Starting phenix.real_space_refine on Fri Jun 13 01:14:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7s_41991/06_2025/8u7s_41991.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7s_41991/06_2025/8u7s_41991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u7s_41991/06_2025/8u7s_41991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7s_41991/06_2025/8u7s_41991.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7s_41991/06_2025/8u7s_41991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7s_41991/06_2025/8u7s_41991.cif" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 2 5.49 5 S 74 5.16 5 C 9562 2.51 5 N 2366 2.21 5 O 2626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14630 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7134 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 880} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 7134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7134 Classifications: {'peptide': 908} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 880} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 207 Unusual residues: {'AJP': 2, 'POV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 19 Chain: "B" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'AJP': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 24 Time building chain proxies: 10.47, per 1000 atoms: 0.72 Number of scatterers: 14630 At special positions: 0 Unit cell: (109.02, 120.06, 128.34, 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 2 15.00 O 2626 8.00 N 2366 7.00 C 9562 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: 4.40 Conformation dependent library (CDL) restraints added in 2.0 seconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3412 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 8 sheets defined 74.4% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 77 through 94 Processing helix chain 'A' and resid 102 through 120 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 134 through 151 removed outlier: 3.646A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.811A pdb=" N SER A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 207 removed outlier: 4.355A pdb=" N MET A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.514A pdb=" N VAL A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASP A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 253 removed outlier: 3.658A pdb=" N GLY A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 291 removed outlier: 4.295A pdb=" N LEU A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.724A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 4.043A pdb=" N LEU A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.506A pdb=" N ALA A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 380 " --> pdb=" O LEU A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 380' Processing helix chain 'A' and resid 381 through 414 removed outlier: 3.986A pdb=" N LEU A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE A 389 " --> pdb=" O TRP A 385 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.917A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 removed outlier: 3.956A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 3.797A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.767A pdb=" N CYS A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 601 removed outlier: 3.600A pdb=" N GLY A 601 " --> pdb=" O GLN A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.713A pdb=" N GLU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.765A pdb=" N LEU A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 653 removed outlier: 3.978A pdb=" N LEU A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 854 removed outlier: 3.682A pdb=" N LEU A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Proline residue: A 819 - end of helix removed outlier: 3.639A pdb=" N ASN A 831 " --> pdb=" O GLY A 827 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLN A 832 " --> pdb=" O LYS A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.505A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 4.055A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.597A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 959 Processing helix chain 'A' and resid 960 through 964 removed outlier: 3.791A pdb=" N LEU A 963 " --> pdb=" O VAL A 960 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 964 " --> pdb=" O SER A 961 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 960 through 964' Processing helix chain 'A' and resid 966 through 977 removed outlier: 3.782A pdb=" N ILE A 970 " --> pdb=" O ASP A 966 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1049 removed outlier: 3.816A pdb=" N LEU A1048 " --> pdb=" O GLU A1044 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A1049 " --> pdb=" O MET A1045 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1044 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 removed outlier: 3.930A pdb=" N GLN A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1123 Processing helix chain 'B' and resid 77 through 94 Processing helix chain 'B' and resid 102 through 120 Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.631A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Proline residue: B 144 - end of helix removed outlier: 3.688A pdb=" N SER B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 151 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.866A pdb=" N SER B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 removed outlier: 3.508A pdb=" N VAL B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 207 removed outlier: 4.219A pdb=" N MET B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 removed outlier: 5.216A pdb=" N ASP B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 253 removed outlier: 3.814A pdb=" N GLY B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 291 removed outlier: 3.539A pdb=" N ASN B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLY B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 298 through 319 removed outlier: 3.733A pdb=" N THR B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 4.066A pdb=" N LEU B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 375 Processing helix chain 'B' and resid 376 through 380 removed outlier: 3.526A pdb=" N ALA B 379 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 380 " --> pdb=" O LEU B 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 376 through 380' Processing helix chain 'B' and resid 381 through 414 removed outlier: 3.870A pdb=" N LEU B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE B 389 " --> pdb=" O TRP B 385 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 427 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.908A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 481 removed outlier: 3.966A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 485 removed outlier: 3.602A pdb=" N ASP B 485 " --> pdb=" O GLY B 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 482 through 485' Processing helix chain 'B' and resid 487 through 514 removed outlier: 3.752A pdb=" N SER B 514 " --> pdb=" O ASN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 530 removed outlier: 3.525A pdb=" N ALA B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 601 removed outlier: 3.576A pdb=" N GLY B 601 " --> pdb=" O GLN B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 621 removed outlier: 3.710A pdb=" N GLU B 621 " --> pdb=" O VAL B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.737A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 640 Processing helix chain 'B' and resid 641 through 653 Processing helix chain 'B' and resid 813 through 854 removed outlier: 3.586A pdb=" N LEU B 817 " --> pdb=" O LEU B 813 " (cutoff:3.500A) Proline residue: B 819 - end of helix removed outlier: 4.309A pdb=" N GLN B 832 " --> pdb=" O LYS B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.509A pdb=" N HIS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 removed outlier: 4.054A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.596A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 959 Processing helix chain 'B' and resid 960 through 964 removed outlier: 3.733A pdb=" N LEU B 963 " --> pdb=" O VAL B 960 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 964 " --> pdb=" O SER B 961 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 960 through 964' Processing helix chain 'B' and resid 966 through 977 removed outlier: 3.583A pdb=" N ILE B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG B 976 " --> pdb=" O PHE B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1049 removed outlier: 3.739A pdb=" N LEU B1048 " --> pdb=" O GLU B1044 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B1049 " --> pdb=" O MET B1045 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1044 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 removed outlier: 3.928A pdb=" N GLN B1106 " --> pdb=" O LEU B1102 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1123 Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.489A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 999 " --> pdb=" O ILE A1042 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A1042 " --> pdb=" O PHE A 999 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1033 through 1035 Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1127 removed outlier: 3.807A pdb=" N TYR A1125 " --> pdb=" O VAL A1188 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL A1188 " --> pdb=" O TYR A1125 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A1127 " --> pdb=" O LEU A1186 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU A1186 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137 Processing sheet with id=AA5, first strand: chain 'B' and resid 978 through 982 removed outlier: 6.502A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 999 " --> pdb=" O ILE B1042 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B1042 " --> pdb=" O PHE B 999 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1033 through 1035 Processing sheet with id=AA7, first strand: chain 'B' and resid 1126 through 1127 removed outlier: 3.765A pdb=" N VAL B1127 " --> pdb=" O LEU B1186 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU B1186 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG B1185 " --> pdb=" O ILE B1148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1135 through 1137 989 hydrogen bonds defined for protein. 2940 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: 5.23 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2553 1.33 - 1.45: 3587 1.45 - 1.57: 8655 1.57 - 1.69: 3 1.69 - 1.82: 136 Bond restraints: 14934 Sorted by residual: bond pdb=" O12 POV A1401 " pdb=" P POV A1401 " ideal model delta sigma weight residual 1.657 1.495 0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C ILE B 818 " pdb=" N PRO B 819 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.28e-02 6.10e+03 5.63e+00 bond pdb=" N PRO B 951 " pdb=" CD PRO B 951 " ideal model delta sigma weight residual 1.473 1.451 0.022 1.40e-02 5.10e+03 2.43e+00 bond pdb=" C TYR A 641 " pdb=" N PRO A 642 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.39e+00 bond pdb=" C26 AJP B1403 " pdb=" O25 AJP B1403 " ideal model delta sigma weight residual 1.375 1.405 -0.030 2.00e-02 2.50e+03 2.30e+00 ... (remaining 14929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 20011 2.72 - 5.44: 241 5.44 - 8.16: 37 8.16 - 10.88: 7 10.88 - 13.59: 1 Bond angle restraints: 20297 Sorted by residual: angle pdb=" O11 POV A1401 " pdb=" P POV A1401 " pdb=" O12 POV A1401 " ideal model delta sigma weight residual 97.67 111.26 -13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C LYS B 622 " pdb=" N ASP B 623 " pdb=" CA ASP B 623 " ideal model delta sigma weight residual 121.54 128.65 -7.11 1.91e+00 2.74e-01 1.39e+01 angle pdb=" C LYS A 622 " pdb=" N ASP A 623 " pdb=" CA ASP A 623 " ideal model delta sigma weight residual 121.54 128.58 -7.04 1.91e+00 2.74e-01 1.36e+01 angle pdb=" N ILE A 829 " pdb=" CA ILE A 829 " pdb=" C ILE A 829 " ideal model delta sigma weight residual 112.96 109.37 3.59 1.00e+00 1.00e+00 1.29e+01 angle pdb=" CB MET A 160 " pdb=" CG MET A 160 " pdb=" SD MET A 160 " ideal model delta sigma weight residual 112.70 122.76 -10.06 3.00e+00 1.11e-01 1.12e+01 ... (remaining 20292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.67: 8825 25.67 - 51.34: 512 51.34 - 77.01: 70 77.01 - 102.68: 11 102.68 - 128.35: 18 Dihedral angle restraints: 9436 sinusoidal: 4166 harmonic: 5270 Sorted by residual: dihedral pdb=" C55 AJP A1403 " pdb=" C59 AJP A1403 " pdb=" O60 AJP A1403 " pdb=" C58 AJP A1403 " ideal model delta sinusoidal sigma weight residual -60.14 68.21 -128.35 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C59 AJP B1403 " pdb=" C55 AJP B1403 " pdb=" O60 AJP B1403 " pdb=" O54 AJP B1403 " ideal model delta sinusoidal sigma weight residual 177.58 61.18 116.40 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C59 AJP A1404 " pdb=" C55 AJP A1404 " pdb=" O60 AJP A1404 " pdb=" O54 AJP A1404 " ideal model delta sinusoidal sigma weight residual 177.58 61.18 116.40 1 3.00e+01 1.11e-03 1.54e+01 ... (remaining 9433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1733 0.041 - 0.083: 548 0.083 - 0.124: 164 0.124 - 0.165: 21 0.165 - 0.206: 14 Chirality restraints: 2480 Sorted by residual: chirality pdb=" C10 AJP A1403 " pdb=" C08 AJP A1403 " pdb=" C11 AJP A1403 " pdb=" O82 AJP A1403 " both_signs ideal model delta sigma weight residual False 2.61 2.40 0.21 2.00e-01 2.50e+01 1.07e+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 2.40 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C10 AJP A1404 " pdb=" C08 AJP A1404 " pdb=" C11 AJP A1404 " pdb=" O82 AJP A1404 " both_signs ideal model delta sigma weight residual False 2.61 2.41 0.20 2.00e-01 2.50e+01 9.97e-01 ... (remaining 2477 not shown) Planarity restraints: 2449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 635 " 0.023 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP B 635 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 635 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP B 635 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 635 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 635 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 635 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 635 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 635 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 635 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B1083 " -0.046 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO B1084 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B1084 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B1084 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A1083 " 0.046 5.00e-02 4.00e+02 7.07e-02 7.99e+00 pdb=" N PRO A1084 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A1084 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A1084 " 0.040 5.00e-02 4.00e+02 ... (remaining 2446 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3074 2.78 - 3.31: 14485 3.31 - 3.84: 23453 3.84 - 4.37: 23728 4.37 - 4.90: 42935 Nonbonded interactions: 107675 Sorted by model distance: nonbonded pdb=" OG1 THR B1179 " pdb=" O GLU B1182 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR A1179 " pdb=" O GLU A1182 " model vdw 2.255 3.040 nonbonded pdb=" NZ LYS A 897 " pdb=" OD2 ASP B 520 " model vdw 2.289 3.120 nonbonded pdb=" OD2 ASP A 520 " pdb=" NZ LYS B 897 " model vdw 2.311 3.120 nonbonded pdb=" NZ LYS A 937 " pdb=" O GLU B 531 " model vdw 2.318 3.120 ... (remaining 107670 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 76 through 1192 or (resid 1401 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 or n \ ame O21 or name O22 or name O31 or name O32 or name C210 or name C211 or name C2 \ 12 or name C213 or name C214 or name C215 or name C216 or name C310 or name C311 \ or name C312 or name C313 or name C314)) or resid 1403)) selection = (chain 'B' and (resid 76 through 1192 or resid 1401 or (resid 1403 and (name C01 \ or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name \ C08 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 \ or name C23 or name C24 or name C26 or name C27 or name C28 or name C29 or name \ C30 or name C32 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C41 or name C55 or name C56 or name C57 or name C58 or name C59 or name C80 \ or name C81 or name C83 or name C85 or name O09 or name O25 or name O31 or name \ O33 or name O34 or name O40 or name O42 or name O43 or name O44 or name O54 or \ name O60 or name O63 or name O64 or name O76 or name O77 or name O78 or name O79 \ or name O82 or name O84)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.940 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 0.162 14934 Z= 0.195 Angle : 0.746 13.594 20297 Z= 0.365 Chirality : 0.046 0.206 2480 Planarity : 0.005 0.071 2449 Dihedral : 16.685 128.348 6024 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.20), residues: 1800 helix: 1.36 (0.14), residues: 1236 sheet: 0.08 (0.51), residues: 100 loop : -1.09 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP B 635 HIS 0.003 0.001 HIS B 350 PHE 0.041 0.002 PHE A 195 TYR 0.017 0.001 TYR B 309 ARG 0.002 0.000 ARG B1162 Details of bonding type rmsd hydrogen bonds : bond 0.12653 ( 989) hydrogen bonds : angle 5.10878 ( 2940) covalent geometry : bond 0.00406 (14934) covalent geometry : angle 0.74574 (20297) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.7879 (mmm) cc_final: 0.7592 (ttp) REVERT: A 578 MET cc_start: 0.8078 (ppp) cc_final: 0.7863 (ppp) REVERT: A 971 ASP cc_start: 0.7380 (p0) cc_final: 0.6940 (p0) REVERT: B 160 MET cc_start: 0.7829 (mmm) cc_final: 0.7617 (ttp) REVERT: B 643 TRP cc_start: 0.4990 (t-100) cc_final: 0.4468 (t-100) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2248 time to fit residues: 78.8592 Evaluate side-chains 165 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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: 0.4980 chunk 75 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.147380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.121303 restraints weight = 23652.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.120174 restraints weight = 27313.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121219 restraints weight = 26340.491| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14934 Z= 0.131 Angle : 0.570 6.549 20297 Z= 0.284 Chirality : 0.039 0.151 2480 Planarity : 0.004 0.071 2449 Dihedral : 9.576 89.460 2692 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.71 (0.20), residues: 1800 helix: 1.99 (0.14), residues: 1248 sheet: 0.05 (0.54), residues: 92 loop : -1.06 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 635 HIS 0.003 0.001 HIS B 350 PHE 0.026 0.001 PHE B 195 TYR 0.017 0.001 TYR B 309 ARG 0.002 0.000 ARG A 420 Details of bonding type rmsd hydrogen bonds : bond 0.05303 ( 989) hydrogen bonds : angle 3.98879 ( 2940) covalent geometry : bond 0.00274 (14934) covalent geometry : angle 0.57025 (20297) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.623 Fit side-chains revert: symmetry clash REVERT: A 578 MET cc_start: 0.7920 (ppp) cc_final: 0.7605 (ppp) REVERT: A 854 ILE cc_start: 0.9082 (tp) cc_final: 0.8846 (tp) REVERT: B 643 TRP cc_start: 0.4764 (t-100) cc_final: 0.4237 (t-100) REVERT: B 848 GLU cc_start: 0.7852 (tt0) cc_final: 0.7393 (tt0) REVERT: B 1107 MET cc_start: 0.7951 (ttt) cc_final: 0.7751 (ttm) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.3018 time to fit residues: 106.2098 Evaluate side-chains 153 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 68 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 889 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115145 restraints weight = 23921.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115393 restraints weight = 30850.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.116352 restraints weight = 29967.277| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14934 Z= 0.197 Angle : 0.624 7.146 20297 Z= 0.312 Chirality : 0.041 0.147 2480 Planarity : 0.004 0.074 2449 Dihedral : 8.623 87.501 2692 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1800 helix: 2.13 (0.14), residues: 1246 sheet: 0.12 (0.55), residues: 92 loop : -1.07 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 635 HIS 0.004 0.001 HIS A 350 PHE 0.022 0.001 PHE B 195 TYR 0.020 0.001 TYR B 309 ARG 0.003 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.05832 ( 989) hydrogen bonds : angle 3.99530 ( 2940) covalent geometry : bond 0.00464 (14934) covalent geometry : angle 0.62363 (20297) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.684 Fit side-chains REVERT: A 97 LYS cc_start: 0.8192 (mmmt) cc_final: 0.7901 (pttp) REVERT: A 295 ASN cc_start: 0.8436 (t0) cc_final: 0.8163 (t0) REVERT: A 578 MET cc_start: 0.7925 (ppp) cc_final: 0.7548 (ppp) REVERT: A 848 GLU cc_start: 0.7901 (tt0) cc_final: 0.7448 (mt-10) REVERT: B 295 ASN cc_start: 0.8430 (t0) cc_final: 0.8186 (t0) REVERT: B 643 TRP cc_start: 0.4976 (t-100) cc_final: 0.4537 (t-100) REVERT: B 1107 MET cc_start: 0.8027 (ttt) cc_final: 0.7815 (ttm) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2247 time to fit residues: 70.2410 Evaluate side-chains 148 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 176 optimal weight: 0.9980 chunk 174 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 889 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120519 restraints weight = 23634.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119806 restraints weight = 27078.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.120956 restraints weight = 25564.165| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 0.031 14934 Z= 0.115 Angle : 0.547 7.677 20297 Z= 0.269 Chirality : 0.038 0.144 2480 Planarity : 0.004 0.074 2449 Dihedral : 7.568 78.895 2692 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 2.19 (0.20), residues: 1800 helix: 2.43 (0.15), residues: 1232 sheet: 0.34 (0.56), residues: 92 loop : -1.01 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 635 HIS 0.003 0.001 HIS A 889 PHE 0.020 0.001 PHE B 195 TYR 0.015 0.001 TYR B 309 ARG 0.003 0.000 ARG B 646 Details of bonding type rmsd hydrogen bonds : bond 0.04702 ( 989) hydrogen bonds : angle 3.69039 ( 2940) covalent geometry : bond 0.00237 (14934) covalent geometry : angle 0.54714 (20297) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.710 Fit side-chains REVERT: A 199 MET cc_start: 0.8791 (mpp) cc_final: 0.8485 (mpp) REVERT: A 295 ASN cc_start: 0.8334 (t0) cc_final: 0.8128 (t0) REVERT: A 848 GLU cc_start: 0.7653 (tt0) cc_final: 0.7237 (tt0) REVERT: A 857 MET cc_start: 0.7267 (mmp) cc_final: 0.6992 (tpt) REVERT: B 154 MET cc_start: 0.8170 (tpp) cc_final: 0.7842 (tpt) REVERT: B 199 MET cc_start: 0.8848 (mpp) cc_final: 0.8594 (mpp) REVERT: B 349 LEU cc_start: 0.9344 (mm) cc_final: 0.9042 (mt) REVERT: B 643 TRP cc_start: 0.4754 (t-100) cc_final: 0.4357 (t-100) REVERT: B 882 LEU cc_start: 0.9202 (tp) cc_final: 0.8940 (tp) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2215 time to fit residues: 77.0808 Evaluate side-chains 155 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.152099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.135844 restraints weight = 24069.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134605 restraints weight = 32401.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134742 restraints weight = 32165.897| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14934 Z= 0.119 Angle : 0.545 7.165 20297 Z= 0.270 Chirality : 0.038 0.142 2480 Planarity : 0.004 0.076 2449 Dihedral : 7.449 79.898 2692 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 2.28 (0.20), residues: 1800 helix: 2.42 (0.14), residues: 1248 sheet: 0.37 (0.56), residues: 92 loop : -0.86 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 635 HIS 0.002 0.001 HIS A 350 PHE 0.039 0.001 PHE B 195 TYR 0.017 0.001 TYR B 309 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 989) hydrogen bonds : angle 3.67467 ( 2940) covalent geometry : bond 0.00253 (14934) covalent geometry : angle 0.54544 (20297) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.823 Fit side-chains revert: symmetry clash REVERT: A 848 GLU cc_start: 0.7672 (tt0) cc_final: 0.7398 (tt0) REVERT: B 154 MET cc_start: 0.8189 (tpp) cc_final: 0.7859 (tpt) REVERT: B 643 TRP cc_start: 0.4220 (t-100) cc_final: 0.3849 (t-100) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2168 time to fit residues: 71.8821 Evaluate side-chains 156 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 22 optimal weight: 0.0370 chunk 14 optimal weight: 0.0980 chunk 18 optimal weight: 0.1980 chunk 68 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.148460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.120783 restraints weight = 23827.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119891 restraints weight = 25915.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.121336 restraints weight = 26054.882| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14934 Z= 0.112 Angle : 0.533 6.799 20297 Z= 0.264 Chirality : 0.038 0.144 2480 Planarity : 0.004 0.077 2449 Dihedral : 7.177 76.837 2692 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 2.32 (0.20), residues: 1800 helix: 2.44 (0.14), residues: 1248 sheet: 0.59 (0.51), residues: 112 loop : -0.95 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 635 HIS 0.002 0.000 HIS A 350 PHE 0.041 0.001 PHE B 195 TYR 0.015 0.001 TYR B 309 ARG 0.002 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 989) hydrogen bonds : angle 3.60797 ( 2940) covalent geometry : bond 0.00235 (14934) covalent geometry : angle 0.53334 (20297) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.771 Fit side-chains revert: symmetry clash REVERT: A 178 SER cc_start: 0.9405 (m) cc_final: 0.8695 (t) REVERT: A 199 MET cc_start: 0.8529 (mpp) cc_final: 0.8159 (mpp) REVERT: A 848 GLU cc_start: 0.7751 (tt0) cc_final: 0.7420 (tt0) REVERT: B 199 MET cc_start: 0.8316 (mpp) cc_final: 0.8102 (mpp) REVERT: B 578 MET cc_start: 0.7671 (ppp) cc_final: 0.7280 (ppp) REVERT: B 643 TRP cc_start: 0.4894 (t-100) cc_final: 0.4441 (t-100) REVERT: B 882 LEU cc_start: 0.9189 (tp) cc_final: 0.8966 (tp) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2275 time to fit residues: 79.0710 Evaluate side-chains 161 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 139 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 170 optimal weight: 0.3980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.148690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120536 restraints weight = 23781.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.119361 restraints weight = 27648.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121025 restraints weight = 27668.569| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14934 Z= 0.117 Angle : 0.548 6.575 20297 Z= 0.270 Chirality : 0.038 0.145 2480 Planarity : 0.004 0.077 2449 Dihedral : 7.086 75.768 2692 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 2.35 (0.20), residues: 1800 helix: 2.46 (0.14), residues: 1248 sheet: 0.40 (0.55), residues: 92 loop : -0.80 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 635 HIS 0.002 0.000 HIS A 350 PHE 0.032 0.001 PHE B 195 TYR 0.015 0.001 TYR B 309 ARG 0.003 0.000 ARG B 976 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 989) hydrogen bonds : angle 3.62580 ( 2940) covalent geometry : bond 0.00253 (14934) covalent geometry : angle 0.54794 (20297) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 SER cc_start: 0.9395 (m) cc_final: 0.8683 (t) REVERT: A 295 ASN cc_start: 0.8221 (t0) cc_final: 0.7980 (t0) REVERT: A 848 GLU cc_start: 0.7666 (tt0) cc_final: 0.7303 (tt0) REVERT: A 857 MET cc_start: 0.7358 (mmp) cc_final: 0.7091 (tpt) REVERT: B 295 ASN cc_start: 0.8127 (t0) cc_final: 0.7875 (t0) REVERT: B 578 MET cc_start: 0.7609 (ppp) cc_final: 0.7264 (ppp) REVERT: B 643 TRP cc_start: 0.5138 (t-100) cc_final: 0.4579 (t-100) REVERT: B 857 MET cc_start: 0.7871 (tpt) cc_final: 0.7670 (mmp) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2529 time to fit residues: 85.1082 Evaluate side-chains 161 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 172 optimal weight: 0.5980 chunk 118 optimal weight: 0.7980 chunk 109 optimal weight: 0.2980 chunk 173 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 158 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.150421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.122239 restraints weight = 23638.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.121799 restraints weight = 24142.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.123133 restraints weight = 23818.909| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14934 Z= 0.107 Angle : 0.539 6.994 20297 Z= 0.264 Chirality : 0.038 0.176 2480 Planarity : 0.004 0.078 2449 Dihedral : 6.885 73.841 2692 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 2.43 (0.20), residues: 1800 helix: 2.51 (0.14), residues: 1248 sheet: 0.86 (0.58), residues: 80 loop : -0.81 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 635 HIS 0.002 0.000 HIS A 126 PHE 0.037 0.001 PHE B 195 TYR 0.012 0.001 TYR B 309 ARG 0.001 0.000 ARG B 646 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 989) hydrogen bonds : angle 3.54661 ( 2940) covalent geometry : bond 0.00218 (14934) covalent geometry : angle 0.53932 (20297) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 2.780 Fit side-chains REVERT: A 178 SER cc_start: 0.9396 (m) cc_final: 0.8710 (t) REVERT: A 199 MET cc_start: 0.8510 (mpp) cc_final: 0.8206 (mpp) REVERT: A 295 ASN cc_start: 0.8186 (t0) cc_final: 0.7939 (t0) REVERT: A 848 GLU cc_start: 0.7635 (tt0) cc_final: 0.7260 (tt0) REVERT: A 882 LEU cc_start: 0.9210 (tp) cc_final: 0.8933 (tp) REVERT: B 154 MET cc_start: 0.8003 (tpp) cc_final: 0.7359 (tpt) REVERT: B 295 ASN cc_start: 0.8109 (t0) cc_final: 0.7880 (t0) REVERT: B 371 VAL cc_start: 0.8168 (t) cc_final: 0.7939 (t) REVERT: B 578 MET cc_start: 0.7486 (ppp) cc_final: 0.7030 (ppp) REVERT: B 643 TRP cc_start: 0.5159 (t-100) cc_final: 0.4628 (t-100) REVERT: B 848 GLU cc_start: 0.7525 (tt0) cc_final: 0.7159 (tt0) REVERT: B 857 MET cc_start: 0.7852 (tpt) cc_final: 0.7588 (mmp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3698 time to fit residues: 131.5781 Evaluate side-chains 162 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 52 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 37 optimal weight: 0.0070 chunk 54 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.149849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.122099 restraints weight = 23591.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122013 restraints weight = 25644.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123363 restraints weight = 23916.522| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14934 Z= 0.110 Angle : 0.551 9.388 20297 Z= 0.269 Chirality : 0.038 0.165 2480 Planarity : 0.004 0.078 2449 Dihedral : 6.944 74.688 2692 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1800 helix: 2.50 (0.14), residues: 1248 sheet: 0.85 (0.58), residues: 80 loop : -0.79 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B 635 HIS 0.002 0.000 HIS A 350 PHE 0.047 0.001 PHE A 195 TYR 0.018 0.001 TYR A 309 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 989) hydrogen bonds : angle 3.56358 ( 2940) covalent geometry : bond 0.00235 (14934) covalent geometry : angle 0.55080 (20297) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.913 Fit side-chains revert: symmetry clash REVERT: A 295 ASN cc_start: 0.8209 (t0) cc_final: 0.7970 (t0) REVERT: A 848 GLU cc_start: 0.7601 (tt0) cc_final: 0.7208 (tt0) REVERT: A 882 LEU cc_start: 0.9202 (tp) cc_final: 0.8927 (tp) REVERT: B 295 ASN cc_start: 0.8128 (t0) cc_final: 0.7906 (t0) REVERT: B 371 VAL cc_start: 0.8177 (t) cc_final: 0.7953 (t) REVERT: B 578 MET cc_start: 0.7453 (ppp) cc_final: 0.7008 (ppp) REVERT: B 643 TRP cc_start: 0.5233 (t-100) cc_final: 0.4655 (t-100) REVERT: B 848 GLU cc_start: 0.7512 (tt0) cc_final: 0.7149 (tt0) REVERT: B 857 MET cc_start: 0.7887 (tpt) cc_final: 0.7620 (mmp) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2904 time to fit residues: 103.3368 Evaluate side-chains 162 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 166 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 chunk 132 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.149960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120606 restraints weight = 23835.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.121051 restraints weight = 26604.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.122398 restraints weight = 22667.232| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14934 Z= 0.112 Angle : 0.564 8.533 20297 Z= 0.275 Chirality : 0.038 0.164 2480 Planarity : 0.004 0.077 2449 Dihedral : 6.802 75.326 2692 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 2.41 (0.20), residues: 1800 helix: 2.49 (0.14), residues: 1248 sheet: 0.85 (0.58), residues: 80 loop : -0.81 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP B 635 HIS 0.002 0.000 HIS A 350 PHE 0.041 0.001 PHE A 195 TYR 0.017 0.001 TYR A 309 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 989) hydrogen bonds : angle 3.59788 ( 2940) covalent geometry : bond 0.00242 (14934) covalent geometry : angle 0.56424 (20297) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.552 Fit side-chains REVERT: A 97 LYS cc_start: 0.8321 (mmmt) cc_final: 0.7983 (pttp) REVERT: A 295 ASN cc_start: 0.8222 (t0) cc_final: 0.7986 (t0) REVERT: A 578 MET cc_start: 0.8007 (ppp) cc_final: 0.7628 (ppp) REVERT: A 848 GLU cc_start: 0.7673 (tt0) cc_final: 0.7288 (tt0) REVERT: A 857 MET cc_start: 0.7303 (mmp) cc_final: 0.7090 (tpt) REVERT: A 882 LEU cc_start: 0.9185 (tp) cc_final: 0.8923 (tp) REVERT: A 1034 ASP cc_start: 0.8819 (t70) cc_final: 0.8425 (t70) REVERT: B 295 ASN cc_start: 0.8141 (t0) cc_final: 0.7912 (t0) REVERT: B 371 VAL cc_start: 0.8208 (t) cc_final: 0.7970 (t) REVERT: B 578 MET cc_start: 0.7578 (ppp) cc_final: 0.7160 (ppp) REVERT: B 643 TRP cc_start: 0.5383 (t-100) cc_final: 0.4777 (t-100) REVERT: B 848 GLU cc_start: 0.7522 (tt0) cc_final: 0.7147 (tt0) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2000 time to fit residues: 69.6351 Evaluate side-chains 160 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 125 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.148925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.121151 restraints weight = 23830.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.120357 restraints weight = 27160.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.121798 restraints weight = 27535.434| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14934 Z= 0.121 Angle : 0.564 8.846 20297 Z= 0.277 Chirality : 0.039 0.162 2480 Planarity : 0.004 0.077 2449 Dihedral : 6.765 76.348 2692 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 2.38 (0.20), residues: 1800 helix: 2.48 (0.15), residues: 1248 sheet: 0.84 (0.58), residues: 80 loop : -0.81 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 635 HIS 0.002 0.000 HIS A 350 PHE 0.038 0.001 PHE A 195 TYR 0.018 0.001 TYR A 309 ARG 0.001 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 989) hydrogen bonds : angle 3.62923 ( 2940) covalent geometry : bond 0.00269 (14934) covalent geometry : angle 0.56365 (20297) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4362.66 seconds wall clock time: 79 minutes 34.42 seconds (4774.42 seconds total)