Starting phenix.real_space_refine on Fri Jun 20 00:41:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mf3_23810/06_2025/7mf3_23810.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mf3_23810/06_2025/7mf3_23810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mf3_23810/06_2025/7mf3_23810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mf3_23810/06_2025/7mf3_23810.map" model { file = "/net/cci-nas-00/data/ceres_data/7mf3_23810/06_2025/7mf3_23810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mf3_23810/06_2025/7mf3_23810.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 4 5.21 5 S 129 5.16 5 C 14359 2.51 5 N 3965 2.21 5 O 4475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22938 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7230 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 24, 'TRANS': 865} Chain breaks: 2 Chain: "B" Number of atoms: 7276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 896, 7276 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 24, 'TRANS': 871} Chain breaks: 2 Chain: "C" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1169 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "D" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1277 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "E" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1270 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "F" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1169 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1742 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1737 Classifications: {'peptide': 211} Link IDs: {'TRANS': 210} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.50, per 1000 atoms: 0.68 Number of scatterers: 22938 At special positions: 0 Unit cell: (101.587, 172.608, 229.245, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 129 16.00 P 6 15.00 Mg 4 11.99 O 4475 8.00 N 3965 7.00 C 14359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.40 Conformation dependent library (CDL) restraints added in 3.2 seconds 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5380 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 14 sheets defined 64.0% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.676A pdb=" N GLU A 91 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 110 removed outlier: 3.907A pdb=" N PHE A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 152 through 168 removed outlier: 3.555A pdb=" N ILE A 156 " --> pdb=" O HIS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 Processing helix chain 'A' and resid 219 through 235 removed outlier: 3.860A pdb=" N GLN A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASN A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 3.834A pdb=" N PHE A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 4.023A pdb=" N TYR A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.568A pdb=" N ASN A 312 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 313 " --> pdb=" O PHE A 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 309 through 313' Processing helix chain 'A' and resid 327 through 343 removed outlier: 3.907A pdb=" N MET A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 362 removed outlier: 3.610A pdb=" N GLN A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 394 through 404 Processing helix chain 'A' and resid 419 through 449 Processing helix chain 'A' and resid 476 through 498 Processing helix chain 'A' and resid 498 through 508 removed outlier: 3.603A pdb=" N GLU A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 529 Processing helix chain 'A' and resid 537 through 546 removed outlier: 4.179A pdb=" N TRP A 546 " --> pdb=" O ASP A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 564 removed outlier: 3.670A pdb=" N VAL A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'A' and resid 606 through 615 removed outlier: 4.073A pdb=" N GLN A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 627 removed outlier: 3.938A pdb=" N TRP A 625 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP A 627 " --> pdb=" O ASP A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 677 removed outlier: 3.966A pdb=" N LEU A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 707 removed outlier: 4.878A pdb=" N GLU A 703 " --> pdb=" O HIS A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 719 Processing helix chain 'A' and resid 727 through 735 Processing helix chain 'A' and resid 748 through 761 removed outlier: 3.879A pdb=" N CYS A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'A' and resid 778 through 783 removed outlier: 4.039A pdb=" N LEU A 781 " --> pdb=" O THR A 778 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 783 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 792 removed outlier: 4.020A pdb=" N ARG A 788 " --> pdb=" O LEU A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 840 removed outlier: 4.464A pdb=" N TRP A 838 " --> pdb=" O LYS A 834 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TRP A 840 " --> pdb=" O ARG A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 846 Processing helix chain 'A' and resid 847 through 854 removed outlier: 4.244A pdb=" N LEU A 851 " --> pdb=" O VAL A 847 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN A 852 " --> pdb=" O LYS A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 949 removed outlier: 4.016A pdb=" N LYS A 871 " --> pdb=" O LEU A 867 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A 872 " --> pdb=" O GLN A 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 removed outlier: 3.547A pdb=" N SER B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.725A pdb=" N TYR B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 198 Processing helix chain 'B' and resid 218 through 234 removed outlier: 4.056A pdb=" N ASN B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Proline residue: B 229 - end of helix Processing helix chain 'B' and resid 273 through 277 removed outlier: 3.586A pdb=" N ALA B 277 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.672A pdb=" N TYR B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 328 through 343 removed outlier: 3.984A pdb=" N PHE B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 364 Processing helix chain 'B' and resid 381 through 390 removed outlier: 3.797A pdb=" N GLN B 385 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 404 Processing helix chain 'B' and resid 419 through 450 Processing helix chain 'B' and resid 476 through 509 removed outlier: 3.684A pdb=" N LEU B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 527 removed outlier: 3.773A pdb=" N LEU B 527 " --> pdb=" O PRO B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 547 removed outlier: 4.128A pdb=" N TRP B 546 " --> pdb=" O ASP B 542 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 564 Processing helix chain 'B' and resid 596 through 602 removed outlier: 3.688A pdb=" N MET B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 615 removed outlier: 3.892A pdb=" N GLN B 615 " --> pdb=" O SER B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 627 removed outlier: 3.984A pdb=" N LEU B 624 " --> pdb=" O PHE B 620 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP B 625 " --> pdb=" O VAL B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 675 Processing helix chain 'B' and resid 697 through 709 removed outlier: 4.073A pdb=" N VAL B 701 " --> pdb=" O ASP B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 720 removed outlier: 3.704A pdb=" N GLY B 713 " --> pdb=" O GLY B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 734 Processing helix chain 'B' and resid 748 through 761 Processing helix chain 'B' and resid 763 through 767 Processing helix chain 'B' and resid 779 through 839 removed outlier: 3.873A pdb=" N THR B 793 " --> pdb=" O ASP B 789 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP B 794 " --> pdb=" O LEU B 790 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL B 795 " --> pdb=" O LYS B 791 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN B 828 " --> pdb=" O VAL B 824 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA B 830 " --> pdb=" O GLN B 826 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA B 831 " --> pdb=" O ARG B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 845 removed outlier: 3.984A pdb=" N PHE B 844 " --> pdb=" O TRP B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 853 Processing helix chain 'B' and resid 855 through 948 removed outlier: 4.227A pdb=" N GLU B 859 " --> pdb=" O ARG B 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 18 removed outlier: 4.241A pdb=" N THR C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 45 through 52 removed outlier: 4.129A pdb=" N LYS C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 78 removed outlier: 3.617A pdb=" N LEU C 70 " --> pdb=" O PHE C 66 " (cutoff:3.500A) Proline residue: C 71 - end of helix Processing helix chain 'C' and resid 84 through 96 removed outlier: 4.005A pdb=" N TYR C 88 " --> pdb=" O CYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.574A pdb=" N ARG C 109 " --> pdb=" O GLY C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 140 through 148 Processing helix chain 'D' and resid 27 through 41 removed outlier: 3.500A pdb=" N GLN D 31 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 61 removed outlier: 3.870A pdb=" N ASP D 55 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA D 58 " --> pdb=" O HIS D 54 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET D 60 " --> pdb=" O MET D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 76 Processing helix chain 'D' and resid 81 through 91 Processing helix chain 'D' and resid 98 through 110 removed outlier: 4.115A pdb=" N ILE D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP D 110 " --> pdb=" O PHE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 removed outlier: 3.709A pdb=" N THR D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'E' and resid 26 through 41 removed outlier: 4.419A pdb=" N GLN E 31 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 61 removed outlier: 3.834A pdb=" N ASP E 55 " --> pdb=" O GLU E 51 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER E 59 " --> pdb=" O ASP E 55 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N MET E 60 " --> pdb=" O MET E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 74 Processing helix chain 'E' and resid 83 through 93 removed outlier: 3.866A pdb=" N THR E 87 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE E 89 " --> pdb=" O PHE E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 110 removed outlier: 4.454A pdb=" N PHE E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP E 110 " --> pdb=" O PHE E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 127 Processing helix chain 'E' and resid 135 through 145 removed outlier: 3.588A pdb=" N GLU E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N MET E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA E 145 " --> pdb=" O MET E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 154 through 164 Processing helix chain 'F' and resid 4 through 18 removed outlier: 4.250A pdb=" N THR F 8 " --> pdb=" O SER F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 38 Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 65 through 77 Proline residue: F 71 - end of helix Processing helix chain 'F' and resid 84 through 96 removed outlier: 3.978A pdb=" N TYR F 88 " --> pdb=" O CYS F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 115 Processing helix chain 'F' and resid 120 through 128 removed outlier: 3.674A pdb=" N VAL F 124 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL F 128 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 148 Processing helix chain 'G' and resid 1413 through 1527 removed outlier: 3.507A pdb=" N LYS G1417 " --> pdb=" O GLN G1413 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP G1527 " --> pdb=" O VAL G1523 " (cutoff:3.500A) Processing helix chain 'G' and resid 1532 through 1623 removed outlier: 4.041A pdb=" N LEU G1536 " --> pdb=" O ASN G1532 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR G1542 " --> pdb=" O LYS G1538 " (cutoff:3.500A) Processing helix chain 'H' and resid 1414 through 1524 removed outlier: 4.358A pdb=" N ALA H1418 " --> pdb=" O PHE H1414 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA H1419 " --> pdb=" O GLU H1415 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER H1524 " --> pdb=" O GLU H1520 " (cutoff:3.500A) Processing helix chain 'H' and resid 1535 through 1621 removed outlier: 3.620A pdb=" N SER H1539 " --> pdb=" O GLU H1535 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 71 removed outlier: 4.290A pdb=" N GLN A 76 " --> pdb=" O TRP A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 117 removed outlier: 6.087A pdb=" N CYS A 121 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE A 685 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 123 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 174 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N CYS A 684 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR A 176 " --> pdb=" O CYS A 684 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 removed outlier: 7.449A pdb=" N GLN A 171 " --> pdb=" O GLY A 462 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 249 through 255 removed outlier: 3.518A pdb=" N GLY A 264 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 368 through 369 Processing sheet with id=AA6, first strand: chain 'A' and resid 406 through 407 removed outlier: 3.899A pdb=" N VAL A 414 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 583 through 584 removed outlier: 3.783A pdb=" N ILE A 583 " --> pdb=" O VAL A 590 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 723 through 726 removed outlier: 3.634A pdb=" N ASN A 723 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 775 " --> pdb=" O ARG A 768 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 35 through 38 Processing sheet with id=AB1, first strand: chain 'B' and resid 57 through 60 Processing sheet with id=AB2, first strand: chain 'B' and resid 116 through 117 removed outlier: 6.619A pdb=" N CYS B 121 " --> pdb=" O ARG B 683 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE B 685 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 123 " --> pdb=" O ILE B 685 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL B 682 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU B 174 " --> pdb=" O VAL B 682 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N CYS B 684 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR B 176 " --> pdb=" O CYS B 684 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 171 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 464 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS B 175 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER B 459 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE B 251 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU B 268 " --> pdb=" O PHE B 251 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 579 through 585 removed outlier: 5.985A pdb=" N PHE B 581 " --> pdb=" O TYR B 592 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TYR B 592 " --> pdb=" O PHE B 581 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 588 " --> pdb=" O HIS B 585 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 724 through 726 removed outlier: 3.691A pdb=" N ILE B 725 " --> pdb=" O ILE B 774 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 117 through 118 removed outlier: 3.571A pdb=" N ILE E 117 " --> pdb=" O PHE E 153 " (cutoff:3.500A) 1349 hydrogen bonds defined for protein. 3999 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: 8.34 Time building geometry restraints manager: 7.47 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: 7480 1.34 - 1.46: 2872 1.46 - 1.58: 12700 1.58 - 1.70: 6 1.70 - 1.82: 220 Bond restraints: 23278 Sorted by residual: bond pdb=" O3 PO4 A2002 " pdb=" P PO4 A2002 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.47e+00 bond pdb=" O3 PO4 B2002 " pdb=" P PO4 B2002 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.95e+00 bond pdb=" O4 PO4 A2002 " pdb=" P PO4 A2002 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.70e+00 bond pdb=" O2 PO4 A2002 " pdb=" P PO4 A2002 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" O4 PO4 B2002 " pdb=" P PO4 B2002 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.30e+00 ... (remaining 23273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 30600 2.05 - 4.11: 537 4.11 - 6.16: 104 6.16 - 8.21: 20 8.21 - 10.27: 5 Bond angle restraints: 31266 Sorted by residual: angle pdb=" C GLN B 327 " pdb=" N ASP B 328 " pdb=" CA ASP B 328 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C THR B 176 " pdb=" CA THR B 176 " pdb=" CB THR B 176 " ideal model delta sigma weight residual 109.80 102.34 7.46 1.70e+00 3.46e-01 1.93e+01 angle pdb=" N GLY B 182 " pdb=" CA GLY B 182 " pdb=" C GLY B 182 " ideal model delta sigma weight residual 115.36 109.63 5.73 1.33e+00 5.65e-01 1.86e+01 angle pdb=" N LYS B 183 " pdb=" CA LYS B 183 " pdb=" C LYS B 183 " ideal model delta sigma weight residual 113.19 108.39 4.80 1.19e+00 7.06e-01 1.63e+01 angle pdb=" O ARG A 815 " pdb=" C ARG A 815 " pdb=" N GLN A 816 " ideal model delta sigma weight residual 122.03 126.10 -4.07 1.04e+00 9.25e-01 1.53e+01 ... (remaining 31261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 14110 35.84 - 71.68: 260 71.68 - 107.51: 38 107.51 - 143.35: 2 143.35 - 179.19: 1 Dihedral angle restraints: 14411 sinusoidal: 6156 harmonic: 8255 Sorted by residual: dihedral pdb=" C5' ADP A2001 " pdb=" O5' ADP A2001 " pdb=" PA ADP A2001 " pdb=" O2A ADP A2001 " ideal model delta sinusoidal sigma weight residual 300.00 120.81 179.19 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP B2001 " pdb=" O5' ADP B2001 " pdb=" PA ADP B2001 " pdb=" O2A ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 -176.24 116.24 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" O2A ADP A2001 " pdb=" O3A ADP A2001 " pdb=" PA ADP A2001 " pdb=" PB ADP A2001 " ideal model delta sinusoidal sigma weight residual -60.00 49.62 -109.62 1 2.00e+01 2.50e-03 3.21e+01 ... (remaining 14408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3050 0.067 - 0.134: 331 0.134 - 0.202: 17 0.202 - 0.269: 0 0.269 - 0.336: 2 Chirality restraints: 3400 Sorted by residual: chirality pdb=" CA ARG A 815 " pdb=" N ARG A 815 " pdb=" C ARG A 815 " pdb=" CB ARG A 815 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA THR B 176 " pdb=" N THR B 176 " pdb=" C THR B 176 " pdb=" CB THR B 176 " both_signs ideal model delta sigma weight residual False 2.53 2.80 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB THR A 404 " pdb=" CA THR A 404 " pdb=" OG1 THR A 404 " pdb=" CG2 THR A 404 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.80e-01 ... (remaining 3397 not shown) Planarity restraints: 4115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 327 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C GLN B 327 " -0.051 2.00e-02 2.50e+03 pdb=" O GLN B 327 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP B 328 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 97 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO E 98 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 98 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 98 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 228 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO B 229 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " 0.029 5.00e-02 4.00e+02 ... (remaining 4112 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 285 2.57 - 3.15: 19789 3.15 - 3.73: 37739 3.73 - 4.32: 47656 4.32 - 4.90: 74084 Nonbonded interactions: 179553 Sorted by model distance: nonbonded pdb=" O ILE D 48 " pdb=" OD1 ASP D 49 " model vdw 1.985 3.040 nonbonded pdb=" OD1 ASP E 41 " pdb="MG MG E 200 " model vdw 2.078 2.170 nonbonded pdb=" OD1 ASP E 45 " pdb="MG MG E 200 " model vdw 2.100 2.170 nonbonded pdb=" CB SER A 246 " pdb="MG MG A2003 " model vdw 2.129 2.570 nonbonded pdb=" O ASP B 618 " pdb=" OD1 ASP B 618 " model vdw 2.152 3.040 ... (remaining 179548 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 29 through 200 or resid 218 through 636 or resid 651 throu \ gh 949 or resid 2001 through 2003)) } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'D' and (resid 15 through 171 or resid 200)) selection = chain 'E' } ncs_group { reference = (chain 'G' and resid 1413 through 1623) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.020 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: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.180 Set scattering table: 0.260 Process input model: 55.600 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.003 0.062 23278 Z= 0.148 Angle : 0.682 10.266 31266 Z= 0.361 Chirality : 0.042 0.336 3400 Planarity : 0.004 0.052 4115 Dihedral : 15.412 179.189 9031 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.04 % Allowed : 0.28 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2798 helix: 1.04 (0.13), residues: 1601 sheet: -1.60 (0.41), residues: 148 loop : -2.05 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 840 HIS 0.006 0.001 HIS B 783 PHE 0.018 0.001 PHE A 493 TYR 0.029 0.001 TYR G1473 ARG 0.012 0.000 ARG H1477 Details of bonding type rmsd hydrogen bonds : bond 0.13360 ( 1349) hydrogen bonds : angle 6.19864 ( 3999) covalent geometry : bond 0.00282 (23278) covalent geometry : angle 0.68193 (31266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 2.695 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: A 149 MET cc_start: 0.8015 (mpp) cc_final: 0.7812 (mpp) REVERT: B 637 MET cc_start: 0.6967 (mtp) cc_final: 0.5942 (mmm) REVERT: C 16 GLN cc_start: 0.9014 (mp10) cc_final: 0.8714 (pp30) REVERT: C 73 MET cc_start: 0.8597 (mmp) cc_final: 0.8230 (mmp) REVERT: D 24 MET cc_start: 0.6846 (ppp) cc_final: 0.6189 (ppp) REVERT: E 141 MET cc_start: 0.8018 (mpp) cc_final: 0.7516 (tmm) REVERT: G 1462 MET cc_start: 0.9103 (mmp) cc_final: 0.8843 (mpp) REVERT: G 1578 MET cc_start: 0.9529 (mtm) cc_final: 0.9262 (tpp) REVERT: H 1462 MET cc_start: 0.9455 (mmp) cc_final: 0.9042 (mmm) REVERT: H 1514 MET cc_start: 0.8759 (mmm) cc_final: 0.8370 (tmm) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.4409 time to fit residues: 161.7176 Evaluate side-chains 144 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN B 636 GLN D 27 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1447 GLN G1605 HIS H1607 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.053997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.044606 restraints weight = 239286.817| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 5.04 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 23278 Z= 0.229 Angle : 0.750 11.005 31266 Z= 0.392 Chirality : 0.044 0.189 3400 Planarity : 0.005 0.068 4115 Dihedral : 6.731 144.021 3051 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.09 % Allowed : 9.93 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2798 helix: 0.70 (0.13), residues: 1602 sheet: -2.02 (0.40), residues: 145 loop : -2.01 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 840 HIS 0.008 0.002 HIS A 102 PHE 0.023 0.002 PHE A 493 TYR 0.041 0.002 TYR G1473 ARG 0.010 0.001 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.05175 ( 1349) hydrogen bonds : angle 5.56441 ( 3999) covalent geometry : bond 0.00479 (23278) covalent geometry : angle 0.74970 (31266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 3.343 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: B 391 MET cc_start: 0.7374 (tpp) cc_final: 0.7135 (tpt) REVERT: B 655 MET cc_start: 0.7076 (ttt) cc_final: 0.6400 (ptt) REVERT: B 747 MET cc_start: 0.7671 (pmm) cc_final: 0.7097 (pmm) REVERT: D 73 MET cc_start: 0.6943 (mmt) cc_final: 0.6223 (ptp) REVERT: D 89 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: E 141 MET cc_start: 0.8089 (mpp) cc_final: 0.7614 (tmm) REVERT: F 59 MET cc_start: 0.7414 (mmp) cc_final: 0.7196 (mmp) REVERT: F 61 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8634 (mm) REVERT: F 73 MET cc_start: 0.3094 (mmm) cc_final: 0.2854 (tpt) REVERT: G 1578 MET cc_start: 0.9576 (mtm) cc_final: 0.9369 (ttm) REVERT: H 1462 MET cc_start: 0.9409 (mmp) cc_final: 0.8975 (mmm) REVERT: H 1514 MET cc_start: 0.8763 (mmm) cc_final: 0.8346 (tmm) REVERT: H 1550 MET cc_start: 0.8664 (ppp) cc_final: 0.7964 (ppp) outliers start: 27 outliers final: 14 residues processed: 161 average time/residue: 0.4450 time to fit residues: 116.2470 Evaluate side-chains 143 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 5.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain G residue 1605 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 219 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 246 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1605 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.052941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.042025 restraints weight = 247967.755| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 7.49 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 23278 Z= 0.208 Angle : 0.717 12.312 31266 Z= 0.372 Chirality : 0.042 0.149 3400 Planarity : 0.005 0.054 4115 Dihedral : 6.751 138.289 3051 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 1.41 % Allowed : 14.21 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), residues: 2798 helix: 0.62 (0.13), residues: 1605 sheet: -2.18 (0.39), residues: 145 loop : -2.11 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 625 HIS 0.012 0.002 HIS G1605 PHE 0.020 0.002 PHE G1459 TYR 0.034 0.002 TYR G1473 ARG 0.013 0.001 ARG A 916 Details of bonding type rmsd hydrogen bonds : bond 0.04992 ( 1349) hydrogen bonds : angle 5.49980 ( 3999) covalent geometry : bond 0.00435 (23278) covalent geometry : angle 0.71699 (31266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.9170 (mmp) cc_final: 0.8929 (mmp) REVERT: A 497 MET cc_start: 0.8146 (mmm) cc_final: 0.7925 (mtp) REVERT: B 391 MET cc_start: 0.7699 (tpp) cc_final: 0.7416 (tpt) REVERT: B 785 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: D 89 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: E 72 MET cc_start: 0.5226 (ptm) cc_final: 0.4989 (ptm) REVERT: E 141 MET cc_start: 0.8079 (mpp) cc_final: 0.7544 (tmm) REVERT: F 35 MET cc_start: 0.8689 (tpp) cc_final: 0.8249 (tpp) REVERT: F 61 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8609 (mm) REVERT: G 1488 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: H 1462 MET cc_start: 0.9391 (mmp) cc_final: 0.9029 (mmm) REVERT: H 1514 MET cc_start: 0.8811 (mmm) cc_final: 0.8407 (tmm) outliers start: 35 outliers final: 21 residues processed: 164 average time/residue: 0.3403 time to fit residues: 91.7824 Evaluate side-chains 156 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain G residue 1488 GLU Chi-restraints excluded: chain G residue 1583 GLU Chi-restraints excluded: chain G residue 1605 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 183 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 208 optimal weight: 0.4980 chunk 150 optimal weight: 0.0020 chunk 11 optimal weight: 1.9990 chunk 265 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 258 optimal weight: 0.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.054544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.045106 restraints weight = 239436.175| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 5.23 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23278 Z= 0.131 Angle : 0.655 10.522 31266 Z= 0.334 Chirality : 0.040 0.202 3400 Planarity : 0.004 0.059 4115 Dihedral : 6.487 129.097 3051 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.65 % Allowed : 16.14 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2798 helix: 0.92 (0.13), residues: 1636 sheet: -2.00 (0.40), residues: 152 loop : -2.13 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 625 HIS 0.005 0.001 HIS B 152 PHE 0.018 0.001 PHE C 69 TYR 0.027 0.001 TYR G1473 ARG 0.005 0.000 ARG A 916 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 1349) hydrogen bonds : angle 5.19336 ( 3999) covalent geometry : bond 0.00268 (23278) covalent geometry : angle 0.65536 (31266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 766 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7989 (mm) REVERT: B 342 MET cc_start: 0.8202 (mmt) cc_final: 0.7743 (mmt) REVERT: B 655 MET cc_start: 0.6856 (ttt) cc_final: 0.6323 (ptt) REVERT: B 747 MET cc_start: 0.7538 (pmm) cc_final: 0.6937 (pmm) REVERT: D 60 MET cc_start: 0.7236 (mmp) cc_final: 0.6277 (pmm) REVERT: D 73 MET cc_start: 0.7076 (mmt) cc_final: 0.6453 (mtt) REVERT: D 89 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7954 (m-80) REVERT: D 129 MET cc_start: 0.7942 (tpt) cc_final: 0.6972 (tpp) REVERT: E 141 MET cc_start: 0.8065 (mpp) cc_final: 0.7510 (tmm) REVERT: F 61 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8523 (mm) REVERT: G 1462 MET cc_start: 0.9217 (mmp) cc_final: 0.8722 (ppp) REVERT: G 1488 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: G 1578 MET cc_start: 0.9285 (ttm) cc_final: 0.8818 (tpp) REVERT: H 1462 MET cc_start: 0.9337 (mmp) cc_final: 0.8959 (mmm) REVERT: H 1514 MET cc_start: 0.8789 (mmm) cc_final: 0.8407 (tmm) outliers start: 41 outliers final: 18 residues processed: 171 average time/residue: 0.3229 time to fit residues: 90.2721 Evaluate side-chains 152 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain G residue 1488 GLU Chi-restraints excluded: chain G residue 1583 GLU Chi-restraints excluded: chain G residue 1605 HIS Chi-restraints excluded: chain H residue 1597 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 102 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1605 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.053318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.043891 restraints weight = 243292.232| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 5.17 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23278 Z= 0.188 Angle : 0.695 11.974 31266 Z= 0.358 Chirality : 0.042 0.418 3400 Planarity : 0.004 0.054 4115 Dihedral : 6.611 129.186 3051 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.38 % Allowed : 17.68 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 2798 helix: 0.81 (0.13), residues: 1634 sheet: -2.17 (0.39), residues: 147 loop : -2.23 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 625 HIS 0.008 0.001 HIS A 102 PHE 0.031 0.002 PHE F 66 TYR 0.022 0.002 TYR G1473 ARG 0.007 0.001 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.04744 ( 1349) hydrogen bonds : angle 5.29825 ( 3999) covalent geometry : bond 0.00392 (23278) covalent geometry : angle 0.69502 (31266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 132 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 766 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8133 (mm) REVERT: B 342 MET cc_start: 0.8173 (mmt) cc_final: 0.7808 (mmt) REVERT: B 655 MET cc_start: 0.6888 (ttt) cc_final: 0.6386 (ptt) REVERT: B 747 MET cc_start: 0.7769 (pmm) cc_final: 0.7021 (pmm) REVERT: C 48 MET cc_start: 0.8847 (ppp) cc_final: 0.8613 (ppp) REVERT: D 60 MET cc_start: 0.7368 (mmp) cc_final: 0.6218 (pmm) REVERT: D 73 MET cc_start: 0.6967 (mmt) cc_final: 0.6349 (mtt) REVERT: D 89 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: E 141 MET cc_start: 0.8048 (mpp) cc_final: 0.7509 (tmm) REVERT: F 61 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8488 (mm) REVERT: G 1488 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7441 (mt-10) REVERT: G 1578 MET cc_start: 0.9282 (ttm) cc_final: 0.8831 (tpp) REVERT: H 1462 MET cc_start: 0.9327 (mmp) cc_final: 0.8953 (mmm) REVERT: H 1514 MET cc_start: 0.8886 (mmm) cc_final: 0.8515 (tmm) outliers start: 59 outliers final: 33 residues processed: 183 average time/residue: 0.3422 time to fit residues: 101.2228 Evaluate side-chains 167 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 126 GLN Chi-restraints excluded: chain G residue 1488 GLU Chi-restraints excluded: chain G residue 1583 GLU Chi-restraints excluded: chain G residue 1605 HIS Chi-restraints excluded: chain H residue 1597 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 181 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 277 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 233 optimal weight: 0.0470 chunk 76 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1605 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.054145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.044715 restraints weight = 239699.917| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 5.22 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23278 Z= 0.130 Angle : 0.664 10.718 31266 Z= 0.335 Chirality : 0.040 0.235 3400 Planarity : 0.004 0.059 4115 Dihedral : 6.435 124.314 3051 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.86 % Allowed : 19.29 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2798 helix: 1.00 (0.13), residues: 1632 sheet: -2.12 (0.40), residues: 152 loop : -2.12 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 625 HIS 0.011 0.001 HIS B 147 PHE 0.026 0.001 PHE F 66 TYR 0.018 0.001 TYR G1473 ARG 0.004 0.000 ARG H1496 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 1349) hydrogen bonds : angle 5.12525 ( 3999) covalent geometry : bond 0.00268 (23278) covalent geometry : angle 0.66430 (31266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 766 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8020 (mm) REVERT: A 933 MET cc_start: 0.9365 (ppp) cc_final: 0.8817 (mmt) REVERT: B 342 MET cc_start: 0.8210 (mmt) cc_final: 0.7888 (mmt) REVERT: B 747 MET cc_start: 0.7560 (pmm) cc_final: 0.6869 (pmm) REVERT: C 140 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: D 24 MET cc_start: 0.7185 (ppp) cc_final: 0.6842 (ppp) REVERT: D 60 MET cc_start: 0.7210 (mmp) cc_final: 0.6176 (pmm) REVERT: D 73 MET cc_start: 0.7124 (mmt) cc_final: 0.6527 (mtt) REVERT: D 89 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: E 73 MET cc_start: 0.8129 (mpp) cc_final: 0.7693 (ptp) REVERT: E 141 MET cc_start: 0.8051 (mpp) cc_final: 0.7435 (tmm) REVERT: F 35 MET cc_start: 0.8502 (tpp) cc_final: 0.8022 (tpp) REVERT: F 61 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8513 (mm) REVERT: G 1462 MET cc_start: 0.9233 (mmp) cc_final: 0.8668 (ppp) REVERT: G 1488 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: G 1578 MET cc_start: 0.9308 (ttm) cc_final: 0.8890 (tpp) REVERT: H 1462 MET cc_start: 0.9296 (mmp) cc_final: 0.8864 (mmm) REVERT: H 1514 MET cc_start: 0.9029 (mmm) cc_final: 0.8724 (tmm) outliers start: 46 outliers final: 31 residues processed: 174 average time/residue: 0.3250 time to fit residues: 92.2914 Evaluate side-chains 167 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 126 GLN Chi-restraints excluded: chain G residue 1488 GLU Chi-restraints excluded: chain G residue 1612 GLU Chi-restraints excluded: chain H residue 1597 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 148 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 275 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 723 ASN D 42 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1433 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.052337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.042978 restraints weight = 245646.922| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 5.01 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 23278 Z= 0.248 Angle : 0.766 13.494 31266 Z= 0.397 Chirality : 0.043 0.202 3400 Planarity : 0.005 0.050 4115 Dihedral : 6.888 131.413 3051 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.78 % Allowed : 19.41 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.16), residues: 2798 helix: 0.63 (0.12), residues: 1630 sheet: -2.43 (0.39), residues: 136 loop : -2.34 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 625 HIS 0.011 0.002 HIS B 147 PHE 0.022 0.002 PHE A 493 TYR 0.019 0.002 TYR G1473 ARG 0.009 0.001 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.05040 ( 1349) hydrogen bonds : angle 5.47981 ( 3999) covalent geometry : bond 0.00517 (23278) covalent geometry : angle 0.76608 (31266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 130 time to evaluate : 2.778 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: A 135 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: A 822 MET cc_start: 0.7862 (tpt) cc_final: 0.7645 (tpt) REVERT: D 60 MET cc_start: 0.7737 (mmp) cc_final: 0.7535 (mmp) REVERT: D 73 MET cc_start: 0.6984 (mmt) cc_final: 0.6352 (mtt) REVERT: D 89 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: E 141 MET cc_start: 0.8184 (mpp) cc_final: 0.7579 (tmm) REVERT: G 1488 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: G 1578 MET cc_start: 0.9325 (ttm) cc_final: 0.8873 (tpp) REVERT: H 1462 MET cc_start: 0.9324 (mmp) cc_final: 0.8926 (mmm) REVERT: H 1514 MET cc_start: 0.9037 (mmm) cc_final: 0.8755 (tmm) outliers start: 69 outliers final: 40 residues processed: 192 average time/residue: 0.3421 time to fit residues: 106.8241 Evaluate side-chains 169 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 126 GLN Chi-restraints excluded: chain G residue 1433 GLN Chi-restraints excluded: chain G residue 1488 GLU Chi-restraints excluded: chain G residue 1612 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 199 optimal weight: 0.6980 chunk 176 optimal weight: 9.9990 chunk 223 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 221 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.053083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.043677 restraints weight = 241435.015| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 5.14 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23278 Z= 0.161 Angle : 0.712 11.476 31266 Z= 0.361 Chirality : 0.042 0.188 3400 Planarity : 0.005 0.132 4115 Dihedral : 6.708 128.486 3051 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.14 % Allowed : 21.07 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.16), residues: 2798 helix: 0.81 (0.13), residues: 1629 sheet: -2.33 (0.39), residues: 147 loop : -2.30 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 625 HIS 0.009 0.001 HIS B 147 PHE 0.016 0.001 PHE C 69 TYR 0.018 0.002 TYR C 140 ARG 0.006 0.000 ARG H1597 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 1349) hydrogen bonds : angle 5.28959 ( 3999) covalent geometry : bond 0.00335 (23278) covalent geometry : angle 0.71235 (31266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 131 time to evaluate : 3.052 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: A 78 MET cc_start: 0.5797 (mpp) cc_final: 0.4813 (mpt) REVERT: A 915 MET cc_start: 0.9148 (ppp) cc_final: 0.8261 (ttt) REVERT: A 933 MET cc_start: 0.9407 (ppp) cc_final: 0.8714 (mmm) REVERT: B 428 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8036 (mm-30) REVERT: B 933 MET cc_start: 0.7315 (mmm) cc_final: 0.7044 (mmm) REVERT: D 60 MET cc_start: 0.7445 (mmp) cc_final: 0.6338 (pmm) REVERT: D 73 MET cc_start: 0.6972 (mmt) cc_final: 0.6444 (mtt) REVERT: D 89 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7920 (m-80) REVERT: E 69 LEU cc_start: 0.8611 (pt) cc_final: 0.7991 (pt) REVERT: E 73 MET cc_start: 0.8057 (mpp) cc_final: 0.7723 (ptp) REVERT: E 141 MET cc_start: 0.8247 (mpp) cc_final: 0.7557 (tmm) REVERT: F 61 LEU cc_start: 0.8948 (pp) cc_final: 0.8567 (mm) REVERT: G 1488 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: G 1578 MET cc_start: 0.9345 (ttm) cc_final: 0.8900 (tpp) REVERT: H 1462 MET cc_start: 0.9272 (mmp) cc_final: 0.8888 (mmm) REVERT: H 1514 MET cc_start: 0.9030 (mmm) cc_final: 0.8779 (tmm) outliers start: 53 outliers final: 40 residues processed: 180 average time/residue: 0.3239 time to fit residues: 96.7689 Evaluate side-chains 170 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 126 GLN Chi-restraints excluded: chain G residue 1488 GLU Chi-restraints excluded: chain G residue 1612 GLU Chi-restraints excluded: chain H residue 1421 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 56 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 222 optimal weight: 0.1980 chunk 134 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 225 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.052827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.043450 restraints weight = 242266.646| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 5.10 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23278 Z= 0.177 Angle : 0.729 12.267 31266 Z= 0.369 Chirality : 0.042 0.285 3400 Planarity : 0.005 0.143 4115 Dihedral : 6.707 128.217 3051 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 1.98 % Allowed : 21.63 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.16), residues: 2798 helix: 0.79 (0.13), residues: 1627 sheet: -2.45 (0.39), residues: 142 loop : -2.32 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 625 HIS 0.008 0.001 HIS B 147 PHE 0.016 0.002 PHE C 15 TYR 0.023 0.002 TYR B 592 ARG 0.005 0.001 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.04724 ( 1349) hydrogen bonds : angle 5.31609 ( 3999) covalent geometry : bond 0.00371 (23278) covalent geometry : angle 0.72900 (31266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 2.917 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: A 78 MET cc_start: 0.5842 (mpp) cc_final: 0.4837 (mpt) REVERT: A 339 MET cc_start: 0.9088 (mmp) cc_final: 0.8818 (mmp) REVERT: A 933 MET cc_start: 0.9411 (ppp) cc_final: 0.8749 (mmm) REVERT: B 428 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8027 (mm-30) REVERT: D 24 MET cc_start: 0.7338 (ppp) cc_final: 0.6759 (ppp) REVERT: D 56 MET cc_start: 0.8403 (mmm) cc_final: 0.7730 (mpp) REVERT: D 60 MET cc_start: 0.7543 (mmp) cc_final: 0.7313 (mmp) REVERT: D 73 MET cc_start: 0.7073 (mmt) cc_final: 0.6497 (mtt) REVERT: D 89 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: E 73 MET cc_start: 0.8045 (mpp) cc_final: 0.7722 (ptp) REVERT: E 141 MET cc_start: 0.8261 (mpp) cc_final: 0.7590 (tmm) REVERT: G 1488 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: G 1578 MET cc_start: 0.9345 (ttm) cc_final: 0.8899 (tpp) REVERT: H 1462 MET cc_start: 0.9255 (mmp) cc_final: 0.8876 (mmm) REVERT: H 1514 MET cc_start: 0.9028 (mmm) cc_final: 0.8777 (tmm) outliers start: 49 outliers final: 42 residues processed: 174 average time/residue: 0.3079 time to fit residues: 89.2234 Evaluate side-chains 174 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 126 GLN Chi-restraints excluded: chain G residue 1488 GLU Chi-restraints excluded: chain G residue 1612 GLU Chi-restraints excluded: chain H residue 1421 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 214 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 233 optimal weight: 0.0010 chunk 124 optimal weight: 7.9990 chunk 274 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.052493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.041632 restraints weight = 249528.650| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 7.45 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23278 Z= 0.157 Angle : 0.720 11.638 31266 Z= 0.363 Chirality : 0.042 0.255 3400 Planarity : 0.004 0.130 4115 Dihedral : 6.618 126.307 3051 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.10 % Allowed : 21.71 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 2798 helix: 0.85 (0.13), residues: 1628 sheet: -2.38 (0.39), residues: 146 loop : -2.29 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 625 HIS 0.008 0.001 HIS B 147 PHE 0.015 0.001 PHE C 69 TYR 0.024 0.002 TYR B 592 ARG 0.004 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.04625 ( 1349) hydrogen bonds : angle 5.25425 ( 3999) covalent geometry : bond 0.00328 (23278) covalent geometry : angle 0.72022 (31266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 129 time to evaluate : 4.419 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: A 78 MET cc_start: 0.7728 (mpp) cc_final: 0.6968 (mpt) REVERT: A 106 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8355 (pp20) REVERT: A 135 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8441 (mt-10) REVERT: A 933 MET cc_start: 0.9406 (ppp) cc_final: 0.8793 (mmm) REVERT: B 428 GLU cc_start: 0.9415 (OUTLIER) cc_final: 0.8753 (mm-30) REVERT: B 933 MET cc_start: 0.6657 (mmm) cc_final: 0.6090 (mmm) REVERT: D 24 MET cc_start: 0.7332 (ppp) cc_final: 0.6871 (ppp) REVERT: D 56 MET cc_start: 0.8574 (mmm) cc_final: 0.7948 (mpp) REVERT: D 60 MET cc_start: 0.8736 (mmp) cc_final: 0.7268 (pmm) REVERT: D 73 MET cc_start: 0.7706 (mmt) cc_final: 0.7204 (mtt) REVERT: D 89 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8404 (m-80) REVERT: E 141 MET cc_start: 0.8363 (mpp) cc_final: 0.7803 (tmm) REVERT: G 1462 MET cc_start: 0.9180 (mmp) cc_final: 0.8687 (ppp) REVERT: G 1488 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6570 (mt-10) REVERT: G 1578 MET cc_start: 0.9465 (ttm) cc_final: 0.9218 (tpp) REVERT: H 1462 MET cc_start: 0.9260 (mmp) cc_final: 0.8733 (mmm) outliers start: 52 outliers final: 44 residues processed: 176 average time/residue: 0.4061 time to fit residues: 118.8222 Evaluate side-chains 176 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 472 PHE Chi-restraints excluded: chain B residue 495 HIS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 730 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 126 GLN Chi-restraints excluded: chain G residue 1433 GLN Chi-restraints excluded: chain G residue 1488 GLU Chi-restraints excluded: chain G residue 1612 GLU Chi-restraints excluded: chain H residue 1421 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 263 optimal weight: 9.9990 chunk 219 optimal weight: 0.0980 chunk 166 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 277 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 262 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.052570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.041694 restraints weight = 248771.712| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 7.42 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.232 23278 Z= 0.230 Angle : 0.889 59.189 31266 Z= 0.485 Chirality : 0.043 0.472 3400 Planarity : 0.005 0.174 4115 Dihedral : 6.623 126.274 3051 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.18 % Allowed : 21.83 % Favored : 75.99 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 2798 helix: 0.87 (0.13), residues: 1632 sheet: -2.38 (0.39), residues: 146 loop : -2.29 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 625 HIS 0.007 0.001 HIS B 147 PHE 0.015 0.001 PHE C 69 TYR 0.052 0.002 TYR G1473 ARG 0.005 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 1349) hydrogen bonds : angle 5.26136 ( 3999) covalent geometry : bond 0.00468 (23278) covalent geometry : angle 0.88888 (31266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12214.22 seconds wall clock time: 216 minutes 46.49 seconds (13006.49 seconds total)