Starting phenix.real_space_refine on Sun Aug 24 00:05:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7r_41990/08_2025/8u7r_41990.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7r_41990/08_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_41990/08_2025/8u7r_41990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7r_41990/08_2025/8u7r_41990.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7r_41990/08_2025/8u7r_41990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7r_41990/08_2025/8u7r_41990.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'ARG:plan': 3, 'TYR: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, 'ARG:plan': 3, 'TYR: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: 4.55, per 1000 atoms: 0.29 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: 1.38 Conformation dependent library (CDL) restraints added in 706.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.54 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: 3.18 Time building geometry restraints manager: 1.84 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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.120 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.610 ------------------------------------------------------------------------------- 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 : 6.45 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.003 0.000 ARG A 585 TYR 0.014 0.001 TYR B 309 PHE 0.018 0.001 PHE B 248 TRP 0.024 0.001 TRP B 635 HIS 0.006 0.001 HIS B1120 Details of bonding type rmsd covalent geometry : bond 0.00343 (15920) covalent geometry : angle 0.67706 (21657) hydrogen bonds : bond 0.11349 ( 1106) hydrogen bonds : angle 4.37670 ( 3273) *********************** 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 : 0.588 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: 0.1158 time to fit residues: 27.2542 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 : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.0050 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.147706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114255 restraints weight = 25294.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114165 restraints weight = 25906.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115357 restraints weight = 25573.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.116087 restraints weight = 17411.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116531 restraints weight = 15843.679| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15920 Z= 0.168 Angle : 0.599 11.822 21657 Z= 0.298 Chirality : 0.038 0.151 2651 Planarity : 0.004 0.071 2627 Dihedral : 9.791 80.201 2887 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.88 % Allowed : 26.41 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.19), residues: 1947 helix: 2.11 (0.14), residues: 1398 sheet: 1.27 (0.49), residues: 94 loop : -1.32 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 646 TYR 0.025 0.001 TYR B 309 PHE 0.011 0.001 PHE A 248 TRP 0.015 0.001 TRP B 419 HIS 0.005 0.001 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00389 (15920) covalent geometry : angle 0.59869 (21657) hydrogen bonds : bond 0.05770 ( 1106) hydrogen bonds : angle 3.78586 ( 3273) *********************** 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 185 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 0.470 Fit side-chains REVERT: A 199 MET cc_start: 0.8595 (mmm) cc_final: 0.8102 (tpp) REVERT: B 199 MET cc_start: 0.8420 (mmm) cc_final: 0.7709 (mpp) REVERT: B 295 ASN cc_start: 0.7530 (t0) cc_final: 0.7290 (t0) REVERT: B 579 MET cc_start: 0.8135 (mmm) cc_final: 0.7903 (mmt) outliers start: 46 outliers final: 18 residues processed: 180 average time/residue: 0.1014 time to fit residues: 29.0277 Evaluate side-chains 143 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 230 ILE 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 178 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 134 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 164 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1120 HIS B1120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.151259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.117879 restraints weight = 25187.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.116370 restraints weight = 25805.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.118357 restraints weight = 23471.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.118764 restraints weight = 16818.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.119432 restraints weight = 15679.340| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15920 Z= 0.110 Angle : 0.501 8.401 21657 Z= 0.254 Chirality : 0.036 0.134 2651 Planarity : 0.004 0.076 2627 Dihedral : 7.844 82.771 2887 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.75 % Allowed : 26.85 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.19), residues: 1947 helix: 2.36 (0.14), residues: 1401 sheet: 1.06 (0.49), residues: 98 loop : -1.20 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 573 TYR 0.016 0.001 TYR B 309 PHE 0.017 0.001 PHE B 575 TRP 0.016 0.001 TRP A 635 HIS 0.008 0.001 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00213 (15920) covalent geometry : angle 0.50115 (21657) hydrogen bonds : bond 0.04550 ( 1106) hydrogen bonds : angle 3.49027 ( 3273) *********************** 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 193 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.632 Fit side-chains REVERT: A 199 MET cc_start: 0.8609 (mmm) cc_final: 0.7988 (tpp) REVERT: B 199 MET cc_start: 0.8419 (mmm) cc_final: 0.8004 (tpp) REVERT: B 295 ASN cc_start: 0.7484 (t0) cc_final: 0.7235 (t0) REVERT: B 512 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8997 (tp) outliers start: 44 outliers final: 18 residues processed: 186 average time/residue: 0.1071 time to fit residues: 31.9413 Evaluate side-chains 152 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 PHE 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 884 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 401 MET 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 1081 THR Chi-restraints excluded: chain B residue 1145 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.149950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.116382 restraints weight = 25497.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.117279 restraints weight = 26862.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118668 restraints weight = 23378.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118715 restraints weight = 15575.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119212 restraints weight = 14636.794| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15920 Z= 0.123 Angle : 0.518 12.847 21657 Z= 0.261 Chirality : 0.037 0.144 2651 Planarity : 0.004 0.079 2627 Dihedral : 7.501 81.582 2887 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.69 % Allowed : 26.16 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.19), residues: 1947 helix: 2.40 (0.14), residues: 1403 sheet: 1.10 (0.49), residues: 98 loop : -1.21 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 856 TYR 0.020 0.001 TYR B 309 PHE 0.008 0.001 PHE A 248 TRP 0.012 0.001 TRP B 635 HIS 0.003 0.000 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00272 (15920) covalent geometry : angle 0.51776 (21657) hydrogen bonds : bond 0.04691 ( 1106) hydrogen bonds : angle 3.47834 ( 3273) *********************** 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 194 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 135 time to evaluate : 0.428 Fit side-chains REVERT: A 199 MET cc_start: 0.8604 (mmm) cc_final: 0.8135 (tpp) REVERT: A 512 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9054 (tp) REVERT: A 586 MET cc_start: 0.7485 (ttm) cc_final: 0.7181 (ttt) REVERT: B 199 MET cc_start: 0.8427 (mmm) cc_final: 0.8082 (tpp) REVERT: B 295 ASN cc_start: 0.7538 (t0) cc_final: 0.7286 (t0) REVERT: B 451 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7416 (mm) outliers start: 59 outliers final: 32 residues processed: 189 average time/residue: 0.0976 time to fit residues: 30.0477 Evaluate side-chains 166 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 268 PHE 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 512 LEU Chi-restraints excluded: chain A residue 518 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 989 VAL Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1081 THR 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 268 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 518 LEU 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 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 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 20 optimal weight: 0.2980 chunk 143 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 109 optimal weight: 0.0980 chunk 165 optimal weight: 5.9990 chunk 100 optimal weight: 0.0270 chunk 55 optimal weight: 9.9990 chunk 176 optimal weight: 0.6980 chunk 182 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1120 HIS B1120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.152872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.118662 restraints weight = 25476.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117475 restraints weight = 28041.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.119577 restraints weight = 22563.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119804 restraints weight = 16426.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.120251 restraints weight = 15918.063| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15920 Z= 0.101 Angle : 0.485 8.821 21657 Z= 0.246 Chirality : 0.036 0.161 2651 Planarity : 0.003 0.079 2627 Dihedral : 7.037 85.011 2887 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.44 % Allowed : 25.78 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.20), residues: 1947 helix: 2.53 (0.14), residues: 1403 sheet: 1.10 (0.50), residues: 98 loop : -1.13 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 573 TYR 0.015 0.001 TYR A 312 PHE 0.008 0.001 PHE A 455 TRP 0.016 0.001 TRP A 635 HIS 0.006 0.000 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00197 (15920) covalent geometry : angle 0.48517 (21657) hydrogen bonds : bond 0.03971 ( 1106) hydrogen bonds : angle 3.33284 ( 3273) *********************** 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 198 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 143 time to evaluate : 0.596 Fit side-chains REVERT: A 152 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.9045 (t80) REVERT: A 199 MET cc_start: 0.8459 (mmm) cc_final: 0.8017 (tpp) REVERT: A 512 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9000 (tp) REVERT: B 199 MET cc_start: 0.8360 (mmm) cc_final: 0.8073 (tpp) REVERT: B 295 ASN cc_start: 0.7499 (t0) cc_final: 0.7234 (t0) REVERT: B 451 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7321 (mm) REVERT: B 512 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8908 (tp) REVERT: B 579 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7958 (mmm) outliers start: 55 outliers final: 29 residues processed: 188 average time/residue: 0.1009 time to fit residues: 30.5022 Evaluate side-chains 171 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 268 PHE 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 518 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 268 PHE 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 579 MET 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 969 LEU Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1081 THR 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 26 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 128 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.151897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.117607 restraints weight = 25188.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116788 restraints weight = 25711.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.118531 restraints weight = 22737.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.118961 restraints weight = 16307.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.119391 restraints weight = 15738.805| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15920 Z= 0.106 Angle : 0.494 13.891 21657 Z= 0.248 Chirality : 0.036 0.160 2651 Planarity : 0.003 0.079 2627 Dihedral : 6.941 84.458 2887 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.32 % Allowed : 26.35 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.20), residues: 1947 helix: 2.56 (0.14), residues: 1404 sheet: 1.32 (0.51), residues: 96 loop : -1.16 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 573 TYR 0.016 0.001 TYR B 309 PHE 0.007 0.001 PHE A 248 TRP 0.012 0.001 TRP A 635 HIS 0.006 0.000 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00226 (15920) covalent geometry : angle 0.49416 (21657) hydrogen bonds : bond 0.04101 ( 1106) hydrogen bonds : angle 3.30953 ( 3273) *********************** 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 200 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 147 time to evaluate : 0.580 Fit side-chains REVERT: A 152 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.9001 (t80) REVERT: A 199 MET cc_start: 0.8472 (mmm) cc_final: 0.8070 (tpp) REVERT: A 512 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8987 (tp) REVERT: A 979 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6009 (tt) REVERT: B 199 MET cc_start: 0.8415 (mmm) cc_final: 0.8107 (tpp) REVERT: B 295 ASN cc_start: 0.7516 (t0) cc_final: 0.7247 (t0) REVERT: B 451 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7346 (mm) REVERT: B 512 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8944 (tp) REVERT: B 579 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7770 (mmm) REVERT: B 625 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6876 (m-80) REVERT: B 979 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.5939 (tt) outliers start: 53 outliers final: 32 residues processed: 191 average time/residue: 0.0972 time to fit residues: 30.2546 Evaluate side-chains 177 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 PHE 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 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 979 LEU Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 205 MET 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 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 575 PHE Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 625 PHE 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 969 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1081 THR 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 62 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 139 optimal weight: 0.3980 chunk 73 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1120 HIS B1120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.151833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.117956 restraints weight = 25057.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.116573 restraints weight = 27148.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.118687 restraints weight = 22005.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.119075 restraints weight = 16037.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119369 restraints weight = 15384.530| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15920 Z= 0.104 Angle : 0.492 10.603 21657 Z= 0.248 Chirality : 0.036 0.169 2651 Planarity : 0.003 0.079 2627 Dihedral : 6.777 85.078 2887 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.44 % Allowed : 26.97 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.20), residues: 1947 helix: 2.58 (0.14), residues: 1404 sheet: 1.41 (0.52), residues: 96 loop : -1.14 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 573 TYR 0.017 0.001 TYR B 309 PHE 0.007 0.001 PHE A 248 TRP 0.012 0.001 TRP A 635 HIS 0.004 0.000 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00222 (15920) covalent geometry : angle 0.49249 (21657) hydrogen bonds : bond 0.04079 ( 1106) hydrogen bonds : angle 3.29542 ( 3273) *********************** 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 201 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 146 time to evaluate : 0.590 Fit side-chains REVERT: A 152 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.9006 (t80) REVERT: A 199 MET cc_start: 0.8486 (mmm) cc_final: 0.8169 (tpp) REVERT: A 512 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8932 (tp) REVERT: A 979 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6019 (tt) REVERT: B 199 MET cc_start: 0.8399 (mmm) cc_final: 0.8102 (tpp) REVERT: B 295 ASN cc_start: 0.7533 (t0) cc_final: 0.7265 (t0) REVERT: B 451 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7287 (mm) REVERT: B 512 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8961 (tp) REVERT: B 575 PHE cc_start: 0.6375 (OUTLIER) cc_final: 0.5991 (m-80) REVERT: B 579 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7708 (mmm) REVERT: B 584 LEU cc_start: 0.8533 (mm) cc_final: 0.8206 (mm) REVERT: B 625 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6869 (m-80) REVERT: B 979 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.5952 (tt) outliers start: 55 outliers final: 32 residues processed: 193 average time/residue: 0.0978 time to fit residues: 30.5467 Evaluate side-chains 179 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 PHE 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 373 THR 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 979 LEU Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 373 THR 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 575 PHE Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 625 PHE 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 969 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1081 THR 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 61 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 191 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.151830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.117999 restraints weight = 25507.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117176 restraints weight = 27652.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.118838 restraints weight = 23840.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.119572 restraints weight = 17233.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.119944 restraints weight = 16136.015| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15920 Z= 0.107 Angle : 0.513 11.455 21657 Z= 0.257 Chirality : 0.036 0.171 2651 Planarity : 0.003 0.079 2627 Dihedral : 6.699 84.730 2887 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.88 % Allowed : 27.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.20), residues: 1947 helix: 2.58 (0.14), residues: 1405 sheet: 1.46 (0.53), residues: 96 loop : -1.13 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 573 TYR 0.017 0.001 TYR B 309 PHE 0.007 0.001 PHE A 248 TRP 0.012 0.001 TRP B 635 HIS 0.003 0.000 HIS B1120 Details of bonding type rmsd covalent geometry : bond 0.00231 (15920) covalent geometry : angle 0.51293 (21657) hydrogen bonds : bond 0.04069 ( 1106) hydrogen bonds : angle 3.30660 ( 3273) *********************** 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 191 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.577 Fit side-chains REVERT: A 152 PHE cc_start: 0.9272 (OUTLIER) cc_final: 0.8958 (t80) REVERT: A 199 MET cc_start: 0.8458 (mmm) cc_final: 0.8151 (tpp) REVERT: A 295 ASN cc_start: 0.7436 (t0) cc_final: 0.7173 (t0) REVERT: A 512 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8975 (tp) REVERT: A 979 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.6022 (tt) REVERT: B 199 MET cc_start: 0.8349 (mmm) cc_final: 0.8079 (tpp) REVERT: B 295 ASN cc_start: 0.7548 (t0) cc_final: 0.7279 (t0) REVERT: B 451 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7316 (mm) REVERT: B 512 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8986 (tp) REVERT: B 575 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: B 579 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7733 (mmm) REVERT: B 584 LEU cc_start: 0.8523 (mm) cc_final: 0.8212 (mm) REVERT: B 625 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6873 (m-80) REVERT: B 979 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6074 (tt) outliers start: 46 outliers final: 34 residues processed: 184 average time/residue: 0.0969 time to fit residues: 28.9827 Evaluate side-chains 186 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 PHE 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 401 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 626 ILE 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 979 LEU Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 268 PHE 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 575 PHE Chi-restraints excluded: chain B residue 579 MET 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 878 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1081 THR 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 82 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 155 optimal weight: 40.0000 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 168 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.147422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.113381 restraints weight = 25680.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.113198 restraints weight = 27026.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114289 restraints weight = 25377.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.115463 restraints weight = 17710.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115758 restraints weight = 15745.380| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15920 Z= 0.173 Angle : 0.582 10.666 21657 Z= 0.293 Chirality : 0.039 0.176 2651 Planarity : 0.004 0.079 2627 Dihedral : 7.136 84.220 2887 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.32 % Allowed : 27.28 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.19), residues: 1947 helix: 2.40 (0.14), residues: 1409 sheet: 1.49 (0.51), residues: 94 loop : -1.26 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 899 TYR 0.026 0.001 TYR B 309 PHE 0.014 0.001 PHE A 195 TRP 0.016 0.001 TRP B 962 HIS 0.002 0.001 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00413 (15920) covalent geometry : angle 0.58243 (21657) hydrogen bonds : bond 0.05370 ( 1106) hydrogen bonds : angle 3.52154 ( 3273) *********************** 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 190 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 0.588 Fit side-chains REVERT: A 152 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8963 (t80) REVERT: A 199 MET cc_start: 0.8522 (mmm) cc_final: 0.8235 (tpp) REVERT: A 295 ASN cc_start: 0.7526 (t0) cc_final: 0.7272 (t0) REVERT: A 512 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9043 (tp) REVERT: A 678 MET cc_start: 0.5294 (ppp) cc_final: 0.4973 (ppp) REVERT: A 979 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6210 (tt) REVERT: B 199 MET cc_start: 0.8515 (mmm) cc_final: 0.8236 (tpp) REVERT: B 295 ASN cc_start: 0.7580 (t0) cc_final: 0.7361 (t0) REVERT: B 451 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7499 (mm) REVERT: B 575 PHE cc_start: 0.6633 (OUTLIER) cc_final: 0.6397 (m-80) REVERT: B 584 LEU cc_start: 0.8532 (mm) cc_final: 0.8217 (mm) REVERT: B 625 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6884 (m-80) REVERT: B 979 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6194 (tt) outliers start: 53 outliers final: 37 residues processed: 183 average time/residue: 0.1018 time to fit residues: 29.8038 Evaluate side-chains 173 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 PHE 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 373 THR 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 878 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 156 VAL 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 373 THR 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 575 PHE Chi-restraints excluded: chain B residue 579 MET 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 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 979 LEU Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1081 THR 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 171 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 36 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.150066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115288 restraints weight = 25203.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114618 restraints weight = 24836.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.116237 restraints weight = 21746.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.116673 restraints weight = 15854.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.117038 restraints weight = 15162.033| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15920 Z= 0.116 Angle : 0.535 12.008 21657 Z= 0.268 Chirality : 0.037 0.203 2651 Planarity : 0.003 0.079 2627 Dihedral : 6.812 86.148 2887 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.75 % Allowed : 27.78 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.20), residues: 1947 helix: 2.52 (0.14), residues: 1408 sheet: 0.86 (0.47), residues: 124 loop : -1.11 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1190 TYR 0.018 0.001 TYR B 309 PHE 0.007 0.001 PHE B 163 TRP 0.013 0.001 TRP A 962 HIS 0.003 0.000 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00254 (15920) covalent geometry : angle 0.53476 (21657) hydrogen bonds : bond 0.04514 ( 1106) hydrogen bonds : angle 3.37866 ( 3273) ********************** 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 182 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8535 (mmm) cc_final: 0.8215 (tpp) REVERT: A 295 ASN cc_start: 0.7519 (t0) cc_final: 0.7290 (t0) REVERT: A 512 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9008 (tp) REVERT: A 678 MET cc_start: 0.5238 (ppp) cc_final: 0.4940 (ppp) REVERT: A 979 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6217 (tt) REVERT: B 295 ASN cc_start: 0.7575 (t0) cc_final: 0.7338 (t0) REVERT: B 451 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7337 (mm) REVERT: B 584 LEU cc_start: 0.8500 (mm) cc_final: 0.8202 (mm) REVERT: B 625 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6857 (m-80) REVERT: B 979 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6115 (tt) REVERT: B 1104 MET cc_start: 0.7999 (tpp) cc_final: 0.7748 (tpt) outliers start: 44 outliers final: 35 residues processed: 175 average time/residue: 0.0989 time to fit residues: 27.5086 Evaluate side-chains 178 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 373 THR 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 878 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 373 THR 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 579 MET 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 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 979 LEU Chi-restraints excluded: chain B residue 1081 THR 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 99 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.146257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.112351 restraints weight = 25386.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111783 restraints weight = 26179.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.113881 restraints weight = 23900.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.113818 restraints weight = 15860.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.114633 restraints weight = 15012.728| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 15920 Z= 0.195 Angle : 0.613 11.753 21657 Z= 0.307 Chirality : 0.040 0.208 2651 Planarity : 0.004 0.078 2627 Dihedral : 7.237 83.911 2887 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.82 % Allowed : 27.72 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.19), residues: 1947 helix: 2.36 (0.14), residues: 1399 sheet: 1.49 (0.51), residues: 94 loop : -1.20 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.027 0.001 TYR B 309 PHE 0.039 0.002 PHE B 195 TRP 0.009 0.001 TRP B 419 HIS 0.003 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00473 (15920) covalent geometry : angle 0.61300 (21657) hydrogen bonds : bond 0.05707 ( 1106) hydrogen bonds : angle 3.60881 ( 3273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1909.99 seconds wall clock time: 34 minutes 6.67 seconds (2046.67 seconds total)