Starting phenix.real_space_refine on Fri May 16 13:58:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7s_41991/05_2025/8u7s_41991.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7s_41991/05_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_41991/05_2025/8u7s_41991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7s_41991/05_2025/8u7s_41991.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7s_41991/05_2025/8u7s_41991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7s_41991/05_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-5687/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: 9.03, per 1000 atoms: 0.62 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: 4.26 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: 1.55 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: 4.94 Time building geometry restraints manager: 4.86 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: 0.300 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: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 35.340 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.180 ------------------------------------------------------------------------------- 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 : 1.575 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: 0.2179 time to fit residues: 76.8179 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 : 1.613 ------------------------------------------------------------------------------- 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 = 0.121304 restraints weight = 23652.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.120123 restraints weight = 27314.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.121178 restraints weight = 26492.663| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 1.568 Fit side-chains revert: symmetry clash REVERT: A 578 MET cc_start: 0.7914 (ppp) cc_final: 0.7593 (ppp) REVERT: A 854 ILE cc_start: 0.9084 (tp) cc_final: 0.8849 (tp) REVERT: B 643 TRP cc_start: 0.4750 (t-100) cc_final: 0.4226 (t-100) REVERT: B 848 GLU cc_start: 0.7845 (tt0) cc_final: 0.7387 (tt0) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2153 time to fit residues: 74.5659 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 : 1.463 ------------------------------------------------------------------------------- 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: 0.7980 chunk 3 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 174 optimal weight: 0.5980 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: 9.9990 chunk 125 optimal weight: 1.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.143590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116240 restraints weight = 23770.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.116541 restraints weight = 30931.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117630 restraints weight = 28991.734| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14934 Z= 0.178 Angle : 0.605 7.157 20297 Z= 0.303 Chirality : 0.040 0.147 2480 Planarity : 0.004 0.073 2449 Dihedral : 8.590 86.397 2692 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % 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: 1.90 (0.20), residues: 1800 helix: 2.16 (0.14), residues: 1246 sheet: 0.13 (0.55), residues: 92 loop : -1.07 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 635 HIS 0.004 0.001 HIS A 350 PHE 0.023 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 0.05633 ( 989) hydrogen bonds : angle 3.94648 ( 2940) covalent geometry : bond 0.00414 (14934) covalent geometry : angle 0.60477 (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 206 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.489 Fit side-chains REVERT: A 97 LYS cc_start: 0.8199 (mmmt) cc_final: 0.7915 (pttp) REVERT: A 295 ASN cc_start: 0.8450 (t0) cc_final: 0.8217 (t0) REVERT: A 578 MET cc_start: 0.7905 (ppp) cc_final: 0.7516 (ppp) REVERT: A 848 GLU cc_start: 0.7870 (tt0) cc_final: 0.7434 (mt-10) REVERT: B 295 ASN cc_start: 0.8387 (t0) cc_final: 0.8141 (t0) REVERT: B 643 TRP cc_start: 0.4855 (t-100) cc_final: 0.4454 (t-100) REVERT: B 848 GLU cc_start: 0.7902 (tt0) cc_final: 0.7627 (tt0) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2133 time to fit residues: 68.9824 Evaluate side-chains 147 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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: 0.8980 chunk 174 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 159 optimal weight: 0.0170 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 889 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.148446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.120263 restraints weight = 23602.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119620 restraints weight = 25158.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.121112 restraints weight = 24072.170| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14934 Z= 0.112 Angle : 0.544 7.527 20297 Z= 0.266 Chirality : 0.038 0.145 2480 Planarity : 0.004 0.072 2449 Dihedral : 7.583 78.844 2692 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % 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: 2.27 (0.20), residues: 1800 helix: 2.48 (0.15), residues: 1230 sheet: 0.33 (0.56), residues: 92 loop : -0.96 (0.28), residues: 478 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 0.021 0.001 PHE B 195 TYR 0.014 0.001 TYR B 309 ARG 0.002 0.000 ARG A 875 Details of bonding type rmsd hydrogen bonds : bond 0.04620 ( 989) hydrogen bonds : angle 3.66618 ( 2940) covalent geometry : bond 0.00223 (14934) covalent geometry : angle 0.54434 (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 219 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.469 Fit side-chains REVERT: A 199 MET cc_start: 0.8752 (mpp) cc_final: 0.8435 (mpp) REVERT: A 578 MET cc_start: 0.8050 (ppp) cc_final: 0.7767 (ppp) REVERT: A 848 GLU cc_start: 0.7629 (tt0) cc_final: 0.7234 (tt0) REVERT: A 857 MET cc_start: 0.7273 (mmp) cc_final: 0.6987 (tpt) REVERT: B 199 MET cc_start: 0.8842 (mpp) cc_final: 0.8523 (mpp) REVERT: B 349 LEU cc_start: 0.9436 (mm) cc_final: 0.9198 (mt) REVERT: B 643 TRP cc_start: 0.4958 (t-100) cc_final: 0.4544 (t-100) REVERT: B 848 GLU cc_start: 0.7778 (tt0) cc_final: 0.7461 (tt0) REVERT: B 882 LEU cc_start: 0.9194 (tp) cc_final: 0.8989 (tp) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2018 time to fit residues: 70.2789 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 : 1.472 ------------------------------------------------------------------------------- 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: 0.9980 chunk 37 optimal weight: 0.7980 chunk 97 optimal weight: 0.0070 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.149054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121578 restraints weight = 23695.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120542 restraints weight = 26978.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122069 restraints weight = 26439.455| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1444 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= 0.113 Angle : 0.536 7.303 20297 Z= 0.265 Chirality : 0.038 0.141 2480 Planarity : 0.004 0.076 2449 Dihedral : 7.371 78.570 2692 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: 2.33 (0.20), residues: 1800 helix: 2.46 (0.14), residues: 1246 sheet: 0.42 (0.56), residues: 92 loop : -0.84 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 635 HIS 0.002 0.000 HIS A 350 PHE 0.039 0.001 PHE B 195 TYR 0.016 0.001 TYR B 309 ARG 0.004 0.000 ARG B 646 Details of bonding type rmsd hydrogen bonds : bond 0.04428 ( 989) hydrogen bonds : angle 3.62402 ( 2940) covalent geometry : bond 0.00234 (14934) covalent geometry : angle 0.53593 (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 217 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.719 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8368 (mmmt) cc_final: 0.7949 (pttp) REVERT: A 295 ASN cc_start: 0.8327 (t0) cc_final: 0.8085 (t0) REVERT: A 578 MET cc_start: 0.7887 (ppp) cc_final: 0.7678 (ppp) REVERT: A 848 GLU cc_start: 0.7816 (tt0) cc_final: 0.7359 (tt0) REVERT: A 857 MET cc_start: 0.7316 (mmp) cc_final: 0.7078 (tpt) REVERT: B 295 ASN cc_start: 0.8258 (t0) cc_final: 0.8028 (t0) REVERT: B 643 TRP cc_start: 0.4882 (t-100) cc_final: 0.4538 (t-100) REVERT: B 848 GLU cc_start: 0.7742 (tt0) cc_final: 0.7418 (tt0) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.2273 time to fit residues: 77.0452 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 : 1.555 ------------------------------------------------------------------------------- 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: 8.9990 chunk 159 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 108 optimal weight: 0.2980 chunk 154 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.147171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119578 restraints weight = 23712.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118954 restraints weight = 28468.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.120303 restraints weight = 27520.406| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14934 Z= 0.132 Angle : 0.553 6.770 20297 Z= 0.274 Chirality : 0.038 0.144 2480 Planarity : 0.004 0.077 2449 Dihedral : 7.259 77.279 2692 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.99 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: 2.33 (0.20), residues: 1800 helix: 2.45 (0.14), residues: 1246 sheet: 0.41 (0.56), residues: 92 loop : -0.82 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 635 HIS 0.002 0.001 HIS A 350 PHE 0.041 0.001 PHE B 195 TYR 0.018 0.001 TYR B 309 ARG 0.002 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04612 ( 989) hydrogen bonds : angle 3.67282 ( 2940) covalent geometry : bond 0.00295 (14934) covalent geometry : angle 0.55312 (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 213 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.543 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8235 (mmmt) cc_final: 0.7915 (pttp) REVERT: A 178 SER cc_start: 0.9381 (m) cc_final: 0.8637 (t) REVERT: A 295 ASN cc_start: 0.8320 (t0) cc_final: 0.8086 (t0) REVERT: A 848 GLU cc_start: 0.7795 (tt0) cc_final: 0.7482 (tt0) REVERT: B 578 MET cc_start: 0.7631 (ppp) cc_final: 0.7229 (ppp) REVERT: B 643 TRP cc_start: 0.5044 (t-100) cc_final: 0.4578 (t-100) REVERT: B 848 GLU cc_start: 0.7661 (tt0) cc_final: 0.7314 (tt0) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2095 time to fit residues: 70.0069 Evaluate side-chains 154 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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: 3.9990 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120490 restraints weight = 23853.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118981 restraints weight = 24861.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.120279 restraints weight = 24049.528| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14934 Z= 0.123 Angle : 0.549 6.602 20297 Z= 0.273 Chirality : 0.038 0.151 2480 Planarity : 0.004 0.077 2449 Dihedral : 7.159 74.847 2692 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 2.27 (0.20), residues: 1800 helix: 2.39 (0.14), residues: 1248 sheet: 0.36 (0.55), residues: 92 loop : -0.79 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 635 HIS 0.002 0.001 HIS A 350 PHE 0.032 0.001 PHE B 195 TYR 0.016 0.001 TYR B 309 ARG 0.004 0.000 ARG B 976 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 989) hydrogen bonds : angle 3.65159 ( 2940) covalent geometry : bond 0.00270 (14934) covalent geometry : angle 0.54907 (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 213 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.610 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7967 (pttp) REVERT: A 178 SER cc_start: 0.9389 (m) cc_final: 0.8669 (t) REVERT: A 848 GLU cc_start: 0.7670 (tt0) cc_final: 0.7317 (tt0) REVERT: B 578 MET cc_start: 0.7666 (ppp) cc_final: 0.7304 (ppp) REVERT: B 643 TRP cc_start: 0.5218 (t-100) cc_final: 0.4737 (t-100) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2123 time to fit residues: 71.3596 Evaluate side-chains 157 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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: 0.3980 chunk 118 optimal weight: 1.9990 chunk 109 optimal weight: 0.2980 chunk 173 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 174 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 158 optimal weight: 0.0000 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.150016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121853 restraints weight = 23479.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.121498 restraints weight = 24146.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.122762 restraints weight = 23341.168| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14934 Z= 0.106 Angle : 0.545 7.241 20297 Z= 0.265 Chirality : 0.038 0.147 2480 Planarity : 0.004 0.078 2449 Dihedral : 6.906 73.742 2692 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: 2.50 (0.15), residues: 1248 sheet: 0.86 (0.58), residues: 80 loop : -0.81 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 635 HIS 0.002 0.000 HIS A 126 PHE 0.037 0.001 PHE B 195 TYR 0.013 0.001 TYR B 309 ARG 0.002 0.000 ARG B 646 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 989) hydrogen bonds : angle 3.56030 ( 2940) covalent geometry : bond 0.00213 (14934) covalent geometry : angle 0.54490 (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 225 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: A 178 SER cc_start: 0.9382 (m) cc_final: 0.8694 (t) REVERT: A 199 MET cc_start: 0.8420 (mpp) cc_final: 0.8094 (mpp) REVERT: A 295 ASN cc_start: 0.8174 (t0) cc_final: 0.7934 (t0) REVERT: A 848 GLU cc_start: 0.7666 (tt0) cc_final: 0.7285 (tt0) REVERT: B 295 ASN cc_start: 0.8110 (t0) cc_final: 0.7887 (t0) REVERT: B 371 VAL cc_start: 0.8255 (t) cc_final: 0.8032 (t) REVERT: B 578 MET cc_start: 0.7500 (ppp) cc_final: 0.7038 (ppp) REVERT: B 643 TRP cc_start: 0.5107 (t-100) cc_final: 0.4634 (t-100) REVERT: B 848 GLU cc_start: 0.7539 (tt0) cc_final: 0.7198 (tt0) REVERT: B 857 MET cc_start: 0.7811 (tpt) cc_final: 0.7533 (mmp) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2148 time to fit residues: 76.9719 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 : 1.717 ------------------------------------------------------------------------------- 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: 0.4980 chunk 160 optimal weight: 0.5980 chunk 150 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.148971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120822 restraints weight = 23477.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120459 restraints weight = 23659.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.121760 restraints weight = 23780.839| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14934 Z= 0.116 Angle : 0.561 8.635 20297 Z= 0.274 Chirality : 0.038 0.173 2480 Planarity : 0.004 0.078 2449 Dihedral : 7.001 74.655 2692 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: 2.47 (0.14), residues: 1248 sheet: 0.82 (0.58), residues: 80 loop : -0.80 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 635 HIS 0.002 0.000 HIS B 350 PHE 0.044 0.001 PHE A 195 TYR 0.019 0.001 TYR A 309 ARG 0.002 0.000 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 989) hydrogen bonds : angle 3.60018 ( 2940) covalent geometry : bond 0.00256 (14934) covalent geometry : angle 0.56117 (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 216 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.397 Fit side-chains REVERT: A 295 ASN cc_start: 0.8171 (t0) cc_final: 0.7929 (t0) REVERT: A 848 GLU cc_start: 0.7653 (tt0) cc_final: 0.7300 (tt0) REVERT: B 154 MET cc_start: 0.7896 (mmm) cc_final: 0.7419 (tpt) REVERT: B 199 MET cc_start: 0.8536 (mpp) cc_final: 0.8263 (mpp) REVERT: B 295 ASN cc_start: 0.8106 (t0) cc_final: 0.7882 (t0) REVERT: B 578 MET cc_start: 0.7572 (ppp) cc_final: 0.7148 (ppp) REVERT: B 643 TRP cc_start: 0.5142 (t-100) cc_final: 0.4685 (t-100) REVERT: B 848 GLU cc_start: 0.7573 (tt0) cc_final: 0.7195 (tt0) REVERT: B 857 MET cc_start: 0.7862 (tpt) cc_final: 0.7611 (mmp) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2461 time to fit residues: 84.0289 Evaluate side-chains 157 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.770 ------------------------------------------------------------------------------- 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: 0.0470 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.149745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121725 restraints weight = 23563.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.121324 restraints weight = 25464.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122826 restraints weight = 24631.752| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1821 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 : 0.563 8.650 20297 Z= 0.274 Chirality : 0.038 0.167 2480 Planarity : 0.004 0.077 2449 Dihedral : 6.804 75.095 2692 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 2.37 (0.20), residues: 1800 helix: 2.46 (0.14), residues: 1246 sheet: 0.38 (0.54), residues: 92 loop : -0.72 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP B 635 HIS 0.002 0.000 HIS A 350 PHE 0.040 0.001 PHE A 195 TYR 0.016 0.001 TYR B 309 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 989) hydrogen bonds : angle 3.61747 ( 2940) covalent geometry : bond 0.00234 (14934) covalent geometry : angle 0.56334 (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 216 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: A 295 ASN cc_start: 0.8180 (t0) cc_final: 0.7951 (t0) REVERT: A 848 GLU cc_start: 0.7719 (tt0) cc_final: 0.7375 (tt0) REVERT: B 154 MET cc_start: 0.7761 (mmm) cc_final: 0.7210 (tpt) REVERT: B 295 ASN cc_start: 0.8122 (t0) cc_final: 0.7895 (t0) REVERT: B 371 VAL cc_start: 0.8210 (t) cc_final: 0.7994 (t) REVERT: B 578 MET cc_start: 0.7540 (ppp) cc_final: 0.7097 (ppp) REVERT: B 643 TRP cc_start: 0.5150 (t-100) cc_final: 0.4659 (t-100) REVERT: B 848 GLU cc_start: 0.7540 (tt0) cc_final: 0.7166 (tt0) REVERT: B 857 MET cc_start: 0.7850 (tpt) cc_final: 0.7604 (mmp) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2053 time to fit residues: 71.0334 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 : 1.461 ------------------------------------------------------------------------------- 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: 6.9990 chunk 3 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.147913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.120217 restraints weight = 23717.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.119522 restraints weight = 26219.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.120999 restraints weight = 27032.435| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14934 Z= 0.127 Angle : 0.568 7.640 20297 Z= 0.280 Chirality : 0.039 0.160 2480 Planarity : 0.004 0.078 2449 Dihedral : 6.793 76.231 2692 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: 2.34 (0.20), residues: 1800 helix: 2.45 (0.14), residues: 1246 sheet: 0.34 (0.55), residues: 92 loop : -0.75 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 635 HIS 0.002 0.001 HIS A 350 PHE 0.038 0.001 PHE A 195 TYR 0.019 0.001 TYR A 309 ARG 0.003 0.000 ARG B 910 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 989) hydrogen bonds : angle 3.65432 ( 2940) covalent geometry : bond 0.00286 (14934) covalent geometry : angle 0.56847 (20297) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3602.95 seconds wall clock time: 64 minutes 15.79 seconds (3855.79 seconds total)