Starting phenix.real_space_refine on Sat May 17 11:06:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7r_41990/05_2025/8u7r_41990.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7r_41990/05_2025/8u7r_41990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u7r_41990/05_2025/8u7r_41990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7r_41990/05_2025/8u7r_41990.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7r_41990/05_2025/8u7r_41990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7r_41990/05_2025/8u7r_41990.cif" } resolution = 3.7 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= 0.010 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 76 5.16 5 C 10156 2.51 5 N 2549 2.21 5 O 2817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 15601 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7601 Classifications: {'peptide': 985} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 955} Chain breaks: 5 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'PHE:plan': 5, 'GLU:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 7615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7615 Classifications: {'peptide': 986} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 956} Chain breaks: 5 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 82 Chain: "A" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 213 Unusual residues: {'AJP': 2, 'POV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 18 Chain: "B" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 172 Unusual residues: {'AJP': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 18 Time building chain proxies: 9.64, per 1000 atoms: 0.62 Number of scatterers: 15601 At special positions: 0 Unit cell: (108.9, 136.4, 128.7, 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 76 16.00 P 3 15.00 O 2817 8.00 N 2549 7.00 C 10156 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: 4.60 Conformation dependent library (CDL) restraints added in 2.0 seconds 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3714 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 8 sheets defined 75.5% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 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 132 removed outlier: 3.501A pdb=" N GLU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 removed outlier: 3.781A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 4.686A 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: 4.007A pdb=" N SER A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 188 removed outlier: 3.580A pdb=" N ASN A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 removed outlier: 3.803A pdb=" N MET A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.888A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 3.809A pdb=" N VAL A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 291 removed outlier: 5.087A 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: 3.655A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 4.293A 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 379 removed outlier: 3.740A pdb=" N ALA A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 381 through 414 removed outlier: 4.322A pdb=" N LEU A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE A 389 " --> pdb=" O TRP A 385 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.730A 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 removed outlier: 3.681A pdb=" N TRP A 427 " --> pdb=" O VAL A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 removed outlier: 4.100A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 481 removed outlier: 4.328A pdb=" N VAL A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 485 removed outlier: 3.644A pdb=" N ASP A 485 " --> pdb=" O GLY A 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 485' Processing helix chain 'A' and resid 487 through 513 Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'A' and resid 571 through 600 Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 637 through 640 removed outlier: 3.894A pdb=" N ILE A 640 " --> pdb=" O ILE A 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 637 through 640' Processing helix chain 'A' and resid 641 through 653 removed outlier: 3.633A pdb=" N LEU A 651 " --> pdb=" O LYS A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 700 removed outlier: 3.719A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 728 through 757 removed outlier: 3.690A pdb=" N ALA A 747 " --> pdb=" O TYR A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 774 removed outlier: 3.872A pdb=" N PHE A 766 " --> pdb=" O HIS A 762 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 769 " --> pdb=" O LYS A 765 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 854 Proline residue: A 819 - end of helix removed outlier: 3.986A 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: 4.061A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 4.162A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.547A pdb=" N ALA A 927 " --> pdb=" O ASP A 923 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 958 Processing helix chain 'A' and resid 966 through 977 removed outlier: 3.693A pdb=" N ARG A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1049 Processing helix chain 'A' and resid 1069 through 1080 removed outlier: 3.591A pdb=" N PHE A1080 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1124 removed outlier: 3.950A pdb=" N GLY A1124 " --> pdb=" O HIS A1120 " (cutoff:3.500A) 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 132 removed outlier: 3.508A pdb=" N GLU B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 153 removed outlier: 3.810A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.986A pdb=" N SER B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 188 removed outlier: 3.592A pdb=" N ASN B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 209 through 220 removed outlier: 4.210A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 254 removed outlier: 3.562A pdb=" N CYS B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 291 removed outlier: 4.721A 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 318 removed outlier: 3.667A pdb=" N THR B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 337 removed outlier: 3.763A pdb=" N GLY B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 4.708A 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 379 removed outlier: 3.713A pdb=" N ALA B 379 " --> pdb=" O ALA B 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 376 through 379' Processing helix chain 'B' and resid 381 through 414 removed outlier: 4.318A pdb=" N LEU B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE B 389 " --> pdb=" O TRP B 385 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) removed outlier: 3.726A 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 removed outlier: 3.690A pdb=" N TRP B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 447 removed outlier: 3.714A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 481 removed outlier: 4.324A pdb=" N VAL B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 485 removed outlier: 3.668A 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 513 Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 571 through 600 removed outlier: 3.510A pdb=" N PHE B 598 " --> pdb=" O TYR B 594 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS B 600 " --> pdb=" O LYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 621 Processing helix chain 'B' and resid 628 through 636 Processing helix chain 'B' and resid 637 through 639 No H-bonds generated for 'chain 'B' and resid 637 through 639' Processing helix chain 'B' and resid 640 through 653 removed outlier: 3.997A pdb=" N LEU B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 651 " --> pdb=" O LYS B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 700 removed outlier: 3.510A pdb=" N VAL B 682 " --> pdb=" O MET B 678 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 728 through 757 Processing helix chain 'B' and resid 761 through 774 Processing helix chain 'B' and resid 808 through 812 removed outlier: 3.790A pdb=" N LEU B 811 " --> pdb=" O LEU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 854 Proline residue: B 819 - end of helix removed outlier: 3.534A pdb=" N GLY B 827 " --> pdb=" O LEU B 823 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN B 832 " --> pdb=" O LYS B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 860 through 889 removed outlier: 4.055A pdb=" N HIS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 removed outlier: 4.173A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.556A pdb=" N ALA B 927 " --> pdb=" O ASP B 923 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 958 Processing helix chain 'B' and resid 966 through 977 removed outlier: 3.679A pdb=" N ARG B 976 " --> pdb=" O PHE B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1049 Processing helix chain 'B' and resid 1069 through 1080 removed outlier: 3.602A pdb=" N PHE B1080 " --> pdb=" O ALA B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1107 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1113 through 1124 removed outlier: 3.870A pdb=" N GLY B1124 " --> pdb=" O HIS B1120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.146A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1032 through 1036 Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1127 removed outlier: 3.514A pdb=" N TYR A1125 " --> pdb=" O VAL A1188 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A1188 " --> pdb=" O TYR A1125 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A1127 " --> pdb=" O LEU A1186 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU A1186 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE A1187 " --> pdb=" O VAL A1145 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL A1145 " --> pdb=" O PHE A1187 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A1189 " --> pdb=" O GLU A1143 " (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: 5.936A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1032 through 1036 Processing sheet with id=AA7, first strand: chain 'B' and resid 1125 through 1127 removed outlier: 3.532A pdb=" N TYR B1125 " --> pdb=" O VAL B1188 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL B1188 " --> pdb=" O TYR B1125 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B1127 " --> pdb=" O LEU B1186 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU B1186 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE B1187 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B1145 " --> pdb=" O PHE B1187 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B1189 " --> pdb=" O GLU B1143 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL B1145 " --> pdb=" O ILE B1167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1135 through 1137 1106 hydrogen bonds defined for protein. 3273 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: 5.16 Time building geometry restraints manager: 5.28 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: 2713 1.33 - 1.45: 3830 1.45 - 1.57: 9231 1.57 - 1.69: 6 1.69 - 1.81: 140 Bond restraints: 15920 Sorted by residual: bond pdb=" CA LYS B 76 " pdb=" C LYS B 76 " ideal model delta sigma weight residual 1.522 1.481 0.042 1.20e-02 6.94e+03 1.20e+01 bond pdb=" CA LYS A 76 " pdb=" C LYS A 76 " ideal model delta sigma weight residual 1.522 1.482 0.041 1.20e-02 6.94e+03 1.14e+01 bond pdb=" C LYS A 76 " pdb=" O LYS A 76 " ideal model delta sigma weight residual 1.236 1.206 0.029 1.21e-02 6.83e+03 5.93e+00 bond pdb=" C LYS B 76 " pdb=" O LYS B 76 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.21e-02 6.83e+03 5.59e+00 bond pdb=" CA LYS B 76 " pdb=" CB LYS B 76 " ideal model delta sigma weight residual 1.531 1.495 0.036 1.52e-02 4.33e+03 5.49e+00 ... (remaining 15915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 21343 2.39 - 4.78: 256 4.78 - 7.16: 46 7.16 - 9.55: 10 9.55 - 11.94: 2 Bond angle restraints: 21657 Sorted by residual: angle pdb=" CA VAL B 693 " pdb=" C VAL B 693 " pdb=" N PRO B 694 " ideal model delta sigma weight residual 120.83 117.55 3.28 6.10e-01 2.69e+00 2.89e+01 angle pdb=" CA VAL A 693 " pdb=" C VAL A 693 " pdb=" N PRO A 694 " ideal model delta sigma weight residual 120.83 117.60 3.23 6.10e-01 2.69e+00 2.80e+01 angle pdb=" N ASN B 685 " pdb=" CA ASN B 685 " pdb=" C ASN B 685 " ideal model delta sigma weight residual 111.11 106.40 4.71 1.20e+00 6.94e-01 1.54e+01 angle pdb=" CA LEU A 216 " pdb=" CB LEU A 216 " pdb=" CG LEU A 216 " ideal model delta sigma weight residual 116.30 128.24 -11.94 3.50e+00 8.16e-02 1.16e+01 angle pdb=" C VAL A 693 " pdb=" CA VAL A 693 " pdb=" CB VAL A 693 " ideal model delta sigma weight residual 114.00 109.54 4.46 1.31e+00 5.83e-01 1.16e+01 ... (remaining 21652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.29: 9032 23.29 - 46.58: 823 46.58 - 69.87: 142 69.87 - 93.16: 14 93.16 - 116.45: 28 Dihedral angle restraints: 10039 sinusoidal: 4316 harmonic: 5723 Sorted by residual: dihedral pdb=" C02 AJP B1402 " pdb=" C85 AJP B1402 " pdb=" O84 AJP B1402 " pdb=" C05 AJP B1402 " ideal model delta sinusoidal sigma weight residual -57.60 58.85 -116.45 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C02 AJP A1404 " pdb=" C85 AJP A1404 " pdb=" O84 AJP A1404 " pdb=" C05 AJP A1404 " ideal model delta sinusoidal sigma weight residual -57.60 58.23 -115.83 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C02 AJP B1403 " pdb=" C85 AJP B1403 " pdb=" O84 AJP B1403 " pdb=" C05 AJP B1403 " ideal model delta sinusoidal sigma weight residual -57.60 57.17 -114.77 1 3.00e+01 1.11e-03 1.51e+01 ... (remaining 10036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1986 0.042 - 0.084: 494 0.084 - 0.126: 139 0.126 - 0.168: 24 0.168 - 0.211: 8 Chirality restraints: 2651 Sorted by residual: 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 0.21 2.00e-01 2.50e+01 1.11e+00 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 1.10e+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 9.74e-01 ... (remaining 2648 not shown) Planarity restraints: 2627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 641 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO B 642 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 642 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 642 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 641 " 0.044 5.00e-02 4.00e+02 6.57e-02 6.92e+00 pdb=" N PRO A 642 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 642 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 642 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 209 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO A 210 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 210 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 210 " 0.024 5.00e-02 4.00e+02 ... (remaining 2624 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2777 2.77 - 3.30: 15054 3.30 - 3.83: 25284 3.83 - 4.37: 25193 4.37 - 4.90: 46557 Nonbonded interactions: 114865 Sorted by model distance: nonbonded pdb=" O LEU A 478 " pdb=" OG SER A 484 " model vdw 2.237 3.040 nonbonded pdb=" O LEU B 478 " pdb=" OG SER B 484 " model vdw 2.269 3.040 nonbonded pdb=" O GLN B 140 " pdb=" OH TYR B 312 " model vdw 2.286 3.040 nonbonded pdb=" NH2 ARG A 646 " pdb=" OD1 ASN A 826 " model vdw 2.287 3.120 nonbonded pdb=" NH2 ARG B 646 " pdb=" OD1 ASN B 826 " model vdw 2.323 3.120 ... (remaining 114860 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 75 through 728 or (resid 729 and (name N or name CA or nam \ e C or name O or name CB )) or resid 730 through 1192 or (resid 1401 and (name C \ 1 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 n \ ame C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name \ O31 or name O32 or name P or name C210 or name C211 or name C212 or name C213 or \ name C214 or name C215 or name C216 or name C310 or name C311 or name C312 or n \ ame C313 or name C314)) or resid 1403)) selection = (chain 'B' and (resid 75 through 676 or resid 678 through 698 or (resid 699 thro \ ugh 700 and (name N or name CA or name C or name O or name CB )) or resid 727 th \ rough 1192 or resid 1401 or resid 1403)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.270 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: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 36.740 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15920 Z= 0.191 Angle : 0.677 11.941 21657 Z= 0.352 Chirality : 0.042 0.211 2651 Planarity : 0.004 0.072 2627 Dihedral : 18.386 116.447 6325 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 25.84 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.19), residues: 1947 helix: 1.73 (0.14), residues: 1391 sheet: 0.44 (0.48), residues: 112 loop : -1.32 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 635 HIS 0.006 0.001 HIS B1120 PHE 0.018 0.001 PHE B 248 TYR 0.014 0.001 TYR B 309 ARG 0.003 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.11349 ( 1106) hydrogen bonds : angle 4.37670 ( 3273) covalent geometry : bond 0.00343 (15920) covalent geometry : angle 0.67706 (21657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.710 Fit side-chains REVERT: A 199 MET cc_start: 0.8361 (mmm) cc_final: 0.7583 (mpp) REVERT: B 295 ASN cc_start: 0.7223 (t0) cc_final: 0.6989 (t0) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2452 time to fit residues: 56.9598 Evaluate side-chains 128 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 8.9990 chunk 148 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 79 optimal weight: 0.0070 chunk 153 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.148276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114897 restraints weight = 25033.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113691 restraints weight = 27517.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115318 restraints weight = 24561.554| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15920 Z= 0.158 Angle : 0.585 11.440 21657 Z= 0.292 Chirality : 0.038 0.149 2651 Planarity : 0.004 0.070 2627 Dihedral : 9.701 80.031 2887 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.88 % Allowed : 26.03 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.19), residues: 1947 helix: 2.13 (0.14), residues: 1398 sheet: 1.29 (0.49), residues: 94 loop : -1.29 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 419 HIS 0.006 0.001 HIS A1120 PHE 0.011 0.001 PHE B 195 TYR 0.023 0.001 TYR B 309 ARG 0.005 0.000 ARG B 646 Details of bonding type rmsd hydrogen bonds : bond 0.05646 ( 1106) hydrogen bonds : angle 3.75573 ( 3273) covalent geometry : bond 0.00363 (15920) covalent geometry : angle 0.58478 (21657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 1.654 Fit side-chains REVERT: A 199 MET cc_start: 0.8623 (mmm) cc_final: 0.7933 (tpp) REVERT: B 199 MET cc_start: 0.8449 (mmm) cc_final: 0.7762 (mpp) REVERT: B 295 ASN cc_start: 0.7548 (t0) cc_final: 0.7308 (t0) outliers start: 46 outliers final: 17 residues processed: 179 average time/residue: 0.2265 time to fit residues: 63.7704 Evaluate side-chains 143 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 1081 THR Chi-restraints excluded: chain B residue 1167 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 185 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 830 ASN A1120 HIS ** B1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.146343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112368 restraints weight = 25146.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.111911 restraints weight = 26019.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113874 restraints weight = 24427.272| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15920 Z= 0.182 Angle : 0.577 8.652 21657 Z= 0.293 Chirality : 0.039 0.137 2651 Planarity : 0.004 0.076 2627 Dihedral : 8.313 81.426 2887 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.01 % Allowed : 25.91 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.19), residues: 1947 helix: 2.17 (0.14), residues: 1399 sheet: 1.59 (0.49), residues: 90 loop : -1.38 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 419 HIS 0.006 0.001 HIS A1120 PHE 0.011 0.001 PHE A 195 TYR 0.024 0.001 TYR B 309 ARG 0.003 0.000 ARG A 646 Details of bonding type rmsd hydrogen bonds : bond 0.05909 ( 1106) hydrogen bonds : angle 3.72922 ( 3273) covalent geometry : bond 0.00430 (15920) covalent geometry : angle 0.57699 (21657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 135 time to evaluate : 1.736 Fit side-chains REVERT: A 199 MET cc_start: 0.8630 (mmm) cc_final: 0.8172 (tpp) REVERT: A 295 ASN cc_start: 0.7426 (t0) cc_final: 0.7188 (t0) REVERT: A 848 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6390 (tt0) REVERT: B 199 MET cc_start: 0.8491 (mmm) cc_final: 0.8146 (tpp) REVERT: B 295 ASN cc_start: 0.7607 (t0) cc_final: 0.7385 (t0) REVERT: B 512 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9053 (tp) REVERT: B 848 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6398 (tt0) REVERT: B 853 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7260 (tp) outliers start: 80 outliers final: 47 residues processed: 207 average time/residue: 0.2173 time to fit residues: 72.4205 Evaluate side-chains 178 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1120 HIS Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 848 GLU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1081 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1167 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.149510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.115380 restraints weight = 25126.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.114620 restraints weight = 26158.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.116164 restraints weight = 24290.321| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15920 Z= 0.117 Angle : 0.520 12.726 21657 Z= 0.264 Chirality : 0.037 0.179 2651 Planarity : 0.004 0.078 2627 Dihedral : 7.605 84.401 2887 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.88 % Allowed : 27.10 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.19), residues: 1947 helix: 2.35 (0.14), residues: 1402 sheet: 1.09 (0.49), residues: 98 loop : -1.25 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 635 HIS 0.004 0.000 HIS A1120 PHE 0.009 0.001 PHE B 575 TYR 0.019 0.001 TYR B 309 ARG 0.002 0.000 ARG A1123 Details of bonding type rmsd hydrogen bonds : bond 0.04905 ( 1106) hydrogen bonds : angle 3.51816 ( 3273) covalent geometry : bond 0.00240 (15920) covalent geometry : angle 0.51979 (21657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 142 time to evaluate : 1.811 Fit side-chains REVERT: A 199 MET cc_start: 0.8541 (mmm) cc_final: 0.8169 (tpp) REVERT: A 295 ASN cc_start: 0.7386 (t0) cc_final: 0.7143 (t0) REVERT: A 512 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9073 (tp) REVERT: A 586 MET cc_start: 0.7483 (ttm) cc_final: 0.7174 (ttt) REVERT: B 199 MET cc_start: 0.8493 (mmm) cc_final: 0.8210 (tpp) REVERT: B 295 ASN cc_start: 0.7591 (t0) cc_final: 0.7362 (t0) REVERT: B 451 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7492 (mm) REVERT: B 512 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9032 (tp) REVERT: B 578 MET cc_start: 0.8599 (mpp) cc_final: 0.8368 (mpp) outliers start: 62 outliers final: 34 residues processed: 196 average time/residue: 0.2325 time to fit residues: 73.3264 Evaluate side-chains 170 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1081 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1167 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 52 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1120 HIS ** 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 = 0.3958 r_free = 0.3958 target = 0.149531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115121 restraints weight = 25388.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113775 restraints weight = 24566.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115609 restraints weight = 22671.490| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15920 Z= 0.117 Angle : 0.502 9.118 21657 Z= 0.256 Chirality : 0.037 0.164 2651 Planarity : 0.004 0.080 2627 Dihedral : 7.329 84.841 2887 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.32 % Allowed : 26.41 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.19), residues: 1947 helix: 2.42 (0.14), residues: 1403 sheet: 1.24 (0.49), residues: 96 loop : -1.23 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 635 HIS 0.004 0.000 HIS A1120 PHE 0.008 0.001 PHE A 248 TYR 0.019 0.001 TYR B 309 ARG 0.002 0.000 ARG B 856 Details of bonding type rmsd hydrogen bonds : bond 0.04721 ( 1106) hydrogen bonds : angle 3.43928 ( 3273) covalent geometry : bond 0.00253 (15920) covalent geometry : angle 0.50162 (21657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 138 time to evaluate : 1.714 Fit side-chains REVERT: A 199 MET cc_start: 0.8555 (mmm) cc_final: 0.8204 (tpp) REVERT: A 295 ASN cc_start: 0.7437 (t0) cc_final: 0.7215 (t0) REVERT: A 512 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9052 (tp) REVERT: A 979 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6149 (tt) REVERT: B 199 MET cc_start: 0.8465 (mmm) cc_final: 0.8182 (tpp) REVERT: B 295 ASN cc_start: 0.7578 (t0) cc_final: 0.7374 (t0) REVERT: B 451 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7523 (mm) REVERT: B 512 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9034 (tp) REVERT: B 872 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7568 (pp20) REVERT: B 979 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6080 (tt) outliers start: 69 outliers final: 41 residues processed: 201 average time/residue: 0.2214 time to fit residues: 70.5634 Evaluate side-chains 181 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 978 SER Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1081 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1167 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 110 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 14 optimal weight: 0.3980 chunk 139 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1120 HIS ** B1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.147738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113858 restraints weight = 25338.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113512 restraints weight = 25357.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114904 restraints weight = 26170.344| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15920 Z= 0.150 Angle : 0.537 13.335 21657 Z= 0.273 Chirality : 0.038 0.165 2651 Planarity : 0.004 0.080 2627 Dihedral : 7.343 83.504 2887 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.38 % Allowed : 25.72 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.19), residues: 1947 helix: 2.37 (0.14), residues: 1402 sheet: 1.37 (0.49), residues: 94 loop : -1.29 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 419 HIS 0.003 0.001 HIS A1120 PHE 0.010 0.001 PHE A 248 TYR 0.022 0.001 TYR B 309 ARG 0.004 0.000 ARG B 573 Details of bonding type rmsd hydrogen bonds : bond 0.05181 ( 1106) hydrogen bonds : angle 3.52512 ( 3273) covalent geometry : bond 0.00352 (15920) covalent geometry : angle 0.53746 (21657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 135 time to evaluate : 1.728 Fit side-chains REVERT: A 199 MET cc_start: 0.8567 (mmm) cc_final: 0.8249 (tpp) REVERT: A 295 ASN cc_start: 0.7505 (t0) cc_final: 0.7303 (t0) REVERT: A 512 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9056 (tp) REVERT: A 848 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6378 (tt0) REVERT: A 872 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7633 (pp20) REVERT: A 979 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6227 (tt) REVERT: B 199 MET cc_start: 0.8490 (mmm) cc_final: 0.8189 (tpp) REVERT: B 295 ASN cc_start: 0.7603 (t0) cc_final: 0.7399 (t0) REVERT: B 451 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7565 (mm) REVERT: B 512 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9031 (tp) REVERT: B 584 LEU cc_start: 0.8560 (mm) cc_final: 0.8214 (mm) REVERT: B 625 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6933 (m-80) REVERT: B 872 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7635 (pp20) REVERT: B 979 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6159 (tt) outliers start: 86 outliers final: 50 residues processed: 215 average time/residue: 0.2193 time to fit residues: 75.7519 Evaluate side-chains 193 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 134 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 625 PHE Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 978 SER Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1081 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1167 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 16 optimal weight: 0.7980 chunk 131 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.148978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.114959 restraints weight = 25527.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114770 restraints weight = 25398.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.115949 restraints weight = 24958.152| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15920 Z= 0.124 Angle : 0.510 11.669 21657 Z= 0.259 Chirality : 0.037 0.150 2651 Planarity : 0.004 0.081 2627 Dihedral : 7.077 84.777 2887 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.44 % Allowed : 27.10 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.19), residues: 1947 helix: 2.44 (0.14), residues: 1403 sheet: 1.37 (0.49), residues: 94 loop : -1.25 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 419 HIS 0.003 0.000 HIS B1120 PHE 0.008 0.001 PHE A 248 TYR 0.019 0.001 TYR B 309 ARG 0.001 0.000 ARG A 646 Details of bonding type rmsd hydrogen bonds : bond 0.04809 ( 1106) hydrogen bonds : angle 3.43764 ( 3273) covalent geometry : bond 0.00278 (15920) covalent geometry : angle 0.51021 (21657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 144 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8530 (mmm) cc_final: 0.8233 (tpp) REVERT: A 512 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9052 (tp) REVERT: A 872 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7641 (pp20) REVERT: A 979 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6231 (tt) REVERT: B 199 MET cc_start: 0.8463 (mmm) cc_final: 0.8230 (tpp) REVERT: B 295 ASN cc_start: 0.7644 (t0) cc_final: 0.7429 (t0) REVERT: B 451 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7426 (mm) REVERT: B 512 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9034 (tp) REVERT: B 584 LEU cc_start: 0.8540 (mm) cc_final: 0.8221 (mm) REVERT: B 625 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6847 (m-80) REVERT: B 979 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6132 (tt) outliers start: 71 outliers final: 50 residues processed: 208 average time/residue: 0.2364 time to fit residues: 77.0771 Evaluate side-chains 196 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 625 PHE Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 834 SER Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 978 SER Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1081 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1167 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 22 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1120 HIS ** 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 = 0.3952 r_free = 0.3952 target = 0.149250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115072 restraints weight = 25064.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114041 restraints weight = 25158.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.115696 restraints weight = 23175.967| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15920 Z= 0.119 Angle : 0.516 12.015 21657 Z= 0.260 Chirality : 0.037 0.218 2651 Planarity : 0.004 0.080 2627 Dihedral : 6.975 84.824 2887 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.26 % Allowed : 27.35 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.20), residues: 1947 helix: 2.46 (0.14), residues: 1406 sheet: 1.44 (0.51), residues: 94 loop : -1.28 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 635 HIS 0.003 0.000 HIS B1120 PHE 0.008 0.001 PHE A 248 TYR 0.020 0.001 TYR A 309 ARG 0.003 0.000 ARG B 573 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 1106) hydrogen bonds : angle 3.41654 ( 3273) covalent geometry : bond 0.00265 (15920) covalent geometry : angle 0.51593 (21657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 139 time to evaluate : 1.916 Fit side-chains revert: symmetry clash REVERT: A 199 MET cc_start: 0.8527 (mmm) cc_final: 0.8242 (tpp) REVERT: A 512 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9033 (tp) REVERT: A 848 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6341 (tt0) REVERT: A 872 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7646 (pp20) REVERT: A 979 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6237 (tt) REVERT: B 199 MET cc_start: 0.8483 (mmm) cc_final: 0.8214 (tpp) REVERT: B 295 ASN cc_start: 0.7631 (t0) cc_final: 0.7418 (t0) REVERT: B 451 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7507 (mm) REVERT: B 512 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9026 (tp) REVERT: B 584 LEU cc_start: 0.8522 (mm) cc_final: 0.8206 (mm) REVERT: B 625 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6832 (m-80) REVERT: B 848 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6382 (tt0) REVERT: B 872 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7574 (pp20) REVERT: B 979 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6133 (tt) outliers start: 68 outliers final: 51 residues processed: 201 average time/residue: 0.2747 time to fit residues: 88.1968 Evaluate side-chains 197 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 136 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 625 PHE Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 848 GLU Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 978 SER Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1081 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1167 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 158 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 24 optimal weight: 0.0770 chunk 174 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1120 HIS ** 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 = 0.3940 r_free = 0.3940 target = 0.148172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114308 restraints weight = 25365.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.113462 restraints weight = 25812.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114981 restraints weight = 23938.150| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15920 Z= 0.141 Angle : 0.546 11.633 21657 Z= 0.273 Chirality : 0.037 0.205 2651 Planarity : 0.004 0.081 2627 Dihedral : 7.024 84.346 2887 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.51 % Allowed : 27.35 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.19), residues: 1947 helix: 2.43 (0.14), residues: 1406 sheet: 1.41 (0.51), residues: 94 loop : -1.32 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 419 HIS 0.001 0.000 HIS B 136 PHE 0.010 0.001 PHE A 248 TYR 0.022 0.001 TYR A 309 ARG 0.001 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.04965 ( 1106) hydrogen bonds : angle 3.46820 ( 3273) covalent geometry : bond 0.00328 (15920) covalent geometry : angle 0.54554 (21657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 135 time to evaluate : 1.746 Fit side-chains REVERT: A 199 MET cc_start: 0.8550 (mmm) cc_final: 0.8259 (tpp) REVERT: A 512 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9062 (tp) REVERT: A 848 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6355 (tt0) REVERT: A 872 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7654 (pp20) REVERT: A 979 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6222 (tt) REVERT: B 199 MET cc_start: 0.8493 (mmm) cc_final: 0.8218 (tpp) REVERT: B 451 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7496 (mm) REVERT: B 512 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9034 (tp) REVERT: B 584 LEU cc_start: 0.8528 (mm) cc_final: 0.8215 (mm) REVERT: B 625 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6834 (m-80) REVERT: B 848 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6408 (tt0) REVERT: B 872 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7620 (pp20) REVERT: B 979 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6165 (tt) outliers start: 72 outliers final: 54 residues processed: 202 average time/residue: 0.2252 time to fit residues: 72.8584 Evaluate side-chains 195 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 131 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 625 PHE Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 834 SER Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 848 GLU Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 978 SER Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1081 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1167 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 184 optimal weight: 0.8980 chunk 142 optimal weight: 0.0770 chunk 117 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1120 HIS ** 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 = 0.3951 r_free = 0.3951 target = 0.149159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115178 restraints weight = 25389.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.114281 restraints weight = 25893.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116131 restraints weight = 23453.893| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15920 Z= 0.123 Angle : 0.533 12.155 21657 Z= 0.268 Chirality : 0.037 0.203 2651 Planarity : 0.004 0.081 2627 Dihedral : 6.907 85.038 2887 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.01 % Allowed : 27.91 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.19), residues: 1947 helix: 2.51 (0.14), residues: 1400 sheet: 1.27 (0.51), residues: 96 loop : -1.25 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 962 HIS 0.002 0.000 HIS A1120 PHE 0.008 0.001 PHE A 248 TYR 0.020 0.001 TYR A 309 ARG 0.002 0.000 ARG B1162 Details of bonding type rmsd hydrogen bonds : bond 0.04692 ( 1106) hydrogen bonds : angle 3.41070 ( 3273) covalent geometry : bond 0.00277 (15920) covalent geometry : angle 0.53263 (21657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 134 time to evaluate : 2.216 Fit side-chains REVERT: A 199 MET cc_start: 0.8527 (mmm) cc_final: 0.8239 (tpp) REVERT: A 512 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9056 (tp) REVERT: A 678 MET cc_start: 0.5357 (ppp) cc_final: 0.5054 (ppp) REVERT: A 848 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6333 (tt0) REVERT: A 872 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7650 (pp20) REVERT: A 979 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6221 (tt) REVERT: B 199 MET cc_start: 0.8457 (mmm) cc_final: 0.8219 (tpp) REVERT: B 451 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7472 (mm) REVERT: B 584 LEU cc_start: 0.8492 (mm) cc_final: 0.8201 (mm) REVERT: B 625 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6813 (m-80) REVERT: B 848 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6374 (tt0) REVERT: B 872 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7571 (pp20) REVERT: B 979 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6169 (tt) outliers start: 64 outliers final: 50 residues processed: 191 average time/residue: 0.2220 time to fit residues: 68.0161 Evaluate side-chains 191 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 132 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 625 PHE Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 848 GLU Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 978 SER Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1081 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1167 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 114 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 190 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 188 optimal weight: 0.0040 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1120 HIS ** 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 = 0.3976 r_free = 0.3976 target = 0.151476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117770 restraints weight = 25378.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116811 restraints weight = 25876.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.118546 restraints weight = 23824.884| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15920 Z= 0.106 Angle : 0.516 12.180 21657 Z= 0.259 Chirality : 0.036 0.202 2651 Planarity : 0.003 0.081 2627 Dihedral : 6.640 85.564 2887 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.00 % Allowed : 28.97 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.20), residues: 1947 helix: 2.61 (0.14), residues: 1399 sheet: 1.29 (0.51), residues: 96 loop : -1.20 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 962 HIS 0.003 0.000 HIS A1120 PHE 0.014 0.001 PHE B 163 TYR 0.017 0.001 TYR A 312 ARG 0.001 0.000 ARG A 573 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 1106) hydrogen bonds : angle 3.31118 ( 3273) covalent geometry : bond 0.00226 (15920) covalent geometry : angle 0.51583 (21657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3997.71 seconds wall clock time: 71 minutes 8.49 seconds (4268.49 seconds total)