Starting phenix.real_space_refine on Sat Sep 12 06:23:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qd8_4521/09_2026/6qd8_4521.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qd8_4521/09_2026/6qd8_4521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qd8_4521/09_2026/6qd8_4521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qd8_4521/09_2026/6qd8_4521.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qd8_4521/09_2026/6qd8_4521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qd8_4521/09_2026/6qd8_4521.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6qd8_4521/09_2026/6qd8_4521.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qd8_4521/09_2026/6qd8_4521.cif" } resolution = 3.3 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= 0.004 sd= 0.089 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 8976 2.51 5 N 2394 2.21 5 O 2739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14154 Number of models: 1 Model: "" Number of chains: 7 Chain: "Z" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 795 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 97} Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1928 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 233} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 44 Classifications: {'peptide': 9} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1032 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "H" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 866 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: Y, L, C, E, F, D, W, Q, I, J Time building chain proxies: 2.98, per 1000 atoms: 0.21 Number of scatterers: 14154 At special positions: 0 Unit cell: (127.5, 136.85, 126.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 2739 8.00 N 2394 7.00 C 8976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.04 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG B 701 " - " ASN B 618 " " NAG D 701 " - " ASN D 618 " " NAG F 701 " - " ASN F 618 " " NAG G 1 " - " ASN B 563 " " NAG I 1 " - " ASN F 563 " " NAG J 1 " - " ASN D 563 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 712.4 milliseconds 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 27 sheets defined 14.8% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.866A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'B' and resid 538 through 541 Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.771A pdb=" N ASN B 563 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 566 " --> pdb=" O ALA B 562 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 598 Processing helix chain 'B' and resid 612 through 622 removed outlier: 4.022A pdb=" N LYS B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.866A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 84 removed outlier: 3.866A pdb=" N LYS E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 264 Processing helix chain 'F' and resid 538 through 541 Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 3.770A pdb=" N ASN F 563 " --> pdb=" O ARG F 559 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR F 566 " --> pdb=" O ALA F 562 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 Processing helix chain 'F' and resid 612 through 622 removed outlier: 4.022A pdb=" N LYS F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 541 Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 576 removed outlier: 3.771A pdb=" N ASN D 563 " --> pdb=" O ARG D 559 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 566 " --> pdb=" O ALA D 562 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 Processing helix chain 'D' and resid 612 through 622 removed outlier: 4.022A pdb=" N LYS D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'Z' and resid 53 through 54 removed outlier: 5.354A pdb=" N PHE Z 46 " --> pdb=" O GLN Z 37 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN Z 37 " --> pdb=" O PHE Z 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.585A pdb=" N ILE A 38 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 103 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.585A pdb=" N ILE A 38 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA6, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.645A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR A 241 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TRP A 275 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 243 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LYS A 272 " --> pdb=" O UNK A 472 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N UNK A 474 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE A 274 " --> pdb=" O UNK A 474 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N UNK A 476 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Y' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'Y' and resid 53 through 54 removed outlier: 5.353A pdb=" N PHE Y 46 " --> pdb=" O GLN Y 37 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN Y 37 " --> pdb=" O PHE Y 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.354A pdb=" N PHE L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN L 37 " --> pdb=" O PHE L 46 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.667A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP H 35 " --> pdb=" O GLU H 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.667A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP H 35 " --> pdb=" O GLU H 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.584A pdb=" N ILE C 38 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 103 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.584A pdb=" N ILE C 38 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB8, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.645A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG C 136 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR C 241 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP C 275 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN C 243 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LYS C 272 " --> pdb=" O UNK C 472 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N UNK C 474 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE C 274 " --> pdb=" O UNK C 474 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N UNK C 476 " --> pdb=" O ILE C 274 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 42 through 45 removed outlier: 3.584A pdb=" N ILE E 38 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU E 103 " --> pdb=" O GLY E 67 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASN E 69 " --> pdb=" O GLU E 103 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 42 through 45 removed outlier: 3.584A pdb=" N ILE E 38 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL E 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AC3, first strand: chain 'E' and resid 105 through 114 removed outlier: 6.645A pdb=" N GLU E 106 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N HIS E 139 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASN E 110 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLY E 143 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU E 112 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG E 136 " --> pdb=" O THR E 216 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE E 218 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL E 138 " --> pdb=" O ILE E 218 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TYR E 220 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS E 140 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA E 222 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SER E 142 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG E 219 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR E 241 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP E 275 " --> pdb=" O TYR E 241 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN E 243 " --> pdb=" O TRP E 275 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS E 272 " --> pdb=" O UNK E 472 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N UNK E 474 " --> pdb=" O LYS E 272 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE E 274 " --> pdb=" O UNK E 474 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N UNK E 476 " --> pdb=" O ILE E 274 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'W' and resid 59 through 60 removed outlier: 6.666A pdb=" N TRP W 37 " --> pdb=" O ILE W 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU W 51 " --> pdb=" O TRP W 35 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP W 35 " --> pdb=" O GLU W 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 59 through 60 removed outlier: 6.666A pdb=" N TRP W 37 " --> pdb=" O ILE W 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU W 51 " --> pdb=" O TRP W 35 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP W 35 " --> pdb=" O GLU W 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'Q' and resid 59 through 60 removed outlier: 6.667A pdb=" N TRP Q 37 " --> pdb=" O ILE Q 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU Q 51 " --> pdb=" O TRP Q 35 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP Q 35 " --> pdb=" O GLU Q 51 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 59 through 60 removed outlier: 6.667A pdb=" N TRP Q 37 " --> pdb=" O ILE Q 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU Q 51 " --> pdb=" O TRP Q 35 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP Q 35 " --> pdb=" O GLU Q 51 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1341 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: 2.38 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4568 1.34 - 1.49: 4726 1.49 - 1.64: 5145 1.64 - 1.79: 24 1.79 - 1.94: 24 Bond restraints: 14487 Sorted by residual: bond pdb=" CD1 TYR L 32 " pdb=" CE1 TYR L 32 " ideal model delta sigma weight residual 1.382 1.248 0.134 3.00e-02 1.11e+03 2.00e+01 bond pdb=" CD1 TYR Z 32 " pdb=" CE1 TYR Z 32 " ideal model delta sigma weight residual 1.382 1.248 0.134 3.00e-02 1.11e+03 2.00e+01 bond pdb=" CD1 TYR Y 32 " pdb=" CE1 TYR Y 32 " ideal model delta sigma weight residual 1.382 1.249 0.133 3.00e-02 1.11e+03 1.98e+01 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.86e+01 ... (remaining 14482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 18997 3.83 - 7.66: 596 7.66 - 11.50: 87 11.50 - 15.33: 21 15.33 - 19.16: 9 Bond angle restraints: 19710 Sorted by residual: angle pdb=" N GLN B 521 " pdb=" CA GLN B 521 " pdb=" C GLN B 521 " ideal model delta sigma weight residual 107.99 119.89 -11.90 1.76e+00 3.23e-01 4.57e+01 angle pdb=" N GLN F 521 " pdb=" CA GLN F 521 " pdb=" C GLN F 521 " ideal model delta sigma weight residual 107.99 119.88 -11.89 1.76e+00 3.23e-01 4.56e+01 angle pdb=" N GLN D 521 " pdb=" CA GLN D 521 " pdb=" C GLN D 521 " ideal model delta sigma weight residual 107.99 119.87 -11.88 1.76e+00 3.23e-01 4.55e+01 angle pdb=" N VAL C 52 " pdb=" CA VAL C 52 " pdb=" C VAL C 52 " ideal model delta sigma weight residual 109.34 96.71 12.63 2.08e+00 2.31e-01 3.68e+01 angle pdb=" N VAL A 52 " pdb=" CA VAL A 52 " pdb=" C VAL A 52 " ideal model delta sigma weight residual 109.34 96.73 12.61 2.08e+00 2.31e-01 3.68e+01 ... (remaining 19705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 7399 16.64 - 33.28: 732 33.28 - 49.92: 224 49.92 - 66.56: 30 66.56 - 83.20: 21 Dihedral angle restraints: 8406 sinusoidal: 3243 harmonic: 5163 Sorted by residual: dihedral pdb=" CA PHE Y 46 " pdb=" C PHE Y 46 " pdb=" N LEU Y 47 " pdb=" CA LEU Y 47 " ideal model delta harmonic sigma weight residual 180.00 149.47 30.53 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA PHE L 46 " pdb=" C PHE L 46 " pdb=" N LEU L 47 " pdb=" CA LEU L 47 " ideal model delta harmonic sigma weight residual 180.00 149.50 30.50 0 5.00e+00 4.00e-02 3.72e+01 dihedral pdb=" CA PHE Z 46 " pdb=" C PHE Z 46 " pdb=" N LEU Z 47 " pdb=" CA LEU Z 47 " ideal model delta harmonic sigma weight residual 180.00 149.50 30.50 0 5.00e+00 4.00e-02 3.72e+01 ... (remaining 8403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1236 0.057 - 0.115: 622 0.115 - 0.172: 253 0.172 - 0.230: 89 0.230 - 0.287: 35 Chirality restraints: 2235 Sorted by residual: chirality pdb=" CB ILE F 610 " pdb=" CA ILE F 610 " pdb=" CG1 ILE F 610 " pdb=" CG2 ILE F 610 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE B 610 " pdb=" CA ILE B 610 " pdb=" CG1 ILE B 610 " pdb=" CG2 ILE B 610 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB ILE D 610 " pdb=" CA ILE D 610 " pdb=" CG1 ILE D 610 " pdb=" CG2 ILE D 610 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 2232 not shown) Planarity restraints: 2523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 274 " 0.022 2.00e-02 2.50e+03 4.40e-02 1.93e+01 pdb=" C ILE E 274 " -0.076 2.00e-02 2.50e+03 pdb=" O ILE E 274 " 0.029 2.00e-02 2.50e+03 pdb=" N TRP E 275 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 274 " -0.022 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C ILE A 274 " 0.076 2.00e-02 2.50e+03 pdb=" O ILE A 274 " -0.029 2.00e-02 2.50e+03 pdb=" N TRP A 275 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 274 " 0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C ILE C 274 " -0.075 2.00e-02 2.50e+03 pdb=" O ILE C 274 " 0.029 2.00e-02 2.50e+03 pdb=" N TRP C 275 " 0.025 2.00e-02 2.50e+03 ... (remaining 2520 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 124 2.55 - 3.14: 10175 3.14 - 3.73: 20540 3.73 - 4.31: 27690 4.31 - 4.90: 48759 Nonbonded interactions: 107288 Sorted by model distance: nonbonded pdb=" SG CYS A 53 " pdb=" SG CYS B 609 " model vdw 1.965 3.760 nonbonded pdb=" SG CYS D 511 " pdb=" SG CYS D 556 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS F 511 " pdb=" SG CYS F 556 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS B 511 " pdb=" SG CYS B 556 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS D 601 " pdb=" SG CYS D 608 " model vdw 2.043 3.760 ... (remaining 107283 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: 0.04 Found NCS groups: ncs_group { reference = chain 'Z' selection = chain 'Y' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'W' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.210 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 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 : 0.015 0.137 14508 Z= 0.615 Angle : 1.687 19.160 19764 Z= 0.893 Chirality : 0.085 0.287 2235 Planarity : 0.011 0.071 2517 Dihedral : 15.247 83.198 5079 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.69 % Favored : 92.80 % Rotamer: Outliers : 3.96 % Allowed : 8.05 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 are not related in a simple way. whole: -2.00 (0.17), residues: 1749 helix: 0.77 (0.32), residues: 186 sheet: -0.70 (0.21), residues: 498 loop : -2.13 (0.16), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.003 ARG B 559 TYR 0.026 0.005 TYR W 54 PHE 0.058 0.007 PHE C 252 TRP 0.049 0.006 TRP C 104 HIS 0.008 0.003 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.01462 / 0.62 (14487) covalent geometry : angle 1.66678 / 0.89 (19710) SS BOND : bond 0.00561 / 0.33 ( 9) SS BOND : angle 2.67662 / 1.43 ( 18) hydrogen bonds : bond 0.15358 / 9.47 ( 474) hydrogen bonds : angle 8.26303 / 5.74 ( 1341) link_BETA1-4 : bond 0.00304 / 0.17 ( 6) link_BETA1-4 : angle 4.46350 / 2.77 ( 18) link_NAG-ASN : bond 0.01278 / 0.68 ( 6) link_NAG-ASN : angle 7.55022 / 4.72 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 212 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 103 LYS cc_start: 0.6613 (mptt) cc_final: 0.6096 (tttp) REVERT: H 35 TRP cc_start: 0.8165 (m100) cc_final: 0.7482 (m100) REVERT: E 56 LYS cc_start: 0.8316 (mmtp) cc_final: 0.8100 (mmtp) REVERT: W 54 TYR cc_start: 0.6568 (p90) cc_final: 0.6308 (p90) REVERT: Q 54 TYR cc_start: 0.7033 (p90) cc_final: 0.6785 (p90) REVERT: Q 60 TYR cc_start: 0.7694 (m-80) cc_final: 0.7367 (m-80) outliers start: 60 outliers final: 18 residues processed: 267 average time/residue: 0.1289 time to fit residues: 50.1716 Evaluate side-chains 170 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 627 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 627 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 93 ASN A 257 ASN ** Y 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 93 ASN B 550 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 61 ASN E 257 ASN F 550 ASN W 3 GLN W 61 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.240039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.187916 restraints weight = 17057.441| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 3.35 r_work: 0.3939 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14508 Z= 0.167 Angle : 0.788 11.346 19764 Z= 0.398 Chirality : 0.049 0.225 2235 Planarity : 0.006 0.056 2517 Dihedral : 8.146 104.129 1975 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.32 % Favored : 94.51 % Rotamer: Outliers : 2.90 % Allowed : 13.20 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: -1.54 (0.18), residues: 1749 helix: 0.81 (0.35), residues: 213 sheet: -0.40 (0.21), residues: 516 loop : -1.84 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 54 TYR 0.020 0.002 TYR A 232 PHE 0.019 0.002 PHE C 252 TRP 0.022 0.002 TRP H 48 HIS 0.004 0.001 HIS W 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (14487) covalent geometry : angle 0.76747 / 0.39 (19710) SS BOND : bond 0.00840 / 0.40 ( 9) SS BOND : angle 1.81630 / 0.99 ( 18) hydrogen bonds : bond 0.04342 / 2.78 ( 474) hydrogen bonds : angle 6.41719 / 4.44 ( 1341) link_BETA1-4 : bond 0.00196 / 0.09 ( 6) link_BETA1-4 : angle 1.93747 / 1.10 ( 18) link_NAG-ASN : bond 0.00630 / 0.31 ( 6) link_NAG-ASN : angle 5.38745 / 3.44 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 137 TYR cc_start: 0.7411 (m-80) cc_final: 0.7140 (m-80) REVERT: A 163 ASP cc_start: 0.8004 (t70) cc_final: 0.7780 (t0) REVERT: B 548 MET cc_start: 0.7083 (ttt) cc_final: 0.6862 (ttt) REVERT: H 35 TRP cc_start: 0.8327 (m100) cc_final: 0.7696 (m100) REVERT: C 56 LYS cc_start: 0.8423 (mmtp) cc_final: 0.8123 (mmtp) REVERT: E 136 ARG cc_start: 0.6770 (mpt-90) cc_final: 0.6467 (mpt-90) REVERT: Q 35 TRP cc_start: 0.7650 (m100) cc_final: 0.7137 (m100) REVERT: Q 60 TYR cc_start: 0.7574 (m-80) cc_final: 0.7137 (m-80) outliers start: 44 outliers final: 24 residues processed: 198 average time/residue: 0.1327 time to fit residues: 38.1222 Evaluate side-chains 175 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain Y residue 3 GLN Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 627 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 627 ILE Chi-restraints excluded: chain W residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 44 optimal weight: 2.9990 chunk 107 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 0.3980 chunk 136 optimal weight: 30.0000 chunk 61 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Z 53 ASN A 257 ASN Y 53 ASN ** Y 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN E 107 ASN E 257 ASN D 550 ASN W 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.238504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.185746 restraints weight = 17143.369| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 3.90 r_work: 0.3891 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14508 Z= 0.165 Angle : 0.754 13.080 19764 Z= 0.375 Chirality : 0.047 0.205 2235 Planarity : 0.005 0.058 2517 Dihedral : 5.531 53.306 1951 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.23 % Favored : 93.60 % Rotamer: Outliers : 2.84 % Allowed : 13.73 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: -1.51 (0.18), residues: 1749 helix: 0.59 (0.33), residues: 213 sheet: -0.42 (0.21), residues: 552 loop : -1.76 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 219 TYR 0.016 0.002 TYR W 60 PHE 0.017 0.002 PHE E 132 TRP 0.020 0.002 TRP H 48 HIS 0.005 0.001 HIS E 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (14487) covalent geometry : angle 0.73681 / 0.37 (19710) SS BOND : bond 0.00480 / 0.25 ( 9) SS BOND : angle 1.41461 / 0.75 ( 18) hydrogen bonds : bond 0.04142 / 2.63 ( 474) hydrogen bonds : angle 6.01235 / 4.18 ( 1341) link_BETA1-4 : bond 0.00203 / 0.11 ( 6) link_BETA1-4 : angle 2.11047 / 1.23 ( 18) link_NAG-ASN : bond 0.00696 / 0.34 ( 6) link_NAG-ASN : angle 4.80052 / 3.04 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.527 Fit side-chains REVERT: A 56 LYS cc_start: 0.7985 (mmtp) cc_final: 0.7607 (mmtp) REVERT: A 111 LEU cc_start: 0.6844 (mp) cc_final: 0.6608 (mp) REVERT: Y 55 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6626 (tt0) REVERT: L 55 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: H 35 TRP cc_start: 0.8317 (m100) cc_final: 0.7687 (m100) REVERT: C 56 LYS cc_start: 0.8518 (mmtp) cc_final: 0.8166 (mmtp) REVERT: E 56 LYS cc_start: 0.8505 (mmtp) cc_final: 0.8201 (mmtp) REVERT: E 84 LYS cc_start: 0.7877 (mttt) cc_final: 0.7605 (mmtp) REVERT: E 136 ARG cc_start: 0.6805 (mpt-90) cc_final: 0.6141 (mpt-90) REVERT: F 548 MET cc_start: 0.7456 (tpt) cc_final: 0.7077 (ttt) REVERT: Q 60 TYR cc_start: 0.7799 (m-80) cc_final: 0.7358 (m-80) outliers start: 43 outliers final: 25 residues processed: 184 average time/residue: 0.1336 time to fit residues: 35.3938 Evaluate side-chains 173 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain Y residue 12 SER Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 164 optimal weight: 0.0030 chunk 84 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 86 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Z 93 ASN ** Y 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 74 GLN W 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.238908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.185058 restraints weight = 17061.790| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 4.06 r_work: 0.3916 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14508 Z= 0.133 Angle : 0.675 14.586 19764 Z= 0.335 Chirality : 0.046 0.188 2235 Planarity : 0.005 0.055 2517 Dihedral : 5.203 59.925 1943 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.90 % Allowed : 13.99 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: -1.25 (0.18), residues: 1749 helix: 0.92 (0.34), residues: 213 sheet: -0.37 (0.21), residues: 558 loop : -1.54 (0.17), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 136 TYR 0.020 0.001 TYR Q 54 PHE 0.011 0.001 PHE A 132 TRP 0.019 0.001 TRP H 48 HIS 0.003 0.001 HIS B 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (14487) covalent geometry : angle 0.66150 / 0.33 (19710) SS BOND : bond 0.00400 / 0.22 ( 9) SS BOND : angle 1.12639 / 0.66 ( 18) hydrogen bonds : bond 0.03492 / 2.25 ( 474) hydrogen bonds : angle 5.55918 / 3.89 ( 1341) link_BETA1-4 : bond 0.00238 / 0.13 ( 6) link_BETA1-4 : angle 1.87671 / 1.07 ( 18) link_NAG-ASN : bond 0.00727 / 0.36 ( 6) link_NAG-ASN : angle 4.13125 / 2.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.598 Fit side-chains REVERT: A 111 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6612 (mp) REVERT: A 136 ARG cc_start: 0.6359 (mtt-85) cc_final: 0.5951 (mpt180) REVERT: B 570 GLN cc_start: 0.7427 (mm110) cc_final: 0.7160 (mt0) REVERT: H 35 TRP cc_start: 0.8156 (m100) cc_final: 0.7730 (m100) REVERT: C 56 LYS cc_start: 0.8568 (mmtp) cc_final: 0.8209 (mmtp) REVERT: E 56 LYS cc_start: 0.8625 (mmtp) cc_final: 0.8295 (mmtp) REVERT: E 84 LYS cc_start: 0.8073 (mttt) cc_final: 0.7840 (mmtp) REVERT: E 136 ARG cc_start: 0.6931 (mpt-90) cc_final: 0.6400 (mpt-90) REVERT: F 548 MET cc_start: 0.7660 (tpt) cc_final: 0.7384 (ttt) REVERT: D 548 MET cc_start: 0.7441 (mmm) cc_final: 0.6551 (mtp) REVERT: W 67 ARG cc_start: 0.7490 (ptt180) cc_final: 0.7282 (ptt90) REVERT: Q 60 TYR cc_start: 0.7835 (m-80) cc_final: 0.7496 (m-80) outliers start: 44 outliers final: 32 residues processed: 182 average time/residue: 0.1183 time to fit residues: 31.8124 Evaluate side-chains 173 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 58 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain Y residue 3 GLN Chi-restraints excluded: chain Y residue 12 SER Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 101 optimal weight: 90.0000 chunk 85 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 128 optimal weight: 0.3980 chunk 84 optimal weight: 0.8980 chunk 171 optimal weight: 8.9990 chunk 123 optimal weight: 40.0000 chunk 66 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 98 optimal weight: 20.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN Q 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.235475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.182279 restraints weight = 17132.674| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 3.36 r_work: 0.3930 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14508 Z= 0.182 Angle : 0.736 15.786 19764 Z= 0.360 Chirality : 0.047 0.212 2235 Planarity : 0.005 0.058 2517 Dihedral : 5.248 52.780 1943 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.56 % Allowed : 15.51 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: -1.35 (0.18), residues: 1749 helix: 0.66 (0.34), residues: 213 sheet: -0.42 (0.21), residues: 558 loop : -1.57 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 587 TYR 0.021 0.002 TYR Q 54 PHE 0.016 0.002 PHE E 132 TRP 0.024 0.002 TRP A 104 HIS 0.003 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (14487) covalent geometry : angle 0.72205 / 0.36 (19710) SS BOND : bond 0.00456 / 0.25 ( 9) SS BOND : angle 1.80682 / 1.00 ( 18) hydrogen bonds : bond 0.03850 / 2.46 ( 474) hydrogen bonds : angle 5.66326 / 3.94 ( 1341) link_BETA1-4 : bond 0.00173 / 0.10 ( 6) link_BETA1-4 : angle 2.29657 / 1.34 ( 18) link_NAG-ASN : bond 0.00798 / 0.40 ( 6) link_NAG-ASN : angle 3.96499 / 2.48 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 143 time to evaluate : 0.391 Fit side-chains REVERT: A 111 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6639 (mp) REVERT: Y 55 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6750 (tt0) REVERT: L 37 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: H 35 TRP cc_start: 0.8260 (m100) cc_final: 0.7764 (m100) REVERT: H 96 CYS cc_start: 0.7069 (p) cc_final: 0.6649 (p) REVERT: C 56 LYS cc_start: 0.8586 (mmtp) cc_final: 0.8235 (mmtp) REVERT: E 56 LYS cc_start: 0.8667 (mmtp) cc_final: 0.8332 (mmtp) REVERT: E 84 LYS cc_start: 0.8242 (mttt) cc_final: 0.7909 (mmtp) REVERT: E 136 ARG cc_start: 0.7002 (mpt-90) cc_final: 0.6348 (mpt-90) REVERT: F 548 MET cc_start: 0.7621 (tpt) cc_final: 0.7186 (ttp) REVERT: F 587 ARG cc_start: 0.8179 (mtp85) cc_final: 0.7948 (mtp-110) REVERT: D 548 MET cc_start: 0.7320 (mmm) cc_final: 0.6461 (mtp) REVERT: W 67 ARG cc_start: 0.7469 (ptt180) cc_final: 0.7246 (ptt90) REVERT: Q 60 TYR cc_start: 0.7929 (m-80) cc_final: 0.7653 (m-80) outliers start: 54 outliers final: 35 residues processed: 179 average time/residue: 0.1249 time to fit residues: 32.6044 Evaluate side-chains 174 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain Y residue 12 SER Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 79 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 128 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 93 ASN ** 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 = 0.4644 r_free = 0.4644 target = 0.230105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.175754 restraints weight = 17162.171| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 4.08 r_work: 0.3757 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14508 Z= 0.131 Angle : 0.664 14.282 19764 Z= 0.329 Chirality : 0.045 0.160 2235 Planarity : 0.005 0.055 2517 Dihedral : 5.017 45.338 1943 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.10 % Allowed : 16.63 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: -1.28 (0.19), residues: 1749 helix: 0.45 (0.34), residues: 231 sheet: -0.27 (0.22), residues: 546 loop : -1.55 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 587 TYR 0.024 0.001 TYR Q 54 PHE 0.011 0.001 PHE D 572 TRP 0.022 0.001 TRP E 104 HIS 0.003 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (14487) covalent geometry : angle 0.65207 / 0.33 (19710) SS BOND : bond 0.00373 / 0.20 ( 9) SS BOND : angle 1.18377 / 0.67 ( 18) hydrogen bonds : bond 0.03357 / 2.16 ( 474) hydrogen bonds : angle 5.41056 / 3.77 ( 1341) link_BETA1-4 : bond 0.00283 / 0.15 ( 6) link_BETA1-4 : angle 2.00739 / 1.15 ( 18) link_NAG-ASN : bond 0.00736 / 0.36 ( 6) link_NAG-ASN : angle 3.60102 / 2.25 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.550 Fit side-chains REVERT: A 56 LYS cc_start: 0.8201 (mmtp) cc_final: 0.7787 (mmtp) REVERT: A 111 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6689 (mp) REVERT: Y 55 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6679 (tt0) REVERT: H 35 TRP cc_start: 0.8088 (m100) cc_final: 0.7713 (m100) REVERT: H 96 CYS cc_start: 0.7105 (p) cc_final: 0.6691 (p) REVERT: C 56 LYS cc_start: 0.8492 (mmtp) cc_final: 0.7789 (mmtt) REVERT: E 56 LYS cc_start: 0.8651 (mmtp) cc_final: 0.8276 (mmtp) REVERT: E 84 LYS cc_start: 0.8277 (mttt) cc_final: 0.7916 (mmtp) REVERT: E 106 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7965 (mm-30) REVERT: E 136 ARG cc_start: 0.6993 (mpt-90) cc_final: 0.6522 (mpt-90) REVERT: F 548 MET cc_start: 0.7700 (tpt) cc_final: 0.7280 (ttp) REVERT: F 595 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7474 (mt0) REVERT: D 548 MET cc_start: 0.7321 (mmm) cc_final: 0.6549 (mtp) REVERT: D 596 ARG cc_start: 0.7475 (ttt90) cc_final: 0.7153 (ttt90) REVERT: Q 60 TYR cc_start: 0.7929 (m-80) cc_final: 0.7594 (m-80) outliers start: 47 outliers final: 36 residues processed: 182 average time/residue: 0.1247 time to fit residues: 33.6686 Evaluate side-chains 180 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 97 optimal weight: 50.0000 chunk 29 optimal weight: 50.0000 chunk 31 optimal weight: 40.0000 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 93 ASN ** 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 = 0.4642 r_free = 0.4642 target = 0.229682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.176238 restraints weight = 17180.085| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 3.93 r_work: 0.3791 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14508 Z= 0.136 Angle : 0.662 12.847 19764 Z= 0.327 Chirality : 0.045 0.158 2235 Planarity : 0.005 0.053 2517 Dihedral : 4.881 34.382 1943 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.17 % Allowed : 17.03 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: -1.21 (0.19), residues: 1749 helix: 0.44 (0.34), residues: 231 sheet: -0.21 (0.22), residues: 546 loop : -1.50 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 587 TYR 0.022 0.001 TYR Q 54 PHE 0.011 0.001 PHE B 572 TRP 0.019 0.001 TRP Q 48 HIS 0.002 0.000 HIS B 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (14487) covalent geometry : angle 0.65002 / 0.32 (19710) SS BOND : bond 0.00353 / 0.21 ( 9) SS BOND : angle 1.77801 / 0.99 ( 18) hydrogen bonds : bond 0.03354 / 2.16 ( 474) hydrogen bonds : angle 5.33731 / 3.73 ( 1341) link_BETA1-4 : bond 0.00212 / 0.13 ( 6) link_BETA1-4 : angle 2.01334 / 1.16 ( 18) link_NAG-ASN : bond 0.00727 / 0.36 ( 6) link_NAG-ASN : angle 3.39903 / 2.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 0.526 Fit side-chains REVERT: A 56 LYS cc_start: 0.8235 (mmtp) cc_final: 0.7824 (mmtp) REVERT: A 111 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6743 (mp) REVERT: Y 55 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6746 (tt0) REVERT: L 37 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: H 35 TRP cc_start: 0.8104 (m100) cc_final: 0.7764 (m100) REVERT: H 96 CYS cc_start: 0.7112 (p) cc_final: 0.6699 (p) REVERT: C 56 LYS cc_start: 0.8500 (mmtp) cc_final: 0.7813 (mmtt) REVERT: E 56 LYS cc_start: 0.8677 (mmtp) cc_final: 0.8267 (mmtp) REVERT: E 84 LYS cc_start: 0.8312 (mttt) cc_final: 0.7991 (mmtp) REVERT: E 106 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7889 (mm-30) REVERT: E 136 ARG cc_start: 0.6953 (mpt-90) cc_final: 0.6375 (mpt-90) REVERT: F 548 MET cc_start: 0.7734 (tpt) cc_final: 0.7398 (ttp) REVERT: Q 60 TYR cc_start: 0.7904 (m-80) cc_final: 0.7640 (m-80) outliers start: 48 outliers final: 41 residues processed: 172 average time/residue: 0.1307 time to fit residues: 32.8421 Evaluate side-chains 183 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain Y residue 3 GLN Chi-restraints excluded: chain Y residue 12 SER Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 138 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 chunk 120 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 121 optimal weight: 0.2980 chunk 136 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.226813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.172628 restraints weight = 17217.499| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 4.32 r_work: 0.3755 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14508 Z= 0.194 Angle : 0.720 11.950 19764 Z= 0.357 Chirality : 0.047 0.162 2235 Planarity : 0.005 0.056 2517 Dihedral : 5.064 26.309 1943 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.10 % Allowed : 17.43 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: -1.27 (0.19), residues: 1749 helix: 0.17 (0.33), residues: 231 sheet: -0.01 (0.23), residues: 501 loop : -1.58 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 587 TYR 0.024 0.002 TYR Q 54 PHE 0.015 0.002 PHE C 132 TRP 0.020 0.002 TRP Q 48 HIS 0.002 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (14487) covalent geometry : angle 0.70729 / 0.35 (19710) SS BOND : bond 0.00501 / 0.28 ( 9) SS BOND : angle 1.99379 / 1.09 ( 18) hydrogen bonds : bond 0.03866 / 2.44 ( 474) hydrogen bonds : angle 5.57044 / 3.89 ( 1341) link_BETA1-4 : bond 0.00315 / 0.19 ( 6) link_BETA1-4 : angle 2.39294 / 1.41 ( 18) link_NAG-ASN : bond 0.00756 / 0.38 ( 6) link_NAG-ASN : angle 3.43089 / 2.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 0.457 Fit side-chains REVERT: A 56 LYS cc_start: 0.8337 (mmtp) cc_final: 0.7910 (mmtp) REVERT: Y 55 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6857 (tt0) REVERT: L 37 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: H 35 TRP cc_start: 0.8201 (m100) cc_final: 0.7794 (m100) REVERT: H 96 CYS cc_start: 0.7214 (p) cc_final: 0.6830 (p) REVERT: C 56 LYS cc_start: 0.8545 (mmtp) cc_final: 0.7868 (mmtt) REVERT: E 56 LYS cc_start: 0.8666 (mmtp) cc_final: 0.8248 (mmtp) REVERT: E 84 LYS cc_start: 0.8378 (mttt) cc_final: 0.8027 (mmtp) REVERT: E 106 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7935 (mm-30) REVERT: E 136 ARG cc_start: 0.6998 (mpt-90) cc_final: 0.6292 (mpt-90) REVERT: Q 60 TYR cc_start: 0.7985 (m-80) cc_final: 0.7742 (m-80) outliers start: 47 outliers final: 32 residues processed: 167 average time/residue: 0.1257 time to fit residues: 30.5022 Evaluate side-chains 169 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain Y residue 12 SER Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 591 ASP Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.224550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.174647 restraints weight = 17407.176| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 2.95 r_work: 0.3727 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14508 Z= 0.248 Angle : 0.778 11.353 19764 Z= 0.387 Chirality : 0.049 0.192 2235 Planarity : 0.006 0.058 2517 Dihedral : 5.343 24.508 1943 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 2.84 % Allowed : 17.95 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: -1.52 (0.18), residues: 1749 helix: -0.08 (0.33), residues: 231 sheet: -0.18 (0.22), residues: 495 loop : -1.72 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 136 TYR 0.026 0.002 TYR Q 54 PHE 0.020 0.002 PHE E 132 TRP 0.023 0.002 TRP Q 48 HIS 0.003 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.25 (14487) covalent geometry : angle 0.76558 / 0.38 (19710) SS BOND : bond 0.00572 / 0.32 ( 9) SS BOND : angle 2.01386 / 1.11 ( 18) hydrogen bonds : bond 0.04307 / 2.72 ( 474) hydrogen bonds : angle 5.85232 / 4.05 ( 1341) link_BETA1-4 : bond 0.00296 / 0.19 ( 6) link_BETA1-4 : angle 2.65036 / 1.57 ( 18) link_NAG-ASN : bond 0.00802 / 0.42 ( 6) link_NAG-ASN : angle 3.54535 / 2.15 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.495 Fit side-chains REVERT: A 56 LYS cc_start: 0.8453 (mmtp) cc_final: 0.8023 (mmtp) REVERT: Y 55 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7024 (tt0) REVERT: L 37 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: H 35 TRP cc_start: 0.8234 (m100) cc_final: 0.7761 (m100) REVERT: H 96 CYS cc_start: 0.7295 (p) cc_final: 0.6929 (p) REVERT: C 56 LYS cc_start: 0.8592 (mmtp) cc_final: 0.7935 (mmtt) REVERT: C 136 ARG cc_start: 0.7115 (mpt-90) cc_final: 0.6649 (ttm110) REVERT: E 56 LYS cc_start: 0.8659 (mmtp) cc_final: 0.8231 (mmtp) REVERT: E 84 LYS cc_start: 0.8311 (mttt) cc_final: 0.8058 (mmtp) REVERT: E 106 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7831 (mm-30) REVERT: E 136 ARG cc_start: 0.7049 (mpt-90) cc_final: 0.6281 (mpt-90) REVERT: W 4 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8068 (mt) outliers start: 43 outliers final: 31 residues processed: 164 average time/residue: 0.1314 time to fit residues: 31.4347 Evaluate side-chains 165 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain Y residue 12 SER Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 114 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 94 optimal weight: 0.0770 chunk 146 optimal weight: 0.0670 chunk 93 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 89 GLN ** Y 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.228932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.175493 restraints weight = 17281.793| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 4.18 r_work: 0.3752 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14508 Z= 0.123 Angle : 0.655 10.473 19764 Z= 0.329 Chirality : 0.045 0.161 2235 Planarity : 0.005 0.054 2517 Dihedral : 4.985 25.156 1943 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.24 % Allowed : 18.55 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: -1.33 (0.19), residues: 1749 helix: 0.36 (0.34), residues: 231 sheet: -0.39 (0.22), residues: 549 loop : -1.52 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 136 TYR 0.032 0.001 TYR H 54 PHE 0.014 0.001 PHE D 572 TRP 0.022 0.002 TRP W 48 HIS 0.002 0.000 HIS D 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (14487) covalent geometry : angle 0.64497 / 0.33 (19710) SS BOND : bond 0.00406 / 0.23 ( 9) SS BOND : angle 1.29937 / 0.74 ( 18) hydrogen bonds : bond 0.03296 / 2.11 ( 474) hydrogen bonds : angle 5.39721 / 3.76 ( 1341) link_BETA1-4 : bond 0.00280 / 0.14 ( 6) link_BETA1-4 : angle 2.11681 / 1.22 ( 18) link_NAG-ASN : bond 0.00676 / 0.33 ( 6) link_NAG-ASN : angle 3.09168 / 1.91 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.509 Fit side-chains REVERT: A 56 LYS cc_start: 0.8374 (mmtp) cc_final: 0.7906 (mmtp) REVERT: A 163 ASP cc_start: 0.7769 (t0) cc_final: 0.7559 (p0) REVERT: Y 33 LEU cc_start: 0.6582 (tp) cc_final: 0.6218 (mp) REVERT: Y 55 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6855 (tt0) REVERT: L 37 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: H 35 TRP cc_start: 0.8039 (m100) cc_final: 0.7672 (m100) REVERT: H 60 TYR cc_start: 0.8175 (m-80) cc_final: 0.7671 (t80) REVERT: H 96 CYS cc_start: 0.7265 (p) cc_final: 0.6922 (p) REVERT: C 56 LYS cc_start: 0.8571 (mmtp) cc_final: 0.7924 (mmtt) REVERT: E 56 LYS cc_start: 0.8626 (mmtp) cc_final: 0.8206 (mmtp) REVERT: E 84 LYS cc_start: 0.8306 (mttt) cc_final: 0.8052 (mmtp) REVERT: E 106 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7907 (mm-30) REVERT: E 136 ARG cc_start: 0.7020 (mpt-90) cc_final: 0.6210 (mpt-90) REVERT: W 4 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8072 (mp) outliers start: 34 outliers final: 29 residues processed: 165 average time/residue: 0.1318 time to fit residues: 31.3795 Evaluate side-chains 170 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 37 GLN Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 105 optimal weight: 3.9990 chunk 153 optimal weight: 0.0870 chunk 110 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 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 = 0.4625 r_free = 0.4625 target = 0.227675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.172843 restraints weight = 17252.499| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 4.23 r_work: 0.3756 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14508 Z= 0.155 Angle : 0.677 10.242 19764 Z= 0.338 Chirality : 0.046 0.191 2235 Planarity : 0.005 0.056 2517 Dihedral : 4.936 24.655 1941 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.71 % Allowed : 18.75 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 are not related in a simple way. whole: -1.22 (0.19), residues: 1749 helix: 0.30 (0.34), residues: 231 sheet: -0.14 (0.23), residues: 513 loop : -1.49 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 587 TYR 0.023 0.002 TYR Q 54 PHE 0.011 0.001 PHE C 132 TRP 0.036 0.002 TRP E 104 HIS 0.002 0.001 HIS D 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (14487) covalent geometry : angle 0.66584 / 0.34 (19710) SS BOND : bond 0.00491 / 0.27 ( 9) SS BOND : angle 1.61324 / 0.89 ( 18) hydrogen bonds : bond 0.03556 / 2.26 ( 474) hydrogen bonds : angle 5.39798 / 3.76 ( 1341) link_BETA1-4 : bond 0.00227 / 0.12 ( 6) link_BETA1-4 : angle 2.24648 / 1.34 ( 18) link_NAG-ASN : bond 0.00691 / 0.35 ( 6) link_NAG-ASN : angle 3.14699 / 1.93 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3722.33 seconds wall clock time: 64 minutes 31.66 seconds (3871.66 seconds total)