Starting phenix.real_space_refine on Fri Sep 19 04:29:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mf3_23810/09_2025/7mf3_23810.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mf3_23810/09_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_23810/09_2025/7mf3_23810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mf3_23810/09_2025/7mf3_23810.map" model { file = "/net/cci-nas-00/data/ceres_data/7mf3_23810/09_2025/7mf3_23810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mf3_23810/09_2025/7mf3_23810.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.17, per 1000 atoms: 0.23 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: 2.13 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.78 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: 4.19 Time building geometry restraints manager: 2.75 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 2003)) } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'D' and resid 15 through 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: 10.910 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: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.320 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.480 ------------------------------------------------------------------------------- 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 : 17.32 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.012 0.000 ARG H1477 TYR 0.029 0.001 TYR G1473 PHE 0.018 0.001 PHE A 493 TRP 0.012 0.001 TRP B 840 HIS 0.006 0.001 HIS B 783 Details of bonding type rmsd covalent geometry : bond 0.00282 (23278) covalent geometry : angle 0.68193 (31266) hydrogen bonds : bond 0.13360 ( 1349) hydrogen bonds : angle 6.19864 ( 3999) *********************** 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 : 0.973 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: 0.2119 time to fit residues: 77.7903 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 : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 HIS B 661 GLN D 27 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1447 GLN G1605 HIS H1607 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.056059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.046660 restraints weight = 235509.779| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 5.11 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23278 Z= 0.141 Angle : 0.675 9.655 31266 Z= 0.348 Chirality : 0.041 0.165 3400 Planarity : 0.004 0.054 4115 Dihedral : 6.405 140.000 3051 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.65 % Allowed : 8.27 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.16), residues: 2798 helix: 0.97 (0.13), residues: 1591 sheet: -1.58 (0.41), residues: 150 loop : -1.93 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H1477 TYR 0.042 0.001 TYR G1473 PHE 0.021 0.001 PHE A 493 TRP 0.012 0.001 TRP B 36 HIS 0.004 0.001 HIS B 585 Details of bonding type rmsd covalent geometry : bond 0.00287 (23278) covalent geometry : angle 0.67451 (31266) hydrogen bonds : bond 0.04841 ( 1349) hydrogen bonds : angle 5.31365 ( 3999) *********************** 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 173 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7681 (mmt) cc_final: 0.7358 (mmm) REVERT: B 391 MET cc_start: 0.7252 (tpp) cc_final: 0.6989 (tpt) REVERT: B 747 MET cc_start: 0.7320 (pmm) cc_final: 0.6727 (pmm) REVERT: C 16 GLN cc_start: 0.9084 (mp10) cc_final: 0.8868 (pp30) REVERT: D 129 MET cc_start: 0.8292 (tpt) cc_final: 0.7247 (tpp) REVERT: E 141 MET cc_start: 0.8179 (mpp) cc_final: 0.7616 (tmm) REVERT: G 1488 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7226 (mt-10) REVERT: G 1557 LEU cc_start: 0.9337 (mt) cc_final: 0.9107 (pp) REVERT: G 1578 MET cc_start: 0.9570 (mtm) cc_final: 0.9337 (tpp) REVERT: H 1462 MET cc_start: 0.9411 (mmp) cc_final: 0.8996 (mmm) REVERT: H 1514 MET cc_start: 0.8798 (mmm) cc_final: 0.8334 (tmm) outliers start: 16 outliers final: 7 residues processed: 170 average time/residue: 0.1671 time to fit residues: 45.7663 Evaluate side-chains 152 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain B residue 69 THR 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 F residue 125 GLU Chi-restraints excluded: chain G residue 1488 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 211 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 94 optimal weight: 0.0270 chunk 82 optimal weight: 0.7980 chunk 273 optimal weight: 6.9990 chunk 200 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 264 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN E 15 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1607 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.056256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.046898 restraints weight = 236050.788| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 5.16 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23278 Z= 0.121 Angle : 0.636 13.334 31266 Z= 0.323 Chirality : 0.040 0.150 3400 Planarity : 0.004 0.050 4115 Dihedral : 6.197 126.066 3051 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.09 % Allowed : 11.66 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.16), residues: 2798 helix: 1.02 (0.13), residues: 1594 sheet: -1.42 (0.42), residues: 148 loop : -1.91 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H1496 TYR 0.033 0.001 TYR G1473 PHE 0.024 0.001 PHE G1459 TRP 0.010 0.001 TRP B 36 HIS 0.011 0.001 HIS H1607 Details of bonding type rmsd covalent geometry : bond 0.00241 (23278) covalent geometry : angle 0.63561 (31266) hydrogen bonds : bond 0.04489 ( 1349) hydrogen bonds : angle 5.07371 ( 3999) *********************** 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 179 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7670 (mmt) cc_final: 0.7278 (mmm) REVERT: A 339 MET cc_start: 0.9172 (mmp) cc_final: 0.8962 (mmm) REVERT: A 916 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8336 (ptp90) REVERT: A 933 MET cc_start: 0.9542 (ppp) cc_final: 0.8924 (mmp) REVERT: B 381 ASN cc_start: 0.8132 (t0) cc_final: 0.7911 (t0) REVERT: B 391 MET cc_start: 0.7287 (tpp) cc_final: 0.7057 (tpt) REVERT: B 747 MET cc_start: 0.7401 (pmm) cc_final: 0.6792 (pmm) REVERT: D 73 MET cc_start: 0.7059 (mmt) cc_final: 0.6601 (mmt) REVERT: D 89 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8031 (m-80) REVERT: D 129 MET cc_start: 0.8091 (tpt) cc_final: 0.7136 (tpp) REVERT: E 141 MET cc_start: 0.8096 (mpp) cc_final: 0.7475 (tmm) REVERT: G 1488 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: G 1578 MET cc_start: 0.9571 (mtm) cc_final: 0.9340 (tpp) REVERT: H 1462 MET cc_start: 0.9398 (mmp) cc_final: 0.9026 (mmm) REVERT: H 1514 MET cc_start: 0.8824 (mmm) cc_final: 0.8410 (tmm) REVERT: H 1550 MET cc_start: 0.8508 (ppp) cc_final: 0.8262 (ppp) outliers start: 27 outliers final: 14 residues processed: 173 average time/residue: 0.1661 time to fit residues: 46.1450 Evaluate side-chains 159 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 40 GLN 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 125 GLU Chi-restraints excluded: chain G residue 1486 GLU Chi-restraints excluded: chain G residue 1488 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 129 optimal weight: 6.9990 chunk 100 optimal weight: 0.0050 chunk 105 optimal weight: 2.9990 chunk 262 optimal weight: 0.8980 chunk 178 optimal weight: 6.9990 chunk 224 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 211 optimal weight: 0.1980 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 GLN D 104 ASN E 15 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1605 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.055835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.046494 restraints weight = 237747.157| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 5.15 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23278 Z= 0.126 Angle : 0.620 10.187 31266 Z= 0.316 Chirality : 0.039 0.146 3400 Planarity : 0.004 0.049 4115 Dihedral : 6.104 118.189 3051 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.53 % Allowed : 13.72 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.16), residues: 2798 helix: 1.13 (0.13), residues: 1632 sheet: -1.43 (0.42), residues: 148 loop : -2.01 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 20 TYR 0.026 0.001 TYR G1473 PHE 0.018 0.001 PHE G1459 TRP 0.010 0.001 TRP B 625 HIS 0.004 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00256 (23278) covalent geometry : angle 0.62036 (31266) hydrogen bonds : bond 0.04323 ( 1349) hydrogen bonds : angle 4.98115 ( 3999) *********************** 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 185 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7768 (mmt) cc_final: 0.7382 (mmm) REVERT: A 655 MET cc_start: 0.8847 (ppp) cc_final: 0.8640 (ppp) REVERT: A 916 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8209 (mtm-85) REVERT: B 381 ASN cc_start: 0.8038 (t0) cc_final: 0.7777 (t0) REVERT: B 391 MET cc_start: 0.7543 (tpp) cc_final: 0.7309 (tpt) REVERT: B 747 MET cc_start: 0.7446 (pmm) cc_final: 0.6866 (pmm) REVERT: D 24 MET cc_start: 0.6871 (ppp) cc_final: 0.6491 (ppp) REVERT: D 60 MET cc_start: 0.6438 (mmp) cc_final: 0.6086 (pmm) REVERT: D 73 MET cc_start: 0.7128 (mmt) cc_final: 0.6551 (mtt) REVERT: D 89 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8030 (m-80) REVERT: D 129 MET cc_start: 0.8125 (tpt) cc_final: 0.7140 (tpp) REVERT: E 141 MET cc_start: 0.8090 (mpp) cc_final: 0.7404 (tmm) REVERT: F 35 MET cc_start: 0.8608 (tpp) cc_final: 0.8222 (tpp) REVERT: F 40 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8222 (mp10) REVERT: G 1488 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7263 (mt-10) REVERT: G 1557 LEU cc_start: 0.9338 (mt) cc_final: 0.9041 (pp) REVERT: G 1578 MET cc_start: 0.9589 (mtm) cc_final: 0.9377 (tpp) REVERT: H 1462 MET cc_start: 0.9371 (mmp) cc_final: 0.8987 (mmm) REVERT: H 1514 MET cc_start: 0.8834 (mmm) cc_final: 0.8421 (tmm) REVERT: H 1550 MET cc_start: 0.8629 (ppp) cc_final: 0.8095 (ppp) outliers start: 38 outliers final: 21 residues processed: 178 average time/residue: 0.1538 time to fit residues: 44.4512 Evaluate side-chains 163 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 428 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain B residue 69 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 510 ILE Chi-restraints excluded: chain B residue 785 GLU Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 7 GLN Chi-restraints excluded: chain F residue 40 GLN Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 126 GLN Chi-restraints excluded: chain G residue 1486 GLU Chi-restraints excluded: chain G residue 1488 GLU Chi-restraints excluded: chain G residue 1565 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 22 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 254 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN D 42 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1432 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.053861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.044448 restraints weight = 240347.282| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 5.18 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 23278 Z= 0.214 Angle : 0.706 11.242 31266 Z= 0.367 Chirality : 0.042 0.239 3400 Planarity : 0.004 0.046 4115 Dihedral : 6.470 120.494 3051 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 1.69 % Allowed : 15.82 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.16), residues: 2798 helix: 0.91 (0.13), residues: 1637 sheet: -1.80 (0.40), residues: 146 loop : -2.16 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 731 TYR 0.020 0.002 TYR G1473 PHE 0.021 0.002 PHE C 15 TRP 0.016 0.002 TRP A 597 HIS 0.023 0.002 HIS G1605 Details of bonding type rmsd covalent geometry : bond 0.00447 (23278) covalent geometry : angle 0.70563 (31266) hydrogen bonds : bond 0.04705 ( 1349) hydrogen bonds : angle 5.23148 ( 3999) *********************** 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 172 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7905 (mmt) cc_final: 0.7681 (mmt) REVERT: A 933 MET cc_start: 0.9484 (ppp) cc_final: 0.8877 (mmm) REVERT: B 381 ASN cc_start: 0.8221 (t0) cc_final: 0.7994 (t0) REVERT: B 391 MET cc_start: 0.7450 (tpp) cc_final: 0.7239 (tpt) REVERT: C 48 MET cc_start: 0.8848 (ppp) cc_final: 0.8547 (ppp) REVERT: D 73 MET cc_start: 0.6942 (mmt) cc_final: 0.6277 (mtt) REVERT: D 89 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.8009 (m-80) REVERT: E 72 MET cc_start: 0.4758 (ptm) cc_final: 0.4451 (ptm) REVERT: E 141 MET cc_start: 0.8033 (mpp) cc_final: 0.7464 (tmm) REVERT: F 35 MET cc_start: 0.8666 (tpp) cc_final: 0.8292 (tpp) REVERT: G 1488 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: G 1578 MET cc_start: 0.9590 (mtm) cc_final: 0.9308 (mtt) REVERT: H 1462 MET cc_start: 0.9347 (mmp) cc_final: 0.8987 (mmm) REVERT: H 1514 MET cc_start: 0.8801 (mmm) cc_final: 0.8389 (tmm) REVERT: H 1550 MET cc_start: 0.8700 (ppp) cc_final: 0.8263 (ppp) outliers start: 42 outliers final: 30 residues processed: 167 average time/residue: 0.1485 time to fit residues: 41.0322 Evaluate side-chains 159 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL 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 553 THR Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 868 GLN 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 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 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 D residue 32 GLU Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 89 PHE 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 1565 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 203 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 143 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 205 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 263 optimal weight: 0.9980 chunk 166 optimal weight: 9.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN D 42 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1605 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.055037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.045679 restraints weight = 238925.038| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 5.13 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23278 Z= 0.120 Angle : 0.646 10.720 31266 Z= 0.326 Chirality : 0.040 0.208 3400 Planarity : 0.004 0.053 4115 Dihedral : 6.246 114.865 3051 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.53 % Allowed : 16.95 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.16), residues: 2798 helix: 1.06 (0.13), residues: 1634 sheet: -1.67 (0.41), residues: 148 loop : -2.07 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H1496 TYR 0.018 0.001 TYR G1473 PHE 0.016 0.001 PHE C 69 TRP 0.013 0.001 TRP B 625 HIS 0.005 0.001 HIS F 131 Details of bonding type rmsd covalent geometry : bond 0.00243 (23278) covalent geometry : angle 0.64637 (31266) hydrogen bonds : bond 0.04328 ( 1349) hydrogen bonds : angle 4.98938 ( 3999) *********************** 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 171 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.9140 (mmp) cc_final: 0.8896 (mmp) REVERT: B 381 ASN cc_start: 0.8211 (t0) cc_final: 0.7951 (t0) REVERT: B 655 MET cc_start: 0.6531 (ttt) cc_final: 0.6154 (ptt) REVERT: C 48 MET cc_start: 0.8875 (ppp) cc_final: 0.8674 (ppp) REVERT: D 24 MET cc_start: 0.6986 (ppp) cc_final: 0.6712 (ppp) REVERT: D 60 MET cc_start: 0.7319 (mmp) cc_final: 0.7002 (pmm) REVERT: D 73 MET cc_start: 0.7093 (mmt) cc_final: 0.6514 (mtt) REVERT: D 89 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: E 72 MET cc_start: 0.4879 (ptm) cc_final: 0.4330 (ptm) REVERT: E 73 MET cc_start: 0.8120 (mpp) cc_final: 0.7621 (ptp) REVERT: E 141 MET cc_start: 0.8029 (mpp) cc_final: 0.7469 (tmm) REVERT: G 1462 MET cc_start: 0.9241 (mmp) cc_final: 0.8699 (ppp) REVERT: G 1488 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: G 1557 LEU cc_start: 0.9379 (mt) cc_final: 0.9024 (pp) REVERT: G 1578 MET cc_start: 0.9595 (mtm) cc_final: 0.9371 (tpp) REVERT: H 1462 MET cc_start: 0.9356 (mmp) cc_final: 0.8932 (mmm) REVERT: H 1514 MET cc_start: 0.8806 (mmm) cc_final: 0.8417 (tmm) REVERT: H 1550 MET cc_start: 0.8690 (ppp) cc_final: 0.8119 (ppp) outliers start: 38 outliers final: 22 residues processed: 165 average time/residue: 0.1428 time to fit residues: 38.4661 Evaluate side-chains 154 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 868 GLN Chi-restraints excluded: chain B residue 89 MET 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 95 PHE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 48 MET 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 1565 GLU Chi-restraints excluded: chain G residue 1605 HIS 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 120 optimal weight: 6.9990 chunk 208 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 175 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.054414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.045018 restraints weight = 240024.796| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 5.23 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23278 Z= 0.148 Angle : 0.652 11.053 31266 Z= 0.333 Chirality : 0.040 0.184 3400 Planarity : 0.004 0.051 4115 Dihedral : 6.254 112.367 3051 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.65 % Allowed : 18.00 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.16), residues: 2798 helix: 1.02 (0.13), residues: 1633 sheet: -1.85 (0.40), residues: 150 loop : -2.10 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 168 TYR 0.016 0.001 TYR G1473 PHE 0.016 0.001 PHE A 493 TRP 0.014 0.001 TRP B 625 HIS 0.006 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00306 (23278) covalent geometry : angle 0.65247 (31266) hydrogen bonds : bond 0.04403 ( 1349) hydrogen bonds : angle 5.01981 ( 3999) *********************** 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 173 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7585 (mmt) cc_final: 0.7210 (mmm) REVERT: A 933 MET cc_start: 0.9328 (ppp) cc_final: 0.8794 (mmt) REVERT: B 381 ASN cc_start: 0.8249 (t0) cc_final: 0.8003 (t0) REVERT: B 428 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8085 (mm-30) REVERT: B 655 MET cc_start: 0.6707 (ttt) cc_final: 0.6304 (ptt) REVERT: D 24 MET cc_start: 0.7259 (ppp) cc_final: 0.6879 (ppp) REVERT: D 60 MET cc_start: 0.7524 (mmp) cc_final: 0.7142 (ptp) REVERT: D 73 MET cc_start: 0.7185 (mmt) cc_final: 0.6603 (mtt) REVERT: D 89 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7940 (m-80) REVERT: E 141 MET cc_start: 0.8022 (mpp) cc_final: 0.7452 (tmm) REVERT: G 1488 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: G 1575 MET cc_start: 0.9398 (ppp) cc_final: 0.9184 (ppp) REVERT: G 1578 MET cc_start: 0.9600 (mtm) cc_final: 0.9310 (mtt) REVERT: H 1462 MET cc_start: 0.9330 (mmp) cc_final: 0.8941 (mmm) REVERT: H 1514 MET cc_start: 0.8859 (mmm) cc_final: 0.8488 (tmm) REVERT: H 1550 MET cc_start: 0.8699 (ppp) cc_final: 0.8225 (ppp) outliers start: 41 outliers final: 30 residues processed: 166 average time/residue: 0.1452 time to fit residues: 40.0396 Evaluate side-chains 162 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 391 MET 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 868 GLN 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 730 PHE 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 D residue 51 GLU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 48 MET 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 1565 GLU Chi-restraints excluded: chain G residue 1605 HIS Chi-restraints excluded: chain H residue 1597 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 75 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 118 optimal weight: 0.2980 chunk 242 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 269 optimal weight: 0.6980 chunk 196 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1605 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.054289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.044882 restraints weight = 239451.681| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 5.19 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23278 Z= 0.151 Angle : 0.665 11.220 31266 Z= 0.340 Chirality : 0.041 0.197 3400 Planarity : 0.004 0.053 4115 Dihedral : 6.281 108.241 3051 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.69 % Allowed : 18.64 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.16), residues: 2798 helix: 1.00 (0.13), residues: 1630 sheet: -1.87 (0.40), residues: 148 loop : -2.12 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 247 TYR 0.016 0.002 TYR G1473 PHE 0.016 0.001 PHE A 493 TRP 0.015 0.001 TRP B 625 HIS 0.007 0.001 HIS H1607 Details of bonding type rmsd covalent geometry : bond 0.00315 (23278) covalent geometry : angle 0.66543 (31266) hydrogen bonds : bond 0.04411 ( 1349) hydrogen bonds : angle 5.05452 ( 3999) *********************** 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 171 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 766 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8076 (mm) REVERT: A 933 MET cc_start: 0.9358 (ppp) cc_final: 0.8832 (mmt) REVERT: B 381 ASN cc_start: 0.8231 (t0) cc_final: 0.7975 (t0) REVERT: B 428 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8078 (mm-30) REVERT: B 655 MET cc_start: 0.6812 (ttt) cc_final: 0.6379 (ptt) REVERT: B 933 MET cc_start: 0.7252 (mmm) cc_final: 0.7019 (mmm) REVERT: C 48 MET cc_start: 0.8856 (ppp) cc_final: 0.8482 (ppp) REVERT: D 24 MET cc_start: 0.7337 (ppp) cc_final: 0.6935 (ppp) REVERT: D 56 MET cc_start: 0.8266 (mmm) cc_final: 0.7596 (mpp) REVERT: D 60 MET cc_start: 0.7430 (mmp) cc_final: 0.7005 (ptp) REVERT: D 73 MET cc_start: 0.7208 (mmt) cc_final: 0.6630 (mtt) REVERT: D 89 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: E 141 MET cc_start: 0.8091 (mpp) cc_final: 0.7491 (tmm) REVERT: G 1488 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: G 1557 LEU cc_start: 0.9367 (mt) cc_final: 0.9028 (pp) REVERT: G 1578 MET cc_start: 0.9608 (mtm) cc_final: 0.9322 (mtt) REVERT: H 1462 MET cc_start: 0.9301 (mmp) cc_final: 0.8905 (mmm) REVERT: H 1514 MET cc_start: 0.8993 (mmm) cc_final: 0.8664 (tmm) REVERT: H 1550 MET cc_start: 0.8689 (ppp) cc_final: 0.8216 (ppp) outliers start: 42 outliers final: 31 residues processed: 164 average time/residue: 0.1558 time to fit residues: 42.4056 Evaluate side-chains 164 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 428 GLU 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 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 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 409 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 730 PHE 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 D residue 51 GLU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 48 MET 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 1565 GLU Chi-restraints excluded: chain G residue 1605 HIS Chi-restraints excluded: chain H residue 1597 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 274 optimal weight: 10.0000 chunk 3 optimal weight: 0.4980 chunk 121 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 231 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1605 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.054276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.044855 restraints weight = 240898.236| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 5.24 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23278 Z= 0.146 Angle : 0.681 16.577 31266 Z= 0.344 Chirality : 0.042 0.576 3400 Planarity : 0.004 0.052 4115 Dihedral : 6.253 104.639 3051 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.49 % Allowed : 19.17 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.16), residues: 2798 helix: 0.99 (0.13), residues: 1629 sheet: -1.93 (0.40), residues: 150 loop : -2.12 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 168 TYR 0.016 0.001 TYR G1473 PHE 0.026 0.001 PHE F 66 TRP 0.014 0.001 TRP B 625 HIS 0.006 0.001 HIS G1605 Details of bonding type rmsd covalent geometry : bond 0.00306 (23278) covalent geometry : angle 0.68052 (31266) hydrogen bonds : bond 0.04425 ( 1349) hydrogen bonds : angle 5.05137 ( 3999) *********************** 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 169 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 933 MET cc_start: 0.9370 (ppp) cc_final: 0.8862 (mmt) REVERT: B 381 ASN cc_start: 0.8338 (t0) cc_final: 0.8087 (t0) REVERT: B 428 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8091 (mm-30) REVERT: B 655 MET cc_start: 0.6777 (ttt) cc_final: 0.6360 (ptt) REVERT: C 48 MET cc_start: 0.8875 (ppp) cc_final: 0.8535 (ppp) REVERT: D 24 MET cc_start: 0.7336 (ppp) cc_final: 0.6921 (ppp) REVERT: D 56 MET cc_start: 0.8308 (mmm) cc_final: 0.7649 (mpp) REVERT: D 60 MET cc_start: 0.7456 (mmp) cc_final: 0.7021 (ptp) REVERT: D 73 MET cc_start: 0.7192 (mmt) cc_final: 0.6633 (mtt) REVERT: D 89 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: E 72 MET cc_start: 0.4654 (ptm) cc_final: 0.4302 (ptm) REVERT: E 141 MET cc_start: 0.8058 (mpp) cc_final: 0.7508 (tmm) REVERT: G 1488 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: G 1557 LEU cc_start: 0.9363 (mt) cc_final: 0.9022 (pp) REVERT: G 1575 MET cc_start: 0.9377 (ppp) cc_final: 0.9123 (ppp) REVERT: G 1578 MET cc_start: 0.9606 (mtm) cc_final: 0.9306 (mtt) REVERT: H 1462 MET cc_start: 0.9297 (mmp) cc_final: 0.8914 (mmm) REVERT: H 1514 MET cc_start: 0.9058 (mmm) cc_final: 0.8746 (tmm) REVERT: H 1550 MET cc_start: 0.8691 (ppp) cc_final: 0.8214 (ppp) outliers start: 37 outliers final: 33 residues processed: 162 average time/residue: 0.1586 time to fit residues: 42.3048 Evaluate side-chains 166 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 413 VAL Chi-restraints excluded: chain A residue 428 GLU 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 868 GLN 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 409 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 510 ILE Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 730 PHE 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 51 GLU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain F residue 48 MET 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 1565 GLU Chi-restraints excluded: chain H residue 1581 GLN Chi-restraints excluded: chain H residue 1597 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 266 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 253 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 211 optimal weight: 0.0970 chunk 122 optimal weight: 4.9990 chunk 274 optimal weight: 5.9990 chunk 161 optimal weight: 0.6980 chunk 236 optimal weight: 5.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- 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 494 ASN ** 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 300 GLN B 636 GLN B 708 ASN D 42 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.053897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.044483 restraints weight = 240388.475| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 5.20 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23278 Z= 0.163 Angle : 0.703 14.019 31266 Z= 0.357 Chirality : 0.042 0.436 3400 Planarity : 0.004 0.051 4115 Dihedral : 6.286 111.030 3051 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 1.53 % Allowed : 19.25 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.16), residues: 2798 helix: 0.91 (0.13), residues: 1631 sheet: -2.11 (0.40), residues: 152 loop : -2.14 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 168 TYR 0.048 0.002 TYR G1473 PHE 0.033 0.002 PHE F 11 TRP 0.015 0.001 TRP B 625 HIS 0.006 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00341 (23278) covalent geometry : angle 0.70262 (31266) hydrogen bonds : bond 0.04499 ( 1349) hydrogen bonds : angle 5.12064 ( 3999) ********************** 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 167 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 1.014 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 766 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8079 (mm) REVERT: A 933 MET cc_start: 0.9375 (ppp) cc_final: 0.8844 (mmt) REVERT: B 381 ASN cc_start: 0.8272 (t0) cc_final: 0.8052 (t0) REVERT: B 428 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8082 (mm-30) REVERT: B 655 MET cc_start: 0.6766 (ttt) cc_final: 0.6371 (ptt) REVERT: B 671 MET cc_start: 0.8472 (mmm) cc_final: 0.8248 (mmm) REVERT: B 933 MET cc_start: 0.7102 (mmm) cc_final: 0.6780 (mmm) REVERT: D 24 MET cc_start: 0.7414 (ppp) cc_final: 0.6937 (ppp) REVERT: D 60 MET cc_start: 0.7431 (mmp) cc_final: 0.7006 (ptp) REVERT: D 73 MET cc_start: 0.7192 (mmt) cc_final: 0.6637 (mtt) REVERT: D 89 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: E 72 MET cc_start: 0.4741 (ptm) cc_final: 0.4534 (ptm) REVERT: E 88 MET cc_start: 0.7556 (ppp) cc_final: 0.7214 (ppp) REVERT: E 141 MET cc_start: 0.8146 (mpp) cc_final: 0.7514 (tmm) REVERT: G 1488 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: G 1575 MET cc_start: 0.9364 (ppp) cc_final: 0.9148 (ppp) REVERT: H 1462 MET cc_start: 0.9294 (mmp) cc_final: 0.8895 (mmm) REVERT: H 1514 MET cc_start: 0.9073 (mmm) cc_final: 0.8776 (tmm) REVERT: H 1550 MET cc_start: 0.8697 (ppp) cc_final: 0.8209 (ppp) outliers start: 38 outliers final: 30 residues processed: 158 average time/residue: 0.1544 time to fit residues: 40.6008 Evaluate side-chains 162 residues out of total 2479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 428 GLU 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 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 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 409 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 730 PHE 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 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 1565 GLU Chi-restraints excluded: chain H residue 1597 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 150 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 235 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 494 ASN ** 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 300 GLN D 42 GLN ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1433 GLN ** 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 = 0.3865 r_free = 0.3865 target = 0.054062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.044656 restraints weight = 239677.609| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 5.20 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23278 Z= 0.147 Angle : 0.698 13.811 31266 Z= 0.353 Chirality : 0.042 0.420 3400 Planarity : 0.004 0.052 4115 Dihedral : 6.165 116.614 3051 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 1.61 % Allowed : 19.29 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.16), residues: 2798 helix: 0.89 (0.13), residues: 1632 sheet: -2.01 (0.41), residues: 150 loop : -2.16 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 168 TYR 0.052 0.002 TYR G1473 PHE 0.036 0.001 PHE F 11 TRP 0.015 0.001 TRP B 625 HIS 0.004 0.001 HIS B 585 Details of bonding type rmsd covalent geometry : bond 0.00307 (23278) covalent geometry : angle 0.69846 (31266) hydrogen bonds : bond 0.04444 ( 1349) hydrogen bonds : angle 5.10969 ( 3999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5301.23 seconds wall clock time: 92 minutes 14.98 seconds (5534.98 seconds total)