_final: 0.7263 (m-80) REVERT: Q 58 TYR cc_start: 0.8252 (t80) cc_final: 0.7951 (t80) REVERT: Q 60 ASN cc_start: 0.8884 (t0) cc_final: 0.8337 (m-40) outliers start: 1 outliers final: 0 residues processed: 713 average time/residue: 0.2394 time to fit residues: 283.5744 Evaluate side-chains 531 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 531 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 459 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 159 optimal weight: 5.9990 chunk 295 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 311 optimal weight: 10.0000 chunk 57 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN A 648 ASN A 944 ASN ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1340 ASN A1385 GLN B 298 GLN B 550 HIS ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 146 HIS ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.097047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.077898 restraints weight = 161920.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079659 restraints weight = 103965.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.080855 restraints weight = 74957.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.081758 restraints weight = 59381.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.082370 restraints weight = 49824.860| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.7663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 39386 Z= 0.141 Angle : 0.873 34.704 53174 Z= 0.407 Chirality : 0.047 0.252 6016 Planarity : 0.005 0.088 6843 Dihedral : 6.147 65.874 5284 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 1.07 % Allowed : 12.09 % Favored : 86.84 % Rotamer: Outliers : 0.02 % Allowed : 1.68 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.12), residues: 4779 helix: -0.45 (0.13), residues: 1520 sheet: -0.93 (0.21), residues: 571 loop : -2.60 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B1038 TYR 0.031 0.001 TYR G 67 PHE 0.033 0.002 PHE E 82 TRP 0.033 0.002 TRP P 183 HIS 0.026 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00307 (39363) covalent geometry : angle 0.79499 (53153) hydrogen bonds : bond 0.04077 ( 1198) hydrogen bonds : angle 5.47734 ( 3405) metal coordination : bond 0.01434 ( 22) metal coordination : angle 18.22408 ( 21) Misc. bond : bond 0.00542 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 729 time to evaluate : 1.319 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: A 17 GLU cc_start: 0.8213 (tt0) cc_final: 0.7985 (tt0) REVERT: A 273 MET cc_start: 0.7779 (ptp) cc_final: 0.6756 (tpp) REVERT: A 274 MET cc_start: 0.6119 (ppp) cc_final: 0.5803 (ppp) REVERT: A 396 ASP cc_start: 0.8295 (p0) cc_final: 0.7989 (t70) REVERT: A 463 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6589 (mm-30) REVERT: A 577 THR cc_start: 0.9288 (m) cc_final: 0.9079 (m) REVERT: A 644 GLU cc_start: 0.9013 (pm20) cc_final: 0.8195 (pm20) REVERT: A 661 SER cc_start: 0.8829 (p) cc_final: 0.8171 (m) REVERT: A 794 MET cc_start: 0.8854 (mtm) cc_final: 0.8624 (mtm) REVERT: A 809 MET cc_start: 0.8241 (mmm) cc_final: 0.7872 (mmm) REVERT: A 835 PHE cc_start: 0.9070 (m-10) cc_final: 0.8146 (m-10) REVERT: A 974 LEU cc_start: 0.8791 (pp) cc_final: 0.8575 (pp) REVERT: A 1163 LYS cc_start: 0.7184 (mppt) cc_final: 0.6559 (tptt) REVERT: A 1260 MET cc_start: 0.6739 (tpt) cc_final: 0.6350 (tpp) REVERT: A 1348 MET cc_start: 0.6723 (pmm) cc_final: 0.6328 (pmm) REVERT: A 1358 LEU cc_start: 0.8527 (mp) cc_final: 0.7858 (tt) REVERT: B 370 ASP cc_start: 0.8166 (t0) cc_final: 0.7892 (t70) REVERT: B 375 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8366 (mmtt) REVERT: B 383 LEU cc_start: 0.9245 (mm) cc_final: 0.8985 (mm) REVERT: B 449 MET cc_start: 0.4760 (tpp) cc_final: 0.4467 (tpp) REVERT: B 469 MET cc_start: 0.8543 (ttt) cc_final: 0.7235 (tmm) REVERT: B 470 MET cc_start: 0.8863 (mtm) cc_final: 0.8008 (mtp) REVERT: B 481 ARG cc_start: 0.3429 (mpt180) cc_final: 0.1652 (ppt170) REVERT: B 490 GLN cc_start: 0.7641 (pm20) cc_final: 0.7435 (pm20) REVERT: B 564 SER cc_start: 0.9044 (t) cc_final: 0.8635 (p) REVERT: B 907 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7960 (tt0) REVERT: B 944 MET cc_start: 0.9071 (ttp) cc_final: 0.8852 (ttm) REVERT: B 987 MET cc_start: 0.9167 (mmm) cc_final: 0.8442 (mtt) REVERT: B 1026 LYS cc_start: 0.8041 (tttm) cc_final: 0.7424 (tttp) REVERT: B 1060 LEU cc_start: 0.8168 (mt) cc_final: 0.7926 (mt) REVERT: B 1084 MET cc_start: 0.7597 (tpp) cc_final: 0.7388 (mmt) REVERT: C 31 TRP cc_start: 0.7706 (t-100) cc_final: 0.7365 (t-100) REVERT: C 70 ILE cc_start: 0.9502 (tp) cc_final: 0.9218 (tp) REVERT: C 93 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7756 (mp10) REVERT: C 112 MET cc_start: 0.9329 (pmm) cc_final: 0.9056 (pmm) REVERT: C 174 ARG cc_start: 0.7744 (mtt180) cc_final: 0.7308 (ptp-170) REVERT: C 248 GLN cc_start: 0.9480 (pt0) cc_final: 0.8633 (pp30) REVERT: D 4 LEU cc_start: 0.8342 (mp) cc_final: 0.7945 (tt) REVERT: D 98 MET cc_start: 0.6456 (mtm) cc_final: 0.6156 (ptm) REVERT: D 108 THR cc_start: 0.7384 (p) cc_final: 0.7105 (p) REVERT: D 131 MET cc_start: 0.7909 (mpp) cc_final: 0.7631 (mpp) REVERT: E 57 MET cc_start: 0.9036 (tpt) cc_final: 0.8626 (tpp) REVERT: E 104 ASN cc_start: 0.7529 (m110) cc_final: 0.6880 (t0) REVERT: E 121 MET cc_start: 0.8962 (mmp) cc_final: 0.8312 (mpp) REVERT: F 145 ASP cc_start: 0.8012 (m-30) cc_final: 0.7656 (m-30) REVERT: G 114 MET cc_start: 0.5422 (ptt) cc_final: 0.4809 (ptm) REVERT: G 130 TRP cc_start: 0.5966 (m-10) cc_final: 0.5715 (m100) REVERT: G 147 ARG cc_start: 0.7241 (tpm170) cc_final: 0.6991 (mmm160) REVERT: G 148 PHE cc_start: 0.7935 (p90) cc_final: 0.7664 (p90) REVERT: G 199 SER cc_start: 0.6315 (m) cc_final: 0.4019 (m) REVERT: G 205 MET cc_start: 0.3442 (mtp) cc_final: 0.2667 (mtp) REVERT: H 14 GLU cc_start: 0.8370 (pm20) cc_final: 0.7917 (pm20) REVERT: H 95 TYR cc_start: 0.7825 (t80) cc_final: 0.7533 (t80) REVERT: H 97 MET cc_start: 0.8802 (mmm) cc_final: 0.8342 (mmt) REVERT: I 12 LEU cc_start: 0.7468 (mt) cc_final: 0.6879 (mt) REVERT: J 39 LEU cc_start: 0.9223 (mt) cc_final: 0.8772 (mt) REVERT: J 51 LEU cc_start: 0.9387 (tt) cc_final: 0.8999 (tp) REVERT: K 56 GLU cc_start: 0.6960 (tm-30) cc_final: 0.6479 (tm-30) REVERT: M 90 TYR cc_start: 0.6998 (p90) cc_final: 0.6502 (p90) REVERT: M 117 HIS cc_start: 0.8244 (p90) cc_final: 0.7826 (p90) REVERT: M 166 MET cc_start: 0.7881 (mmp) cc_final: 0.7276 (ttp) REVERT: M 246 THR cc_start: 0.9141 (p) cc_final: 0.8920 (p) REVERT: N 308 GLN cc_start: 0.7277 (mt0) cc_final: 0.6875 (mm-40) REVERT: N 312 ARG cc_start: 0.8194 (mmt180) cc_final: 0.7551 (ptp-170) REVERT: O 128 HIS cc_start: 0.7548 (t70) cc_final: 0.7079 (t70) REVERT: O 139 GLU cc_start: 0.8931 (pp20) cc_final: 0.8598 (pp20) REVERT: O 140 ILE cc_start: 0.8668 (mm) cc_final: 0.8393 (mm) REVERT: O 144 MET cc_start: 0.7257 (tpp) cc_final: 0.6773 (tpp) REVERT: O 514 ASN cc_start: 0.7927 (t0) cc_final: 0.7615 (p0) REVERT: O 582 GLU cc_start: 0.8327 (pm20) cc_final: 0.7836 (pm20) REVERT: O 629 MET cc_start: 0.8533 (ppp) cc_final: 0.8156 (ppp) REVERT: P 224 PHE cc_start: 0.6575 (m-10) cc_final: 0.6085 (m-80) REVERT: P 261 TYR cc_start: 0.8252 (m-80) cc_final: 0.7147 (m-80) REVERT: Q 51 GLU cc_start: 0.9277 (mt-10) cc_final: 0.9024 (tp30) REVERT: Q 58 TYR cc_start: 0.8291 (t80) cc_final: 0.7980 (t80) outliers start: 1 outliers final: 0 residues processed: 730 average time/residue: 0.2200 time to fit residues: 266.8857 Evaluate side-chains 545 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 238 optimal weight: 0.5980 chunk 110 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 133 optimal weight: 0.6980 chunk 237 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 320 optimal weight: 0.7980 chunk 261 optimal weight: 0.6980 chunk 328 optimal weight: 9.9990 chunk 426 optimal weight: 10.0000 chunk 476 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 386 ASN A 648 ASN A 944 ASN ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 HIS ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 HIS O 584 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.097159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.078584 restraints weight = 160730.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.080279 restraints weight = 102762.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.081448 restraints weight = 73900.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.082273 restraints weight = 58289.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.082888 restraints weight = 49200.044| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.7849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39386 Z= 0.136 Angle : 0.859 34.408 53174 Z= 0.401 Chirality : 0.047 0.240 6016 Planarity : 0.005 0.068 6843 Dihedral : 5.969 66.203 5284 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 1.03 % Allowed : 11.76 % Favored : 87.21 % Rotamer: Outliers : 0.02 % Allowed : 1.45 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.12), residues: 4779 helix: -0.32 (0.13), residues: 1517 sheet: -0.86 (0.21), residues: 587 loop : -2.55 (0.11), residues: 2675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 184 TYR 0.026 0.001 TYR A1060 PHE 0.022 0.001 PHE E 82 TRP 0.039 0.002 TRP O 583 HIS 0.009 0.001 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00298 (39363) covalent geometry : angle 0.78226 (53153) hydrogen bonds : bond 0.03903 ( 1198) hydrogen bonds : angle 5.34973 ( 3405) metal coordination : bond 0.01291 ( 22) metal coordination : angle 17.93124 ( 21) Misc. bond : bond 0.00323 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 710 time to evaluate : 1.740 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: A 17 GLU cc_start: 0.8231 (tt0) cc_final: 0.7966 (tt0) REVERT: A 91 PHE cc_start: 0.7938 (t80) cc_final: 0.7722 (t80) REVERT: A 261 LEU cc_start: 0.8903 (tp) cc_final: 0.8649 (tp) REVERT: A 273 MET cc_start: 0.7749 (ptp) cc_final: 0.6779 (tpp) REVERT: A 396 ASP cc_start: 0.8255 (p0) cc_final: 0.7959 (t70) REVERT: A 463 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6715 (mm-30) REVERT: A 577 THR cc_start: 0.9227 (m) cc_final: 0.8982 (m) REVERT: A 661 SER cc_start: 0.8749 (p) cc_final: 0.8184 (m) REVERT: A 674 LYS cc_start: 0.8283 (mmmt) cc_final: 0.7596 (ptpt) REVERT: A 794 MET cc_start: 0.8939 (mtm) cc_final: 0.8553 (mtm) REVERT: A 835 PHE cc_start: 0.9085 (m-10) cc_final: 0.8126 (m-10) REVERT: A 885 MET cc_start: 0.6838 (tmm) cc_final: 0.6536 (tmm) REVERT: A 974 LEU cc_start: 0.8777 (pp) cc_final: 0.8528 (pp) REVERT: A 1084 GLU cc_start: 0.6940 (tt0) cc_final: 0.6495 (mt-10) REVERT: A 1128 GLU cc_start: 0.8177 (tp30) cc_final: 0.7610 (tt0) REVERT: A 1163 LYS cc_start: 0.6996 (mppt) cc_final: 0.6516 (tptt) REVERT: A 1260 MET cc_start: 0.6879 (tpt) cc_final: 0.6425 (tpp) REVERT: A 1348 MET cc_start: 0.6817 (pmm) cc_final: 0.6463 (pmm) REVERT: A 1358 LEU cc_start: 0.8495 (mp) cc_final: 0.8060 (tt) REVERT: B 155 MET cc_start: 0.8325 (ttp) cc_final: 0.8071 (ttp) REVERT: B 370 ASP cc_start: 0.8162 (t0) cc_final: 0.7859 (t70) REVERT: B 375 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8372 (mmtt) REVERT: B 449 MET cc_start: 0.4997 (tpp) cc_final: 0.4792 (tpp) REVERT: B 469 MET cc_start: 0.8550 (ttt) cc_final: 0.7190 (tmm) REVERT: B 470 MET cc_start: 0.8820 (mtm) cc_final: 0.7975 (mtp) REVERT: B 481 ARG cc_start: 0.3531 (mpt180) cc_final: 0.1694 (ppt170) REVERT: B 597 MET cc_start: 0.8305 (mmt) cc_final: 0.7963 (mmt) REVERT: B 727 LEU cc_start: 0.9111 (mm) cc_final: 0.8905 (mm) REVERT: B 746 TYR cc_start: 0.8311 (t80) cc_final: 0.7867 (t80) REVERT: B 907 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7886 (tt0) REVERT: B 987 MET cc_start: 0.9155 (mmm) cc_final: 0.7868 (mmm) REVERT: B 1026 LYS cc_start: 0.8027 (tttm) cc_final: 0.7544 (tttp) REVERT: B 1060 LEU cc_start: 0.8164 (mt) cc_final: 0.7929 (mt) REVERT: C 70 ILE cc_start: 0.9434 (tp) cc_final: 0.9220 (tp) REVERT: C 174 ARG cc_start: 0.7737 (mtt180) cc_final: 0.7296 (ptp-170) REVERT: C 248 GLN cc_start: 0.9462 (pt0) cc_final: 0.8625 (pp30) REVERT: D 108 THR cc_start: 0.7343 (p) cc_final: 0.7126 (p) REVERT: D 131 MET cc_start: 0.7722 (mpp) cc_final: 0.7519 (mpp) REVERT: E 22 MET cc_start: 0.8540 (ttt) cc_final: 0.7991 (tmm) REVERT: E 57 MET cc_start: 0.8932 (tpt) cc_final: 0.8610 (tpp) REVERT: E 104 ASN cc_start: 0.7510 (m110) cc_final: 0.6897 (t0) REVERT: E 121 MET cc_start: 0.8928 (mmp) cc_final: 0.8286 (mpp) REVERT: F 145 ASP cc_start: 0.8166 (m-30) cc_final: 0.7746 (m-30) REVERT: G 114 MET cc_start: 0.5117 (ptt) cc_final: 0.4898 (ptt) REVERT: G 130 TRP cc_start: 0.5969 (m-10) cc_final: 0.5594 (m100) REVERT: G 148 PHE cc_start: 0.7925 (p90) cc_final: 0.7339 (p90) REVERT: G 155 PHE cc_start: 0.6138 (m-10) cc_final: 0.5808 (m-80) REVERT: G 194 TYR cc_start: 0.6549 (t80) cc_final: 0.6274 (t80) REVERT: G 199 SER cc_start: 0.6564 (m) cc_final: 0.4869 (m) REVERT: G 205 MET cc_start: 0.3466 (mtp) cc_final: 0.2694 (mtp) REVERT: H 14 GLU cc_start: 0.8381 (pm20) cc_final: 0.7963 (pm20) REVERT: I 12 LEU cc_start: 0.7270 (mt) cc_final: 0.6908 (mt) REVERT: J 39 LEU cc_start: 0.9219 (mt) cc_final: 0.8754 (mt) REVERT: K 56 GLU cc_start: 0.6869 (tm-30) cc_final: 0.6406 (tm-30) REVERT: M 90 TYR cc_start: 0.7097 (p90) cc_final: 0.6516 (p90) REVERT: M 117 HIS cc_start: 0.7969 (p90) cc_final: 0.7682 (p90) REVERT: M 166 MET cc_start: 0.7949 (mmp) cc_final: 0.7316 (ttp) REVERT: M 170 LEU cc_start: 0.8501 (mp) cc_final: 0.7743 (tt) REVERT: M 180 LYS cc_start: 0.7216 (mmmt) cc_final: 0.6705 (pttm) REVERT: M 185 TYR cc_start: 0.7777 (m-80) cc_final: 0.7253 (m-80) REVERT: N 308 GLN cc_start: 0.7191 (mt0) cc_final: 0.6894 (mm-40) REVERT: N 312 ARG cc_start: 0.8205 (mmt180) cc_final: 0.7555 (ptp-170) REVERT: O 78 GLU cc_start: 0.8968 (pt0) cc_final: 0.8742 (pt0) REVERT: O 128 HIS cc_start: 0.7480 (t-90) cc_final: 0.6845 (t70) REVERT: O 138 ASP cc_start: 0.9270 (t0) cc_final: 0.9033 (t0) REVERT: O 139 GLU cc_start: 0.8938 (pp20) cc_final: 0.8620 (pp20) REVERT: O 140 ILE cc_start: 0.8682 (mm) cc_final: 0.8451 (mm) REVERT: O 287 PHE cc_start: 0.7449 (t80) cc_final: 0.7229 (t80) REVERT: O 514 ASN cc_start: 0.8000 (t0) cc_final: 0.7785 (p0) REVERT: O 575 ASN cc_start: 0.8030 (m-40) cc_final: 0.7694 (m110) REVERT: O 582 GLU cc_start: 0.8409 (pm20) cc_final: 0.8025 (pm20) REVERT: O 629 MET cc_start: 0.8527 (ppp) cc_final: 0.8211 (ppp) REVERT: O 653 MET cc_start: 0.3790 (mmp) cc_final: 0.3314 (mtp) REVERT: P 224 PHE cc_start: 0.6588 (m-10) cc_final: 0.6067 (m-80) REVERT: P 261 TYR cc_start: 0.8239 (m-80) cc_final: 0.7238 (m-80) REVERT: Q 51 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8938 (tp30) REVERT: Q 58 TYR cc_start: 0.8214 (t80) cc_final: 0.7912 (t80) outliers start: 1 outliers final: 1 residues processed: 711 average time/residue: 0.2431 time to fit residues: 290.1449 Evaluate side-chains 554 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 553 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 338 optimal weight: 9.9990 chunk 191 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 308 optimal weight: 0.0020 chunk 351 optimal weight: 2.9990 chunk 310 optimal weight: 9.9990 chunk 306 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 256 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 ASN A 675 HIS A 944 ASN ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 HIS O 584 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.097222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.079601 restraints weight = 164016.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.080932 restraints weight = 115988.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081805 restraints weight = 79164.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.081941 restraints weight = 73463.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.082027 restraints weight = 67031.475| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.8014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 39386 Z= 0.142 Angle : 0.873 34.891 53174 Z= 0.403 Chirality : 0.047 0.317 6016 Planarity : 0.005 0.068 6843 Dihedral : 5.881 68.842 5284 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 1.05 % Allowed : 11.93 % Favored : 87.03 % Rotamer: Outliers : 0.02 % Allowed : 0.75 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.12), residues: 4779 helix: -0.23 (0.13), residues: 1519 sheet: -0.81 (0.21), residues: 585 loop : -2.57 (0.11), residues: 2675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 628 TYR 0.023 0.001 TYR O 543 PHE 0.016 0.001 PHE O 576 TRP 0.048 0.002 TRP P 183 HIS 0.009 0.001 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00315 (39363) covalent geometry : angle 0.78937 (53153) hydrogen bonds : bond 0.03870 ( 1198) hydrogen bonds : angle 5.29670 ( 3405) metal coordination : bond 0.01478 ( 22) metal coordination : angle 18.77845 ( 21) Misc. bond : bond 0.00144 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 702 time to evaluate : 1.618 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: A 273 MET cc_start: 0.7821 (ptp) cc_final: 0.6867 (tpp) REVERT: A 463 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6673 (mm-30) REVERT: A 577 THR cc_start: 0.9230 (m) cc_final: 0.8939 (m) REVERT: A 661 SER cc_start: 0.8700 (p) cc_final: 0.8031 (m) REVERT: A 835 PHE cc_start: 0.9029 (m-10) cc_final: 0.8096 (m-80) REVERT: A 885 MET cc_start: 0.6944 (tmm) cc_final: 0.6557 (tmm) REVERT: A 974 LEU cc_start: 0.8755 (pp) cc_final: 0.8495 (pp) REVERT: A 1084 GLU cc_start: 0.6787 (tt0) cc_final: 0.6477 (mt-10) REVERT: A 1163 LYS cc_start: 0.6814 (mppt) cc_final: 0.6239 (tptt) REVERT: A 1260 MET cc_start: 0.6844 (tpt) cc_final: 0.6482 (tpp) REVERT: A 1348 MET cc_start: 0.6608 (pmm) cc_final: 0.6324 (pmm) REVERT: A 1358 LEU cc_start: 0.8401 (mp) cc_final: 0.7969 (tt) REVERT: B 204 ARG cc_start: 0.7827 (mmt180) cc_final: 0.7345 (mpt180) REVERT: B 375 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8376 (mmtt) REVERT: B 449 MET cc_start: 0.5021 (tpp) cc_final: 0.4713 (tpp) REVERT: B 469 MET cc_start: 0.8437 (ttt) cc_final: 0.7072 (tmm) REVERT: B 470 MET cc_start: 0.8825 (mtm) cc_final: 0.7881 (mtp) REVERT: B 481 ARG cc_start: 0.3327 (mpt180) cc_final: 0.1570 (ppt170) REVERT: B 727 LEU cc_start: 0.9151 (mm) cc_final: 0.8874 (mm) REVERT: B 746 TYR cc_start: 0.8204 (t80) cc_final: 0.7767 (t80) REVERT: B 907 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7763 (tt0) REVERT: B 1026 LYS cc_start: 0.8013 (tttm) cc_final: 0.7429 (tttp) REVERT: B 1060 LEU cc_start: 0.8284 (mt) cc_final: 0.8040 (mt) REVERT: C 31 TRP cc_start: 0.7738 (t-100) cc_final: 0.7162 (t-100) REVERT: C 70 ILE cc_start: 0.9345 (tp) cc_final: 0.9143 (tp) REVERT: C 93 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7655 (mp10) REVERT: C 112 MET cc_start: 0.9290 (pmm) cc_final: 0.9024 (pmm) REVERT: C 174 ARG cc_start: 0.7770 (mtt180) cc_final: 0.7210 (ptp-170) REVERT: C 248 GLN cc_start: 0.9444 (pt0) cc_final: 0.8664 (pp30) REVERT: D 1 MET cc_start: 0.8221 (ttm) cc_final: 0.7819 (ttt) REVERT: D 131 MET cc_start: 0.7807 (mpp) cc_final: 0.7508 (mpp) REVERT: E 2 ASP cc_start: 0.5800 (m-30) cc_final: 0.5194 (p0) REVERT: E 57 MET cc_start: 0.8933 (tpt) cc_final: 0.8581 (tpp) REVERT: E 75 MET cc_start: 0.8602 (mmp) cc_final: 0.8386 (mmm) REVERT: E 104 ASN cc_start: 0.7468 (m110) cc_final: 0.6899 (t0) REVERT: E 121 MET cc_start: 0.9000 (mmp) cc_final: 0.8280 (mpp) REVERT: E 127 ILE cc_start: 0.9248 (mm) cc_final: 0.8935 (pt) REVERT: E 159 ASP cc_start: 0.8345 (p0) cc_final: 0.7897 (t0) REVERT: E 165 LEU cc_start: 0.9622 (mt) cc_final: 0.9368 (tp) REVERT: F 145 ASP cc_start: 0.8107 (m-30) cc_final: 0.7675 (m-30) REVERT: G 106 ASP cc_start: 0.8643 (p0) cc_final: 0.8372 (p0) REVERT: G 114 MET cc_start: 0.5125 (ptt) cc_final: 0.4883 (ptt) REVERT: G 130 TRP cc_start: 0.6221 (m-10) cc_final: 0.5783 (m100) REVERT: G 148 PHE cc_start: 0.7969 (p90) cc_final: 0.7370 (p90) REVERT: G 155 PHE cc_start: 0.6279 (m-10) cc_final: 0.5934 (m-80) REVERT: G 194 TYR cc_start: 0.6662 (t80) cc_final: 0.6442 (t80) REVERT: G 199 SER cc_start: 0.6632 (m) cc_final: 0.5230 (m) REVERT: G 205 MET cc_start: 0.3420 (mtp) cc_final: 0.2688 (mtp) REVERT: H 14 GLU cc_start: 0.8426 (pm20) cc_final: 0.7993 (pm20) REVERT: I 12 LEU cc_start: 0.7124 (mt) cc_final: 0.6709 (mt) REVERT: J 39 LEU cc_start: 0.9216 (mt) cc_final: 0.8692 (mt) REVERT: K 56 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6572 (tm-30) REVERT: K 114 VAL cc_start: 0.8779 (m) cc_final: 0.8507 (p) REVERT: M 90 TYR cc_start: 0.7191 (p90) cc_final: 0.6574 (p90) REVERT: M 117 HIS cc_start: 0.8031 (p90) cc_final: 0.7761 (p90) REVERT: M 159 TYR cc_start: 0.8757 (m-80) cc_final: 0.8530 (m-80) REVERT: M 180 LYS cc_start: 0.7217 (mmmt) cc_final: 0.6663 (pttm) REVERT: M 185 TYR cc_start: 0.7912 (m-80) cc_final: 0.7429 (m-80) REVERT: N 308 GLN cc_start: 0.7370 (mt0) cc_final: 0.7159 (mt0) REVERT: N 312 ARG cc_start: 0.8209 (mmt180) cc_final: 0.7589 (ptp-170) REVERT: O 128 HIS cc_start: 0.7420 (t70) cc_final: 0.7010 (t70) REVERT: O 138 ASP cc_start: 0.9260 (t0) cc_final: 0.9033 (t0) REVERT: O 139 GLU cc_start: 0.8995 (pp20) cc_final: 0.8726 (pp20) REVERT: O 140 ILE cc_start: 0.8694 (mm) cc_final: 0.8454 (mm) REVERT: O 144 MET cc_start: 0.7021 (tpp) cc_final: 0.6553 (tpp) REVERT: O 288 MET cc_start: 0.9078 (mpp) cc_final: 0.8686 (mpp) REVERT: O 505 MET cc_start: 0.9192 (mmp) cc_final: 0.8499 (mmm) REVERT: O 575 ASN cc_start: 0.8142 (m-40) cc_final: 0.7830 (m-40) REVERT: O 582 GLU cc_start: 0.8420 (pm20) cc_final: 0.7915 (pm20) REVERT: O 629 MET cc_start: 0.8576 (ppp) cc_final: 0.8271 (ppp) REVERT: P 224 PHE cc_start: 0.6503 (m-10) cc_final: 0.6019 (m-80) REVERT: P 261 TYR cc_start: 0.8307 (m-80) cc_final: 0.7228 (m-80) REVERT: Q 51 GLU cc_start: 0.9239 (mt-10) cc_final: 0.9015 (tp30) REVERT: Q 58 TYR cc_start: 0.8237 (t80) cc_final: 0.7951 (t80) outliers start: 1 outliers final: 0 residues processed: 703 average time/residue: 0.2279 time to fit residues: 269.1218 Evaluate side-chains 535 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 535 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 323 optimal weight: 0.5980 chunk 311 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 233 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 312 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 383 optimal weight: 0.7980 chunk 382 optimal weight: 8.9990 chunk 166 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 648 ASN A 675 HIS A 944 ASN ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1149 ASN ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 947 HIS C 137 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 56 HIS O 128 HIS O 584 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.098141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.080541 restraints weight = 162601.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.082073 restraints weight = 109870.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.082708 restraints weight = 79218.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.083228 restraints weight = 66010.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.083330 restraints weight = 61948.717| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.8179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39386 Z= 0.135 Angle : 0.871 37.164 53174 Z= 0.402 Chirality : 0.047 0.279 6016 Planarity : 0.005 0.068 6843 Dihedral : 5.807 69.805 5284 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 1.11 % Allowed : 11.38 % Favored : 87.51 % Rotamer: Outliers : 0.02 % Allowed : 0.44 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.12), residues: 4779 helix: -0.19 (0.13), residues: 1530 sheet: -0.74 (0.21), residues: 582 loop : -2.54 (0.11), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1380 TYR 0.024 0.001 TYR H 93 PHE 0.019 0.001 PHE G 80 TRP 0.056 0.002 TRP O 583 HIS 0.008 0.001 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00295 (39363) covalent geometry : angle 0.78980 (53153) hydrogen bonds : bond 0.03690 ( 1198) hydrogen bonds : angle 5.23629 ( 3405) metal coordination : bond 0.01420 ( 22) metal coordination : angle 18.53629 ( 21) Misc. bond : bond 0.00269 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 712 time to evaluate : 1.581 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: A 261 LEU cc_start: 0.8902 (tp) cc_final: 0.8615 (tp) REVERT: A 273 MET cc_start: 0.7806 (ptp) cc_final: 0.6886 (tpp) REVERT: A 463 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6553 (mm-30) REVERT: A 577 THR cc_start: 0.9209 (m) cc_final: 0.8922 (m) REVERT: A 644 GLU cc_start: 0.9057 (pm20) cc_final: 0.8146 (pm20) REVERT: A 660 LEU cc_start: 0.8836 (mp) cc_final: 0.8626 (mt) REVERT: A 661 SER cc_start: 0.8729 (p) cc_final: 0.8161 (m) REVERT: A 723 LEU cc_start: 0.8560 (pt) cc_final: 0.7960 (tt) REVERT: A 835 PHE cc_start: 0.9069 (m-10) cc_final: 0.8083 (m-10) REVERT: A 885 MET cc_start: 0.6946 (tmm) cc_final: 0.6605 (tmm) REVERT: A 974 LEU cc_start: 0.8704 (pp) cc_final: 0.8442 (pp) REVERT: A 996 ASP cc_start: 0.8260 (p0) cc_final: 0.7965 (p0) REVERT: A 997 GLN cc_start: 0.8250 (pm20) cc_final: 0.7914 (pm20) REVERT: A 1096 SER cc_start: 0.9117 (t) cc_final: 0.8895 (t) REVERT: A 1163 LYS cc_start: 0.6889 (mppt) cc_final: 0.6219 (tptt) REVERT: A 1260 MET cc_start: 0.6750 (tpt) cc_final: 0.6356 (tpp) REVERT: A 1278 ILE cc_start: 0.8853 (mp) cc_final: 0.8631 (mt) REVERT: B 375 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8395 (mmtt) REVERT: B 449 MET cc_start: 0.4971 (tpp) cc_final: 0.4617 (tpp) REVERT: B 451 ARG cc_start: 0.8479 (mmm160) cc_final: 0.7807 (tpp80) REVERT: B 469 MET cc_start: 0.8499 (ttt) cc_final: 0.7138 (tmm) REVERT: B 470 MET cc_start: 0.8768 (mtm) cc_final: 0.7914 (mtp) REVERT: B 481 ARG cc_start: 0.3250 (mpt180) cc_final: 0.1498 (ppt170) REVERT: B 727 LEU cc_start: 0.9084 (mm) cc_final: 0.8799 (mm) REVERT: B 746 TYR cc_start: 0.8324 (t80) cc_final: 0.7955 (t80) REVERT: B 944 MET cc_start: 0.8946 (ttp) cc_final: 0.8442 (ttp) REVERT: B 987 MET cc_start: 0.9240 (mmm) cc_final: 0.8678 (mtt) REVERT: B 1003 MET cc_start: 0.8796 (tmm) cc_final: 0.8390 (tmm) REVERT: B 1026 LYS cc_start: 0.8036 (tttm) cc_final: 0.7514 (tttp) REVERT: B 1060 LEU cc_start: 0.8242 (mt) cc_final: 0.7999 (mt) REVERT: B 1117 ILE cc_start: 0.9138 (mp) cc_final: 0.8542 (mp) REVERT: B 1123 TYR cc_start: 0.7747 (t80) cc_final: 0.7307 (t80) REVERT: C 31 TRP cc_start: 0.7964 (t-100) cc_final: 0.7164 (t-100) REVERT: C 93 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7668 (mp10) REVERT: C 112 MET cc_start: 0.9201 (pmm) cc_final: 0.8927 (pmm) REVERT: C 174 ARG cc_start: 0.7772 (mtt180) cc_final: 0.7186 (ptp-170) REVERT: C 248 GLN cc_start: 0.9469 (pt0) cc_final: 0.9062 (tt0) REVERT: D 108 THR cc_start: 0.7624 (p) cc_final: 0.7412 (p) REVERT: D 131 MET cc_start: 0.7813 (mpp) cc_final: 0.7491 (mpp) REVERT: E 2 ASP cc_start: 0.5853 (m-30) cc_final: 0.5211 (p0) REVERT: E 22 MET cc_start: 0.8591 (ttt) cc_final: 0.7705 (tpp) REVERT: E 57 MET cc_start: 0.8955 (tpt) cc_final: 0.8586 (tpp) REVERT: E 104 ASN cc_start: 0.7452 (m110) cc_final: 0.6894 (t0) REVERT: E 121 MET cc_start: 0.8974 (mmp) cc_final: 0.8273 (mpp) REVERT: E 127 ILE cc_start: 0.9247 (mm) cc_final: 0.8877 (pt) REVERT: E 159 ASP cc_start: 0.8481 (p0) cc_final: 0.8004 (t0) REVERT: E 165 LEU cc_start: 0.9628 (mt) cc_final: 0.9383 (tp) REVERT: E 179 GLN cc_start: 0.7561 (pt0) cc_final: 0.7182 (pt0) REVERT: F 145 ASP cc_start: 0.8253 (m-30) cc_final: 0.7800 (m-30) REVERT: G 106 ASP cc_start: 0.8786 (p0) cc_final: 0.8287 (m-30) REVERT: G 114 MET cc_start: 0.5422 (ptt) cc_final: 0.4689 (ptm) REVERT: G 130 TRP cc_start: 0.6142 (m-10) cc_final: 0.5701 (m100) REVERT: G 148 PHE cc_start: 0.7991 (p90) cc_final: 0.7740 (p90) REVERT: G 155 PHE cc_start: 0.6342 (m-10) cc_final: 0.5853 (m-10) REVERT: G 194 TYR cc_start: 0.6665 (t80) cc_final: 0.6342 (t80) REVERT: G 205 MET cc_start: 0.3594 (mtp) cc_final: 0.2823 (mtp) REVERT: H 14 GLU cc_start: 0.8411 (pm20) cc_final: 0.7967 (pm20) REVERT: H 97 MET cc_start: 0.8458 (mmm) cc_final: 0.8151 (mmm) REVERT: I 12 LEU cc_start: 0.7032 (mt) cc_final: 0.6619 (mt) REVERT: J 39 LEU cc_start: 0.9203 (mt) cc_final: 0.8762 (mt) REVERT: K 56 GLU cc_start: 0.7107 (tm-30) cc_final: 0.6699 (tm-30) REVERT: K 114 VAL cc_start: 0.8573 (m) cc_final: 0.8260 (p) REVERT: M 90 TYR cc_start: 0.7180 (p90) cc_final: 0.6562 (p90) REVERT: M 117 HIS cc_start: 0.8056 (p90) cc_final: 0.7767 (p90) REVERT: M 159 TYR cc_start: 0.8741 (m-80) cc_final: 0.8470 (m-80) REVERT: M 180 LYS cc_start: 0.7296 (mmmt) cc_final: 0.6851 (pttm) REVERT: M 185 TYR cc_start: 0.7965 (m-80) cc_final: 0.7547 (m-80) REVERT: M 246 THR cc_start: 0.9179 (p) cc_final: 0.8915 (p) REVERT: N 308 GLN cc_start: 0.7460 (mt0) cc_final: 0.7237 (mt0) REVERT: N 312 ARG cc_start: 0.8233 (mmt180) cc_final: 0.7542 (ptp-170) REVERT: O 128 HIS cc_start: 0.7468 (t-90) cc_final: 0.6905 (t70) REVERT: O 138 ASP cc_start: 0.9312 (t0) cc_final: 0.9093 (t0) REVERT: O 139 GLU cc_start: 0.9078 (pp20) cc_final: 0.8774 (pp20) REVERT: O 144 MET cc_start: 0.7062 (tpp) cc_final: 0.6551 (tpp) REVERT: O 288 MET cc_start: 0.9209 (mpp) cc_final: 0.8785 (mpp) REVERT: O 361 PHE cc_start: 0.6953 (m-10) cc_final: 0.6661 (m-10) REVERT: O 505 MET cc_start: 0.9234 (mmp) cc_final: 0.8416 (mmm) REVERT: O 575 ASN cc_start: 0.8118 (m-40) cc_final: 0.7752 (m-40) REVERT: O 629 MET cc_start: 0.8640 (ppp) cc_final: 0.8305 (ppp) REVERT: O 653 MET cc_start: 0.4469 (mmp) cc_final: 0.3766 (mtp) REVERT: P 224 PHE cc_start: 0.6594 (m-10) cc_final: 0.6107 (m-80) REVERT: P 249 TYR cc_start: 0.8075 (t80) cc_final: 0.7636 (t80) REVERT: P 261 TYR cc_start: 0.8205 (m-80) cc_final: 0.7371 (m-80) outliers start: 1 outliers final: 0 residues processed: 712 average time/residue: 0.2290 time to fit residues: 275.1092 Evaluate side-chains 544 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 81 optimal weight: 0.2980 chunk 433 optimal weight: 0.0070 chunk 315 optimal weight: 4.9990 chunk 279 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 343 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 419 optimal weight: 6.9990 chunk 291 optimal weight: 3.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 648 ASN A 675 HIS A 843 GLN A 944 ASN ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1385 GLN ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 56 HIS O 128 HIS O 584 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.097629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.079962 restraints weight = 161802.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.081630 restraints weight = 108989.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.082767 restraints weight = 73725.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.082884 restraints weight = 62606.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.083013 restraints weight = 57679.560| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.8327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 39386 Z= 0.135 Angle : 0.858 36.981 53174 Z= 0.396 Chirality : 0.047 0.269 6016 Planarity : 0.005 0.087 6843 Dihedral : 5.735 70.303 5284 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 1.07 % Allowed : 11.86 % Favored : 87.07 % Rotamer: Outliers : 0.02 % Allowed : 0.47 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.12), residues: 4779 helix: -0.10 (0.14), residues: 1521 sheet: -0.70 (0.21), residues: 580 loop : -2.51 (0.11), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 147 TYR 0.026 0.001 TYR J 21 PHE 0.019 0.001 PHE I 33 TRP 0.038 0.002 TRP P 183 HIS 0.008 0.001 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00299 (39363) covalent geometry : angle 0.77886 (53153) hydrogen bonds : bond 0.03684 ( 1198) hydrogen bonds : angle 5.16865 ( 3405) metal coordination : bond 0.01299 ( 22) metal coordination : angle 18.14944 ( 21) Misc. bond : bond 0.00262 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7475.18 seconds wall clock time: 130 minutes 9.52 seconds (7809.52 seconds total)