Starting phenix.real_space_refine on Fri Jun 13 01:19:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u75_41969/06_2025/8u75_41969.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u75_41969/06_2025/8u75_41969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u75_41969/06_2025/8u75_41969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u75_41969/06_2025/8u75_41969.map" model { file = "/net/cci-nas-00/data/ceres_data/8u75_41969/06_2025/8u75_41969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u75_41969/06_2025/8u75_41969.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 74 5.16 5 C 9579 2.51 5 N 2364 2.21 5 O 2636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14656 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 907, 7131 Classifications: {'peptide': 907} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 878} Chain breaks: 3 Chain: "B" Number of atoms: 7131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 907, 7131 Classifications: {'peptide': 907} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 878} Chain breaks: 3 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 154 Unusual residues: {'AJP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 240 Unusual residues: {'AJP': 3, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 27 Time building chain proxies: 12.20, per 1000 atoms: 0.83 Number of scatterers: 14656 At special positions: 0 Unit cell: (107.44, 120.36, 129.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 3 15.00 O 2636 8.00 N 2364 7.00 C 9579 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: 5.65 Conformation dependent library (CDL) restraints added in 1.9 seconds 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 11 sheets defined 74.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 77 through 95 Processing helix chain 'A' and resid 102 through 120 Processing helix chain 'A' and resid 120 through 132 removed outlier: 4.932A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 removed outlier: 3.869A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 156 through 188 removed outlier: 4.750A pdb=" N SER A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLN A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 209 through 221 removed outlier: 4.540A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 3.960A pdb=" N GLY A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 273 through 292 removed outlier: 4.068A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 320 Processing helix chain 'A' and resid 323 through 336 removed outlier: 4.419A pdb=" N VAL A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 376 through 379 removed outlier: 3.606A pdb=" N ALA A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 381 through 413 removed outlier: 3.530A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 396 " --> pdb=" O TYR A 392 " (cutoff:3.500A) Proline residue: A 408 - end of helix removed outlier: 3.675A pdb=" N ILE A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 426 removed outlier: 3.550A pdb=" N ALA A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.851A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 482 removed outlier: 4.441A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 3.950A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.926A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 601 Processing helix chain 'A' and resid 604 through 619 Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.990A pdb=" N SER A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 652 removed outlier: 3.728A pdb=" N LEU A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 858 Proline residue: A 819 - end of helix removed outlier: 3.948A pdb=" N ILE A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 823 " --> pdb=" O PRO A 819 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 824 " --> pdb=" O LYS A 820 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 832 " --> pdb=" O LYS A 828 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 835 " --> pdb=" O ASN A 831 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP A 855 " --> pdb=" O GLY A 851 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ARG A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.535A pdb=" N THR A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 958 Processing helix chain 'A' and resid 966 through 976 removed outlier: 3.724A pdb=" N ARG A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1049 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1123 removed outlier: 3.761A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1158 Processing helix chain 'B' and resid 77 through 95 Processing helix chain 'B' and resid 102 through 120 Processing helix chain 'B' and resid 120 through 132 removed outlier: 4.943A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 removed outlier: 3.872A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 153 Processing helix chain 'B' and resid 155 through 188 removed outlier: 3.831A pdb=" N PHE B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N SER B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLN B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 209 through 221 removed outlier: 4.250A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 254 removed outlier: 3.907A pdb=" N GLY B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 273 through 292 removed outlier: 4.058A pdb=" N HIS B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 320 Processing helix chain 'B' and resid 323 through 336 removed outlier: 4.405A pdb=" N VAL B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 375 Processing helix chain 'B' and resid 376 through 380 removed outlier: 4.117A pdb=" N VAL B 380 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 413 removed outlier: 3.514A pdb=" N TRP B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR B 396 " --> pdb=" O TYR B 392 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 428 removed outlier: 3.582A pdb=" N ALA B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.850A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 481 removed outlier: 4.437A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 514 removed outlier: 3.961A pdb=" N SER B 514 " --> pdb=" O ASN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 530 removed outlier: 3.929A pdb=" N ALA B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 601 Processing helix chain 'B' and resid 604 through 619 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.055A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 652 removed outlier: 3.706A pdb=" N LEU B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 858 Proline residue: B 819 - end of helix removed outlier: 3.931A pdb=" N ILE B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 823 " --> pdb=" O PRO B 819 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL B 824 " --> pdb=" O LYS B 820 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN B 832 " --> pdb=" O LYS B 828 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU B 835 " --> pdb=" O ASN B 831 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 852 " --> pdb=" O GLU B 848 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 853 " --> pdb=" O GLU B 849 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP B 855 " --> pdb=" O GLY B 851 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG B 856 " --> pdb=" O LYS B 852 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET B 857 " --> pdb=" O ILE B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.543A pdb=" N HIS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.515A pdb=" N THR B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 958 Processing helix chain 'B' and resid 966 through 976 removed outlier: 3.750A pdb=" N ARG B 976 " --> pdb=" O PHE B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1049 Processing helix chain 'B' and resid 1070 through 1080 Processing helix chain 'B' and resid 1085 through 1107 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1113 through 1123 Processing helix chain 'B' and resid 1155 through 1158 Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 Processing sheet with id=AA2, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.522A pdb=" N TYR A1066 " --> pdb=" O ILE A1001 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ILE A1001 " --> pdb=" O TYR A1066 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 987 through 989 removed outlier: 7.352A pdb=" N VAL A 987 " --> pdb=" O CYS A1059 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N CYS A1059 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 989 " --> pdb=" O VAL A1057 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1125 through 1127 removed outlier: 4.353A pdb=" N LEU A1186 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1135 through 1137 Processing sheet with id=AA6, first strand: chain 'A' and resid 1151 through 1154 Processing sheet with id=AA7, first strand: chain 'B' and resid 978 through 982 removed outlier: 6.325A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 987 through 989 removed outlier: 7.138A pdb=" N VAL B 987 " --> pdb=" O CYS B1059 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N CYS B1059 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 989 " --> pdb=" O VAL B1057 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1125 through 1127 removed outlier: 4.023A pdb=" N LEU B1186 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG B1185 " --> pdb=" O ILE B1148 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP B1144 " --> pdb=" O VAL B1189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1135 through 1137 Processing sheet with id=AB2, first strand: chain 'B' and resid 1151 through 1154 1046 hydrogen bonds defined for protein. 3075 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: 7.39 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2446 1.32 - 1.44: 3652 1.44 - 1.57: 8721 1.57 - 1.69: 6 1.69 - 1.81: 136 Bond restraints: 14961 Sorted by residual: bond pdb=" C35 AJP B1404 " pdb=" O34 AJP B1404 " ideal model delta sigma weight residual 1.380 1.412 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" C LYS B1051 " pdb=" N PRO B1052 " ideal model delta sigma weight residual 1.331 1.351 -0.019 1.21e-02 6.83e+03 2.58e+00 bond pdb=" C26 AJP B1404 " pdb=" O25 AJP B1404 " ideal model delta sigma weight residual 1.375 1.406 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" C26 AJP B1402 " pdb=" O25 AJP B1402 " ideal model delta sigma weight residual 1.375 1.405 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C26 AJP A1403 " pdb=" O25 AJP A1403 " ideal model delta sigma weight residual 1.375 1.405 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 14956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 19935 2.03 - 4.05: 323 4.05 - 6.08: 57 6.08 - 8.10: 19 8.10 - 10.13: 4 Bond angle restraints: 20338 Sorted by residual: angle pdb=" CA GLU A 233 " pdb=" CB GLU A 233 " pdb=" CG GLU A 233 " ideal model delta sigma weight residual 114.10 121.98 -7.88 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CB GLU A 233 " pdb=" CG GLU A 233 " pdb=" CD GLU A 233 " ideal model delta sigma weight residual 112.60 119.08 -6.48 1.70e+00 3.46e-01 1.45e+01 angle pdb=" N VAL B 130 " pdb=" CA VAL B 130 " pdb=" C VAL B 130 " ideal model delta sigma weight residual 112.96 109.31 3.65 1.00e+00 1.00e+00 1.33e+01 angle pdb=" N VAL A 130 " pdb=" CA VAL A 130 " pdb=" C VAL A 130 " ideal model delta sigma weight residual 112.96 109.34 3.62 1.00e+00 1.00e+00 1.31e+01 angle pdb=" CA MET B1107 " pdb=" CB MET B1107 " pdb=" CG MET B1107 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 ... (remaining 20333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.25: 8760 27.25 - 54.51: 606 54.51 - 81.76: 73 81.76 - 109.01: 26 109.01 - 136.26: 24 Dihedral angle restraints: 9489 sinusoidal: 4227 harmonic: 5262 Sorted by residual: dihedral pdb=" C29 POV A1401 " pdb="C210 POV A1401 " pdb="C211 POV A1401 " pdb="C212 POV A1401 " ideal model delta sinusoidal sigma weight residual 112.25 -111.49 -136.26 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" O31 AJP B1403 " pdb=" C30 AJP B1403 " pdb=" C32 AJP B1403 " pdb=" O33 AJP B1403 " ideal model delta sinusoidal sigma weight residual 177.28 -51.04 -131.68 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C29 AJP B1403 " pdb=" C30 AJP B1403 " pdb=" C32 AJP B1403 " pdb=" O33 AJP B1403 " ideal model delta sinusoidal sigma weight residual -60.96 69.57 -130.53 1 3.00e+01 1.11e-03 1.76e+01 ... (remaining 9486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1792 0.043 - 0.086: 533 0.086 - 0.129: 139 0.129 - 0.172: 15 0.172 - 0.215: 10 Chirality restraints: 2489 Sorted by residual: chirality pdb=" C10 AJP B1402 " pdb=" C08 AJP B1402 " pdb=" C11 AJP B1402 " pdb=" O82 AJP B1402 " both_signs ideal model delta sigma weight residual False 2.61 2.39 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C10 AJP B1404 " pdb=" C08 AJP B1404 " pdb=" C11 AJP B1404 " pdb=" O82 AJP B1404 " both_signs ideal model delta sigma weight residual False 2.61 2.39 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C10 AJP B1403 " pdb=" C08 AJP B1403 " pdb=" C11 AJP B1403 " pdb=" O82 AJP B1403 " both_signs ideal model delta sigma weight residual False 2.61 2.39 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2486 not shown) Planarity restraints: 2449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 641 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO B 642 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 642 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 642 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 949 " 0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO A 950 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 950 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 950 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 268 " -0.010 2.00e-02 2.50e+03 1.55e-02 4.20e+00 pdb=" CG PHE A 268 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 268 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 268 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 268 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 268 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 268 " 0.001 2.00e-02 2.50e+03 ... (remaining 2446 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3685 2.80 - 3.33: 13899 3.33 - 3.85: 23828 3.85 - 4.38: 25804 4.38 - 4.90: 47304 Nonbonded interactions: 114520 Sorted by model distance: nonbonded pdb=" OE1 GLU A 233 " pdb=" ND2 ASN A 237 " model vdw 2.280 3.120 nonbonded pdb=" O GLN B 140 " pdb=" OH TYR B 312 " model vdw 2.303 3.040 nonbonded pdb=" O GLN A 140 " pdb=" OH TYR A 312 " model vdw 2.308 3.040 nonbonded pdb=" O LEU B 174 " pdb=" OG SER B 178 " model vdw 2.311 3.040 nonbonded pdb=" O42 AJP A1403 " pdb=" O64 AJP B1404 " model vdw 2.312 3.040 ... (remaining 114515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 74 through 1192 or resid 1401 or resid 1403)) selection = (chain 'B' and (resid 74 through 1192 or resid 1401 or resid 1403)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 68.340 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: 0.010 Extract box with map and model: 2.270 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 40.260 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14961 Z= 0.188 Angle : 0.674 10.128 20338 Z= 0.336 Chirality : 0.045 0.215 2489 Planarity : 0.005 0.078 2449 Dihedral : 19.444 136.263 6081 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 26.71 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.20), residues: 1798 helix: 1.48 (0.14), residues: 1242 sheet: -0.51 (0.43), residues: 114 loop : -1.06 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 635 HIS 0.002 0.001 HIS A 614 PHE 0.035 0.002 PHE A 268 TYR 0.016 0.001 TYR A 309 ARG 0.003 0.000 ARG B 856 Details of bonding type rmsd hydrogen bonds : bond 0.11196 ( 1040) hydrogen bonds : angle 5.04859 ( 3075) covalent geometry : bond 0.00414 (14961) covalent geometry : angle 0.67380 (20338) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.3440 time to fit residues: 92.1129 Evaluate side-chains 169 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 92 optimal weight: 0.0980 chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS B 889 HIS B 914 HIS B 981 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.224453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.174824 restraints weight = 15224.800| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.20 r_work: 0.3398 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14961 Z= 0.238 Angle : 0.626 7.470 20338 Z= 0.318 Chirality : 0.043 0.143 2489 Planarity : 0.005 0.076 2449 Dihedral : 12.784 142.637 2739 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.90 % Allowed : 23.55 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.20), residues: 1798 helix: 1.76 (0.14), residues: 1248 sheet: -0.62 (0.44), residues: 114 loop : -1.11 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 635 HIS 0.004 0.001 HIS B 614 PHE 0.019 0.002 PHE B 201 TYR 0.017 0.002 TYR A 309 ARG 0.003 0.000 ARG B 976 Details of bonding type rmsd hydrogen bonds : bond 0.05899 ( 1040) hydrogen bonds : angle 4.32367 ( 3075) covalent geometry : bond 0.00596 (14961) covalent geometry : angle 0.62599 (20338) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 169 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 923 ASP cc_start: 0.6393 (OUTLIER) cc_final: 0.6133 (m-30) outliers start: 76 outliers final: 49 residues processed: 221 average time/residue: 0.2287 time to fit residues: 78.7906 Evaluate side-chains 212 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 162 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 923 ASP Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 981 HIS Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 74 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 169 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS A 981 HIS B 292 HIS B 889 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.229603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.185980 restraints weight = 15447.244| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.18 r_work: 0.3574 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14961 Z= 0.117 Angle : 0.511 8.337 20338 Z= 0.260 Chirality : 0.038 0.155 2489 Planarity : 0.004 0.075 2449 Dihedral : 10.523 136.217 2739 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.29 % Allowed : 24.39 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.20), residues: 1798 helix: 2.16 (0.14), residues: 1254 sheet: -0.54 (0.44), residues: 110 loop : -1.11 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 635 HIS 0.004 0.001 HIS B 981 PHE 0.015 0.001 PHE B 201 TYR 0.015 0.001 TYR A 309 ARG 0.002 0.000 ARG B 976 Details of bonding type rmsd hydrogen bonds : bond 0.04581 ( 1040) hydrogen bonds : angle 4.04637 ( 3075) covalent geometry : bond 0.00247 (14961) covalent geometry : angle 0.51118 (20338) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 29 residues processed: 195 average time/residue: 0.2305 time to fit residues: 69.7963 Evaluate side-chains 191 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 65 optimal weight: 0.0470 chunk 47 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 overall best weight: 0.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS A 981 HIS B 292 HIS B 889 HIS B 914 HIS B 981 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.229067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.182744 restraints weight = 15321.994| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 2.21 r_work: 0.3535 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14961 Z= 0.120 Angle : 0.490 8.843 20338 Z= 0.251 Chirality : 0.038 0.140 2489 Planarity : 0.004 0.074 2449 Dihedral : 8.406 130.385 2739 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.94 % Allowed : 24.32 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.20), residues: 1798 helix: 2.33 (0.14), residues: 1256 sheet: -0.43 (0.44), residues: 110 loop : -1.02 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 635 HIS 0.003 0.001 HIS A 614 PHE 0.015 0.001 PHE B 201 TYR 0.020 0.001 TYR B1125 ARG 0.002 0.000 ARG A1092 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 1040) hydrogen bonds : angle 3.89917 ( 3075) covalent geometry : bond 0.00269 (14961) covalent geometry : angle 0.49036 (20338) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 170 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.6963 (mp) REVERT: A 877 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7440 (mm-40) REVERT: A 923 ASP cc_start: 0.6387 (OUTLIER) cc_final: 0.6140 (m-30) REVERT: B 233 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7302 (tm-30) outliers start: 61 outliers final: 38 residues processed: 214 average time/residue: 0.2867 time to fit residues: 96.0163 Evaluate side-chains 202 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 923 ASP Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1166 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 105 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS A 914 HIS A 981 HIS B 889 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.230255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.193985 restraints weight = 15550.296| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 1.92 r_work: 0.3560 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14961 Z= 0.119 Angle : 0.491 7.611 20338 Z= 0.251 Chirality : 0.037 0.140 2489 Planarity : 0.004 0.073 2449 Dihedral : 7.891 128.723 2739 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.81 % Allowed : 24.58 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.20), residues: 1798 helix: 2.39 (0.14), residues: 1256 sheet: -0.42 (0.44), residues: 110 loop : -1.00 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 635 HIS 0.009 0.001 HIS B 914 PHE 0.015 0.001 PHE B 201 TYR 0.015 0.001 TYR A 309 ARG 0.002 0.000 ARG A1092 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 1040) hydrogen bonds : angle 3.87343 ( 3075) covalent geometry : bond 0.00270 (14961) covalent geometry : angle 0.49050 (20338) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 169 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6958 (mp) REVERT: A 877 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7452 (mm-40) REVERT: B 233 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: B 889 HIS cc_start: 0.7101 (OUTLIER) cc_final: 0.6322 (m90) REVERT: B 923 ASP cc_start: 0.6015 (OUTLIER) cc_final: 0.5517 (m-30) outliers start: 59 outliers final: 44 residues processed: 208 average time/residue: 0.2316 time to fit residues: 74.8430 Evaluate side-chains 210 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 914 HIS Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 923 ASP Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 112 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 HIS B 889 HIS B 981 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.227844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.175512 restraints weight = 15396.210| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.40 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14961 Z= 0.149 Angle : 0.523 8.227 20338 Z= 0.267 Chirality : 0.039 0.348 2489 Planarity : 0.004 0.073 2449 Dihedral : 7.706 131.096 2739 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.10 % Allowed : 23.48 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.20), residues: 1798 helix: 2.30 (0.14), residues: 1256 sheet: -0.41 (0.45), residues: 110 loop : -0.98 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 635 HIS 0.010 0.001 HIS B 889 PHE 0.019 0.001 PHE B 268 TYR 0.019 0.001 TYR A 594 ARG 0.005 0.000 ARG B 976 Details of bonding type rmsd hydrogen bonds : bond 0.04574 ( 1040) hydrogen bonds : angle 3.92444 ( 3075) covalent geometry : bond 0.00360 (14961) covalent geometry : angle 0.52338 (20338) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 162 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.6980 (mp) REVERT: B 233 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6681 (tm-30) REVERT: B 405 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7002 (mp) outliers start: 79 outliers final: 55 residues processed: 218 average time/residue: 0.2647 time to fit residues: 90.8485 Evaluate side-chains 218 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 160 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 94 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 179 optimal weight: 30.0000 chunk 143 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 69 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS A 832 GLN A 877 GLN ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 HIS B 292 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.229510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.192669 restraints weight = 15580.621| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 1.98 r_work: 0.3540 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14961 Z= 0.126 Angle : 0.502 8.884 20338 Z= 0.257 Chirality : 0.038 0.230 2489 Planarity : 0.004 0.073 2449 Dihedral : 7.316 129.181 2739 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.19 % Allowed : 24.06 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.20), residues: 1798 helix: 2.37 (0.14), residues: 1256 sheet: -0.39 (0.45), residues: 110 loop : -0.93 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 635 HIS 0.003 0.001 HIS A 614 PHE 0.016 0.001 PHE B 201 TYR 0.015 0.001 TYR A 309 ARG 0.002 0.000 ARG A1092 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 1040) hydrogen bonds : angle 3.88829 ( 3075) covalent geometry : bond 0.00293 (14961) covalent geometry : angle 0.50191 (20338) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 158 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6915 (mp) REVERT: B 233 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: B 405 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6839 (mp) REVERT: B 889 HIS cc_start: 0.7110 (OUTLIER) cc_final: 0.6293 (m90) outliers start: 65 outliers final: 52 residues processed: 204 average time/residue: 0.2512 time to fit residues: 80.8932 Evaluate side-chains 211 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 155 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 981 HIS Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 16 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 144 optimal weight: 20.0000 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 HIS B 292 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.228690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.183881 restraints weight = 15491.743| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.28 r_work: 0.3554 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14961 Z= 0.141 Angle : 0.515 9.406 20338 Z= 0.264 Chirality : 0.038 0.186 2489 Planarity : 0.004 0.072 2449 Dihedral : 7.360 130.417 2739 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.26 % Allowed : 24.06 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.20), residues: 1798 helix: 2.33 (0.14), residues: 1256 sheet: -0.40 (0.45), residues: 110 loop : -0.92 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 635 HIS 0.003 0.001 HIS A 614 PHE 0.018 0.001 PHE B 201 TYR 0.016 0.001 TYR A 309 ARG 0.002 0.000 ARG A1092 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 1040) hydrogen bonds : angle 3.91477 ( 3075) covalent geometry : bond 0.00338 (14961) covalent geometry : angle 0.51466 (20338) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 161 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.6940 (mp) REVERT: A 877 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7447 (mm-40) REVERT: B 233 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: B 405 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6876 (mp) REVERT: B 889 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6422 (m90) outliers start: 66 outliers final: 53 residues processed: 207 average time/residue: 0.2350 time to fit residues: 75.3895 Evaluate side-chains 216 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 159 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 981 HIS Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 70 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 87 optimal weight: 0.1980 chunk 67 optimal weight: 0.3980 chunk 94 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 96 optimal weight: 0.0980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 HIS B 292 HIS B 505 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.232657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.190931 restraints weight = 15468.585| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 2.28 r_work: 0.3584 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14961 Z= 0.100 Angle : 0.480 10.410 20338 Z= 0.245 Chirality : 0.037 0.165 2489 Planarity : 0.004 0.073 2449 Dihedral : 6.704 118.819 2739 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.00 % Allowed : 26.39 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.20), residues: 1798 helix: 2.54 (0.14), residues: 1256 sheet: -0.37 (0.44), residues: 110 loop : -0.86 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 635 HIS 0.002 0.000 HIS A 614 PHE 0.011 0.001 PHE B 201 TYR 0.011 0.001 TYR A 309 ARG 0.003 0.000 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 1040) hydrogen bonds : angle 3.75860 ( 3075) covalent geometry : bond 0.00206 (14961) covalent geometry : angle 0.48041 (20338) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.686 Fit side-chains revert: symmetry clash REVERT: A 405 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6889 (mp) REVERT: A 877 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7422 (mm-40) REVERT: A 923 ASP cc_start: 0.6047 (OUTLIER) cc_final: 0.5685 (m-30) REVERT: A 1115 GLU cc_start: 0.7337 (tt0) cc_final: 0.7101 (pt0) REVERT: B 405 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6818 (mp) outliers start: 31 outliers final: 21 residues processed: 187 average time/residue: 0.2871 time to fit residues: 82.9464 Evaluate side-chains 184 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 50 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 85 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN A 831 ASN ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 HIS B 908 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.231505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.186402 restraints weight = 15517.037| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.23 r_work: 0.3591 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14961 Z= 0.109 Angle : 0.498 10.984 20338 Z= 0.252 Chirality : 0.037 0.148 2489 Planarity : 0.004 0.073 2449 Dihedral : 6.713 117.639 2739 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.00 % Allowed : 26.84 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.20), residues: 1798 helix: 2.57 (0.14), residues: 1250 sheet: -0.31 (0.45), residues: 110 loop : -0.80 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 635 HIS 0.004 0.001 HIS B 600 PHE 0.022 0.001 PHE B 268 TYR 0.015 0.001 TYR A 309 ARG 0.001 0.000 ARG A1092 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 1040) hydrogen bonds : angle 3.77471 ( 3075) covalent geometry : bond 0.00242 (14961) covalent geometry : angle 0.49806 (20338) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.957 Fit side-chains revert: symmetry clash REVERT: A 405 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.6983 (mp) REVERT: A 877 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7433 (mm-40) REVERT: A 923 ASP cc_start: 0.6017 (OUTLIER) cc_final: 0.5604 (m-30) REVERT: A 1115 GLU cc_start: 0.7343 (tt0) cc_final: 0.7100 (pt0) REVERT: B 405 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6871 (mp) outliers start: 31 outliers final: 25 residues processed: 181 average time/residue: 0.2606 time to fit residues: 71.4543 Evaluate side-chains 189 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1166 LEU Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 179 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 175 optimal weight: 0.0470 chunk 30 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 135 optimal weight: 0.0050 chunk 141 optimal weight: 8.9990 overall best weight: 0.4692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 917 GLN A 981 HIS B 908 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.232538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.190077 restraints weight = 15593.564| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 2.27 r_work: 0.3566 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14961 Z= 0.102 Angle : 0.493 11.271 20338 Z= 0.249 Chirality : 0.037 0.142 2489 Planarity : 0.004 0.073 2449 Dihedral : 6.530 111.955 2739 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.06 % Allowed : 26.71 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.20), residues: 1798 helix: 2.64 (0.14), residues: 1250 sheet: -0.27 (0.45), residues: 110 loop : -0.76 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 635 HIS 0.002 0.000 HIS B 908 PHE 0.013 0.001 PHE B 386 TYR 0.013 0.001 TYR A 309 ARG 0.019 0.000 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 1040) hydrogen bonds : angle 3.73215 ( 3075) covalent geometry : bond 0.00219 (14961) covalent geometry : angle 0.49333 (20338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7926.63 seconds wall clock time: 141 minutes 8.52 seconds (8468.52 seconds total)