Starting phenix.real_space_refine on Sat Oct 24 17:02:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qd8_4521/10_2026/6qd8_4521.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qd8_4521/10_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6qd8_4521/10_2026/6qd8_4521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qd8_4521/10_2026/6qd8_4521.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6qd8_4521/10_2026/6qd8_4521.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qd8_4521/10_2026/6qd8_4521.cif" model { file = "/net/cci-nas-00/data/ceres_data/6qd8_4521/10_2026/6qd8_4521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qd8_4521/10_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-2.3rc1-6221/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: 2.94, 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=21, symmetry=0 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=1.96 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 B 511 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS D 609 " distance=2.09 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 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 53 " - pdb=" SG CYS F 609 " distance=2.06 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.04 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.02 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.04 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.02 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.04 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 96 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.05 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: 1.12 Conformation dependent library (CDL) restraints added in 618.5 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: 0.42 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: 1.51 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: 7405 16.64 - 33.28: 753 33.28 - 49.92: 233 49.92 - 66.56: 30 66.56 - 83.20: 21 Dihedral angle restraints: 8442 sinusoidal: 3279 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 8439 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: 2.22 - 2.76: 2252 2.76 - 3.29: 12144 3.29 - 3.83: 22202 3.83 - 4.36: 25061 4.36 - 4.90: 45593 Nonbonded interactions: 107252 Sorted by model distance: nonbonded pdb=" O THR B 616 " pdb=" OG1 THR B 620 " model vdw 2.220 3.040 nonbonded pdb=" O THR F 616 " pdb=" OG1 THR F 620 " model vdw 2.220 3.040 nonbonded pdb=" O THR D 616 " pdb=" OG1 THR D 620 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR L 87 " pdb=" O ARG H 44 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR A 83 " pdb=" OH TYR A 232 " model vdw 2.240 3.040 ... (remaining 107247 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: 2.650 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 13.650 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.190 ------------------------------------------------------------------------------- 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 14520 Z= 0.617 Angle : 1.690 19.160 19788 Z= 0.894 Chirality : 0.085 0.287 2235 Planarity : 0.011 0.071 2517 Dihedral : 15.247 83.198 5079 Min Nonbonded Distance : 2.220 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 0.02237 / 1.49 ( 21) SS BOND : angle 2.85810 / 1.68 ( 42) 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 : 0.504 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: 0.1199 time to fit residues: 46.6346 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 : 0.445 ------------------------------------------------------------------------------- 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: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] 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: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 Y 93 ASN B 550 ASN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 61 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 = 0.4759 r_free = 0.4759 target = 0.240328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.186280 restraints weight = 17071.563| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 3.85 r_work: 0.3902 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14520 Z= 0.177 Angle : 0.803 11.477 19788 Z= 0.407 Chirality : 0.049 0.196 2235 Planarity : 0.006 0.055 2517 Dihedral : 8.204 103.918 1975 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.49 % Favored : 94.34 % Rotamer: Outliers : 2.90 % Allowed : 12.81 % Favored : 84.29 % 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: -1.61 (0.18), residues: 1749 helix: 0.86 (0.35), residues: 213 sheet: -0.41 (0.21), residues: 516 loop : -1.93 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 54 TYR 0.022 0.002 TYR A 232 PHE 0.019 0.002 PHE C 252 TRP 0.022 0.002 TRP H 48 HIS 0.006 0.001 HIS B 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (14487) covalent geometry : angle 0.78308 / 0.40 (19710) SS BOND : bond 0.00491 / 0.29 ( 21) SS BOND : angle 1.44497 / 0.87 ( 42) hydrogen bonds : bond 0.04405 / 2.82 ( 474) hydrogen bonds : angle 6.38988 / 4.42 ( 1341) link_BETA1-4 : bond 0.00365 / 0.21 ( 6) link_BETA1-4 : angle 1.93667 / 1.09 ( 18) link_NAG-ASN : bond 0.00593 / 0.29 ( 6) link_NAG-ASN : angle 5.41673 / 3.46 ( 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 211 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 64 ARG cc_start: 0.8073 (mmt-90) cc_final: 0.7871 (tpp-160) REVERT: A 163 ASP cc_start: 0.8052 (t70) cc_final: 0.7825 (t0) REVERT: B 548 MET cc_start: 0.7157 (ttt) cc_final: 0.6946 (ttt) REVERT: C 56 LYS cc_start: 0.8454 (mmtp) cc_final: 0.8150 (mmtp) REVERT: E 56 LYS cc_start: 0.8493 (mmtp) cc_final: 0.8104 (mmtp) REVERT: Q 60 TYR cc_start: 0.7612 (m-80) cc_final: 0.7206 (m-80) outliers start: 44 outliers final: 23 residues processed: 196 average time/residue: 0.1185 time to fit residues: 33.7412 Evaluate side-chains 172 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 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 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 78 ASP Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 309 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: [44, 107, 4, 165, 1, 121, 40, 62, 136, 61, 115] chunk 44 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 0.0060 chunk 136 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 89 GLN A 257 ASN Y 89 GLN ** Y 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN E 107 ASN W 3 GLN ** Q 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.234125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.179242 restraints weight = 17178.610| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 3.96 r_work: 0.3881 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14520 Z= 0.255 Angle : 0.863 13.619 19788 Z= 0.427 Chirality : 0.051 0.266 2235 Planarity : 0.006 0.065 2517 Dihedral : 5.882 24.962 1950 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.78 % Favored : 92.05 % Rotamer: Outliers : 3.63 % Allowed : 13.93 % Favored : 82.44 % 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: -1.79 (0.17), residues: 1749 helix: 0.25 (0.32), residues: 213 sheet: -0.50 (0.20), residues: 507 loop : -1.95 (0.16), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 219 TYR 0.024 0.002 TYR Q 54 PHE 0.025 0.003 PHE E 132 TRP 0.022 0.002 TRP Q 48 HIS 0.004 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.25 (14487) covalent geometry : angle 0.84518 / 0.42 (19710) SS BOND : bond 0.00602 / 0.39 ( 21) SS BOND : angle 1.55728 / 0.94 ( 42) hydrogen bonds : bond 0.04821 / 3.03 ( 474) hydrogen bonds : angle 6.39708 / 4.43 ( 1341) link_BETA1-4 : bond 0.00208 / 0.13 ( 6) link_BETA1-4 : angle 2.63404 / 1.52 ( 18) link_NAG-ASN : bond 0.00809 / 0.40 ( 6) link_NAG-ASN : angle 4.88729 / 3.06 ( 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 203 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 148 time to evaluate : 0.503 Fit side-chains REVERT: A 56 LYS cc_start: 0.8235 (mmtp) cc_final: 0.7887 (mmtp) REVERT: A 64 ARG cc_start: 0.8465 (mmt-90) cc_final: 0.8210 (tpp-160) REVERT: A 111 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6675 (mp) REVERT: A 162 TYR cc_start: 0.8253 (m-80) cc_final: 0.7931 (m-80) REVERT: Y 55 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6754 (tt0) REVERT: C 56 LYS cc_start: 0.8569 (mmtp) cc_final: 0.8309 (mmtp) REVERT: C 136 ARG cc_start: 0.7202 (mpt-90) cc_final: 0.6822 (mpt180) REVERT: E 56 LYS cc_start: 0.8562 (mmtp) cc_final: 0.8020 (mmtm) REVERT: E 84 LYS cc_start: 0.8212 (mttt) cc_final: 0.7939 (mmtp) REVERT: E 136 ARG cc_start: 0.6695 (mpt-90) cc_final: 0.6140 (mpt180) REVERT: F 548 MET cc_start: 0.7700 (tpt) cc_final: 0.7414 (ttt) REVERT: Q 60 TYR cc_start: 0.7952 (m-80) cc_final: 0.7685 (m-80) outliers start: 55 outliers final: 33 residues processed: 186 average time/residue: 0.1234 time to fit residues: 33.6614 Evaluate side-chains 173 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 A residue 37 VAL 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 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 547 LEU Chi-restraints excluded: chain B residue 577 THR 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 H residue 96 CYS Chi-restraints excluded: chain C residue 37 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 C residue 309 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 309 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: [164, 84, 140, 100, 42, 67, 158, 86, 82, 107, 74] chunk 164 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 chunk 86 optimal weight: 0.1980 chunk 82 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Z 53 ASN Z 89 GLN Y 89 GLN ** Y 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN H 3 GLN W 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.238403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.185373 restraints weight = 17085.699| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 3.67 r_work: 0.3942 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14520 Z= 0.129 Angle : 0.697 15.039 19788 Z= 0.343 Chirality : 0.046 0.174 2235 Planarity : 0.005 0.058 2517 Dihedral : 5.291 25.854 1942 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.77 % Allowed : 15.64 % Favored : 81.58 % 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: 0.79 (0.34), residues: 213 sheet: -0.54 (0.21), residues: 549 loop : -1.73 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 136 TYR 0.021 0.001 TYR Q 54 PHE 0.013 0.001 PHE F 572 TRP 0.021 0.002 TRP H 48 HIS 0.006 0.001 HIS D 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (14487) covalent geometry : angle 0.68244 / 0.34 (19710) SS BOND : bond 0.00437 / 0.28 ( 21) SS BOND : angle 0.98001 / 0.62 ( 42) hydrogen bonds : bond 0.03596 / 2.32 ( 474) hydrogen bonds : angle 5.78859 / 4.03 ( 1341) link_BETA1-4 : bond 0.00219 / 0.11 ( 6) link_BETA1-4 : angle 1.97098 / 1.12 ( 18) link_NAG-ASN : bond 0.00717 / 0.35 ( 6) link_NAG-ASN : angle 4.19875 / 2.66 ( 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 199 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8130 (mmtp) cc_final: 0.7793 (mmtp) REVERT: A 111 LEU cc_start: 0.6966 (mp) cc_final: 0.6742 (mp) REVERT: A 162 TYR cc_start: 0.8157 (m-80) cc_final: 0.7785 (m-80) REVERT: A 163 ASP cc_start: 0.7892 (t0) cc_final: 0.7643 (t0) REVERT: Y 11 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8255 (mp) REVERT: Y 55 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6702 (tt0) REVERT: C 56 LYS cc_start: 0.8562 (mmtp) cc_final: 0.8206 (mmtp) REVERT: E 56 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8066 (mmtm) REVERT: E 84 LYS cc_start: 0.8185 (mttt) cc_final: 0.7950 (mmtp) REVERT: F 548 MET cc_start: 0.7893 (tpt) cc_final: 0.7579 (ttt) REVERT: D 548 MET cc_start: 0.7415 (mmm) cc_final: 0.6613 (mtp) REVERT: Q 60 TYR cc_start: 0.7892 (m-80) cc_final: 0.7685 (m-80) REVERT: Q 96 CYS cc_start: 0.5660 (p) cc_final: 0.5437 (p) outliers start: 42 outliers final: 25 residues processed: 184 average time/residue: 0.1189 time to fit residues: 32.3592 Evaluate side-chains 165 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 2 ILE 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 A residue 79 VAL Chi-restraints excluded: chain Y residue 11 LEU 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 L residue 7 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 29 ILE 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 231 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: [101, 85, 141, 128, 84, 171, 123, 66, 112, 41, 98] chunk 101 optimal weight: 220.0000 chunk 85 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 171 optimal weight: 8.9990 chunk 123 optimal weight: 50.0000 chunk 66 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 30.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Z 89 GLN Y 89 GLN ** Y 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN Q 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.225304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.168355 restraints weight = 17415.006| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 3.84 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14520 Z= 0.254 Angle : 0.823 15.277 19788 Z= 0.403 Chirality : 0.050 0.177 2235 Planarity : 0.006 0.063 2517 Dihedral : 5.633 25.437 1941 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 3.50 % Allowed : 16.37 % Favored : 80.13 % 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: -1.71 (0.18), residues: 1749 helix: 0.37 (0.33), residues: 213 sheet: -0.56 (0.21), residues: 513 loop : -1.83 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 134 TYR 0.021 0.002 TYR Z 36 PHE 0.019 0.002 PHE C 132 TRP 0.023 0.002 TRP Q 48 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.25 (14487) covalent geometry : angle 0.80818 / 0.40 (19710) SS BOND : bond 0.00688 / 0.38 ( 21) SS BOND : angle 1.55340 / 1.12 ( 42) hydrogen bonds : bond 0.04485 / 2.83 ( 474) hydrogen bonds : angle 6.13261 / 4.24 ( 1341) link_BETA1-4 : bond 0.00258 / 0.15 ( 6) link_BETA1-4 : angle 2.65389 / 1.53 ( 18) link_NAG-ASN : bond 0.00877 / 0.45 ( 6) link_NAG-ASN : angle 4.15691 / 2.57 ( 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 194 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 141 time to evaluate : 0.324 Fit side-chains REVERT: A 56 LYS cc_start: 0.8219 (mmtp) cc_final: 0.7747 (mmtp) REVERT: A 111 LEU cc_start: 0.7051 (mp) cc_final: 0.6744 (mp) REVERT: Y 11 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8213 (mt) REVERT: Y 55 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6611 (tt0) REVERT: L 37 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6942 (tt0) REVERT: C 56 LYS cc_start: 0.8405 (mmtp) cc_final: 0.7948 (mmtp) REVERT: E 56 LYS cc_start: 0.8488 (mmtp) cc_final: 0.8107 (mmtp) REVERT: E 84 LYS cc_start: 0.8021 (mttt) cc_final: 0.7719 (mmtp) REVERT: F 548 MET cc_start: 0.7178 (tpt) cc_final: 0.6929 (ttp) REVERT: D 548 MET cc_start: 0.6893 (mmm) cc_final: 0.6513 (mtp) outliers start: 53 outliers final: 38 residues processed: 172 average time/residue: 0.1294 time to fit residues: 32.1785 Evaluate side-chains 171 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 83 PHE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain Y residue 11 LEU 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 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 4 LEU 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 H residue 110 THR Chi-restraints excluded: chain C residue 77 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 77 THR Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 542 ILE 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 D residue 604 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: [79, 66, 168, 130, 122, 166, 24, 17, 109, 136, 128] chunk 79 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 128 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Z 89 GLN Y 89 GLN Y 93 ASN E 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.230296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.175592 restraints weight = 17166.655| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 4.02 r_work: 0.3781 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14520 Z= 0.123 Angle : 0.674 14.876 19788 Z= 0.332 Chirality : 0.046 0.171 2235 Planarity : 0.005 0.058 2517 Dihedral : 5.119 26.194 1941 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.77 % Allowed : 17.16 % Favored : 80.07 % 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: -1.49 (0.18), residues: 1749 helix: 0.79 (0.35), residues: 213 sheet: -0.64 (0.21), residues: 558 loop : -1.63 (0.17), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 67 TYR 0.018 0.001 TYR Q 54 PHE 0.014 0.001 PHE D 572 TRP 0.021 0.001 TRP Q 48 HIS 0.003 0.000 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (14487) covalent geometry : angle 0.66188 / 0.33 (19710) SS BOND : bond 0.00338 / 0.21 ( 21) SS BOND : angle 0.95436 / 0.66 ( 42) hydrogen bonds : bond 0.03349 / 2.15 ( 474) hydrogen bonds : angle 5.56305 / 3.87 ( 1341) link_BETA1-4 : bond 0.00195 / 0.10 ( 6) link_BETA1-4 : angle 2.01752 / 1.14 ( 18) link_NAG-ASN : bond 0.00719 / 0.35 ( 6) link_NAG-ASN : angle 3.59247 / 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 195 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 0.511 Fit side-chains REVERT: A 56 LYS cc_start: 0.8171 (mmtp) cc_final: 0.7776 (mmtp) REVERT: A 111 LEU cc_start: 0.6948 (mp) cc_final: 0.6716 (mp) REVERT: A 162 TYR cc_start: 0.8268 (m-80) cc_final: 0.7888 (m-80) REVERT: Y 11 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8265 (mp) REVERT: Y 55 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6794 (tt0) REVERT: L 37 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: H 29 ILE cc_start: 0.5886 (OUTLIER) cc_final: 0.5646 (mt) REVERT: C 56 LYS cc_start: 0.8442 (mmtp) cc_final: 0.8171 (mmtp) REVERT: E 56 LYS cc_start: 0.8583 (mmtp) cc_final: 0.8215 (mmtp) REVERT: E 84 LYS cc_start: 0.8385 (mttt) cc_final: 0.8012 (mmtp) REVERT: F 595 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7482 (mt0) outliers start: 42 outliers final: 30 residues processed: 178 average time/residue: 0.1229 time to fit residues: 32.1644 Evaluate side-chains 177 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 79 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain Y residue 11 LEU 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 Y residue 93 ASN Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain L residue 7 SER 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 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 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain D residue 505 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain Q residue 11 LEU 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: [114, 47, 96, 52, 3, 97, 29, 31, 42, 39, 119] chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 96 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 97 optimal weight: 50.0000 chunk 29 optimal weight: 50.0000 chunk 31 optimal weight: 50.0000 chunk 42 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.4612 r_free = 0.4612 target = 0.226550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.172471 restraints weight = 17324.328| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 4.09 r_work: 0.3744 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14520 Z= 0.202 Angle : 0.744 14.102 19788 Z= 0.366 Chirality : 0.048 0.160 2235 Planarity : 0.005 0.059 2517 Dihedral : 5.254 25.328 1941 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.63 % Allowed : 17.76 % Favored : 78.61 % 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: 0.59 (0.34), residues: 213 sheet: -0.48 (0.21), residues: 513 loop : -1.70 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 587 TYR 0.027 0.002 TYR H 54 PHE 0.015 0.002 PHE C 132 TRP 0.021 0.002 TRP Q 48 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (14487) covalent geometry : angle 0.73031 / 0.36 (19710) SS BOND : bond 0.00465 / 0.30 ( 21) SS BOND : angle 1.59208 / 1.08 ( 42) hydrogen bonds : bond 0.03969 / 2.51 ( 474) hydrogen bonds : angle 5.74687 / 3.98 ( 1341) link_BETA1-4 : bond 0.00165 / 0.09 ( 6) link_BETA1-4 : angle 2.41990 / 1.42 ( 18) link_NAG-ASN : bond 0.00786 / 0.39 ( 6) link_NAG-ASN : angle 3.62962 / 2.24 ( 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 193 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 138 time to evaluate : 0.520 Fit side-chains REVERT: A 56 LYS cc_start: 0.8269 (mmtp) cc_final: 0.7875 (mmtp) REVERT: Y 11 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8304 (mt) REVERT: Y 55 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6878 (tt0) REVERT: B 596 ARG cc_start: 0.7186 (ttt180) cc_final: 0.6983 (ttt180) REVERT: C 56 LYS cc_start: 0.8460 (mmtp) cc_final: 0.8186 (mmtp) REVERT: E 56 LYS cc_start: 0.8653 (mmtp) cc_final: 0.8208 (mmtp) REVERT: E 84 LYS cc_start: 0.8332 (mttt) cc_final: 0.7992 (mmtp) REVERT: F 548 MET cc_start: 0.7755 (ttt) cc_final: 0.7499 (ttp) REVERT: F 595 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7487 (mt0) REVERT: D 551 GLN cc_start: 0.7884 (pm20) cc_final: 0.7671 (pm20) outliers start: 55 outliers final: 39 residues processed: 173 average time/residue: 0.1145 time to fit residues: 29.1814 Evaluate side-chains 177 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 46 PHE Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 46 PHE Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain L residue 7 SER 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 4 LEU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain C residue 37 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 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 591 ASP Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain F residue 609 CYS 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 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: [138, 47, 120, 30, 165, 121, 136, 20, 109, 86, 89] chunk 138 optimal weight: 30.0000 chunk 47 optimal weight: 0.4980 chunk 120 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 165 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.4608 r_free = 0.4608 target = 0.226198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.172641 restraints weight = 17250.664| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 3.76 r_work: 0.3739 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14520 Z= 0.199 Angle : 0.734 13.637 19788 Z= 0.364 Chirality : 0.047 0.156 2235 Planarity : 0.005 0.060 2517 Dihedral : 5.270 25.536 1941 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.50 % Allowed : 18.42 % Favored : 78.09 % 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: -1.55 (0.18), residues: 1749 helix: 0.50 (0.35), residues: 213 sheet: -0.49 (0.21), residues: 513 loop : -1.71 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 587 TYR 0.028 0.002 TYR W 54 PHE 0.015 0.002 PHE E 132 TRP 0.023 0.002 TRP Q 48 HIS 0.003 0.001 HIS Q 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 (14487) covalent geometry : angle 0.72053 / 0.36 (19710) SS BOND : bond 0.00469 / 0.29 ( 21) SS BOND : angle 1.54827 / 1.08 ( 42) hydrogen bonds : bond 0.03947 / 2.49 ( 474) hydrogen bonds : angle 5.74086 / 3.97 ( 1341) link_BETA1-4 : bond 0.00127 / 0.07 ( 6) link_BETA1-4 : angle 2.44651 / 1.43 ( 18) link_NAG-ASN : bond 0.00748 / 0.38 ( 6) link_NAG-ASN : angle 3.50536 / 2.15 ( 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 190 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 0.436 Fit side-chains REVERT: A 56 LYS cc_start: 0.8267 (mmtp) cc_final: 0.7897 (mmtp) REVERT: A 104 TRP cc_start: 0.7356 (m100) cc_final: 0.6843 (m100) REVERT: Y 11 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8311 (mt) REVERT: Y 55 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.6906 (tt0) REVERT: C 56 LYS cc_start: 0.8467 (mmtp) cc_final: 0.7800 (mmtt) REVERT: E 56 LYS cc_start: 0.8644 (mmtp) cc_final: 0.8262 (mmtp) REVERT: E 84 LYS cc_start: 0.8336 (mttt) cc_final: 0.8102 (mmtp) REVERT: F 595 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7527 (mt0) outliers start: 53 outliers final: 37 residues processed: 172 average time/residue: 0.1161 time to fit residues: 29.3886 Evaluate side-chains 175 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 231 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 12 SER Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 46 PHE Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain L residue 7 SER 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 4 LEU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain C residue 37 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 37 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain F residue 609 CYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: [52, 95, 123, 109, 81, 159, 144, 106, 163, 92, 56] chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 109 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4632 r_free = 0.4632 target = 0.228695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.176040 restraints weight = 17256.773| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 3.38 r_work: 0.3789 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14520 Z= 0.139 Angle : 0.681 14.267 19788 Z= 0.335 Chirality : 0.046 0.159 2235 Planarity : 0.005 0.057 2517 Dihedral : 5.036 25.134 1941 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.97 % Allowed : 19.27 % Favored : 77.76 % 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: -1.53 (0.19), residues: 1749 helix: 0.24 (0.34), residues: 231 sheet: -0.59 (0.22), residues: 546 loop : -1.60 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 596 TYR 0.027 0.002 TYR W 54 PHE 0.015 0.001 PHE F 572 TRP 0.021 0.002 TRP H 48 HIS 0.003 0.000 HIS Q 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (14487) covalent geometry : angle 0.66983 / 0.33 (19710) SS BOND : bond 0.00376 / 0.24 ( 21) SS BOND : angle 1.17658 / 0.82 ( 42) hydrogen bonds : bond 0.03411 / 2.17 ( 474) hydrogen bonds : angle 5.44815 / 3.78 ( 1341) link_BETA1-4 : bond 0.00197 / 0.11 ( 6) link_BETA1-4 : angle 2.15462 / 1.23 ( 18) link_NAG-ASN : bond 0.00700 / 0.35 ( 6) link_NAG-ASN : angle 3.24586 / 2.01 ( 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 183 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 0.630 Fit side-chains REVERT: A 104 TRP cc_start: 0.7263 (m100) cc_final: 0.6744 (m100) REVERT: A 162 TYR cc_start: 0.8287 (m-80) cc_final: 0.7987 (m-80) REVERT: Y 11 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8236 (mp) REVERT: Y 55 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6838 (tt0) REVERT: Y 79 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7076 (mp10) REVERT: L 37 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7258 (tt0) REVERT: C 56 LYS cc_start: 0.8409 (mmtp) cc_final: 0.7736 (mmtt) REVERT: C 136 ARG cc_start: 0.6950 (mpt-90) cc_final: 0.6361 (mtm-85) REVERT: E 56 LYS cc_start: 0.8546 (mmtp) cc_final: 0.8175 (mmtp) REVERT: E 84 LYS cc_start: 0.8297 (mttt) cc_final: 0.7974 (mmtp) REVERT: E 136 ARG cc_start: 0.6668 (mpt-90) cc_final: 0.6217 (mpt180) REVERT: F 595 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7523 (mt0) outliers start: 45 outliers final: 35 residues processed: 168 average time/residue: 0.1214 time to fit residues: 30.0592 Evaluate side-chains 173 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 46 PHE 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 11 LEU Chi-restraints excluded: chain Y residue 37 GLN Chi-restraints excluded: chain Y residue 46 PHE Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain L residue 7 SER 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 4 LEU Chi-restraints excluded: chain H residue 36 THR 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 F residue 540 GLU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain F residue 609 CYS 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 36 THR Chi-restraints excluded: chain Q residue 11 LEU 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: [114, 160, 165, 32, 0, 29, 135, 21, 94, 146, 93] chunk 114 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 50.0000 chunk 135 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.7924 ------------------------------------------------------------------------------- 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 = 0.4607 r_free = 0.4607 target = 0.225850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.171431 restraints weight = 17380.033| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 3.92 r_work: 0.3698 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14520 Z= 0.215 Angle : 0.754 14.059 19788 Z= 0.372 Chirality : 0.048 0.222 2235 Planarity : 0.005 0.061 2517 Dihedral : 5.274 24.988 1941 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.77 % Allowed : 19.74 % Favored : 77.49 % 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: 0.45 (0.35), residues: 213 sheet: -0.56 (0.21), residues: 519 loop : -1.63 (0.17), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 67 TYR 0.026 0.002 TYR W 54 PHE 0.014 0.002 PHE E 132 TRP 0.036 0.002 TRP E 104 HIS 0.003 0.001 HIS Q 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.21 (14487) covalent geometry : angle 0.74088 / 0.37 (19710) SS BOND : bond 0.00515 / 0.32 ( 21) SS BOND : angle 1.58784 / 1.11 ( 42) hydrogen bonds : bond 0.04074 / 2.57 ( 474) hydrogen bonds : angle 5.70284 / 3.95 ( 1341) link_BETA1-4 : bond 0.00203 / 0.11 ( 6) link_BETA1-4 : angle 2.51809 / 1.52 ( 18) link_NAG-ASN : bond 0.00743 / 0.38 ( 6) link_NAG-ASN : angle 3.37402 / 2.06 ( 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 175 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.422 Fit side-chains REVERT: A 104 TRP cc_start: 0.7383 (m100) cc_final: 0.6852 (m100) REVERT: Y 55 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7028 (tt0) REVERT: Y 79 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.6835 (mp10) REVERT: L 37 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: C 56 LYS cc_start: 0.8448 (mmtp) cc_final: 0.7788 (mmtt) REVERT: C 136 ARG cc_start: 0.6951 (mpt-90) cc_final: 0.6523 (ttm110) REVERT: E 56 LYS cc_start: 0.8586 (mmtp) cc_final: 0.8207 (mmtp) REVERT: E 84 LYS cc_start: 0.8374 (mttt) cc_final: 0.8037 (mmtp) REVERT: F 548 MET cc_start: 0.7670 (ttt) cc_final: 0.7423 (ttp) outliers start: 42 outliers final: 36 residues processed: 161 average time/residue: 0.1208 time to fit residues: 28.1659 Evaluate side-chains 171 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 46 PHE 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 46 PHE Chi-restraints excluded: chain Y residue 55 GLN Chi-restraints excluded: chain Y residue 69 THR Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 83 PHE Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 PHE 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 4 LEU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 540 GLU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain F residue 609 CYS 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 36 THR Chi-restraints excluded: chain Q residue 11 LEU 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: [105, 153, 110, 20, 135, 65, 164, 157, 166, 32, 150] chunk 105 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 110 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 164 optimal weight: 0.2980 chunk 157 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 150 optimal weight: 40.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.228552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.176120 restraints weight = 17231.520| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.53 r_work: 0.3755 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14520 Z= 0.134 Angle : 0.675 13.523 19788 Z= 0.334 Chirality : 0.045 0.157 2235 Planarity : 0.005 0.057 2517 Dihedral : 5.022 25.089 1941 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.77 % Allowed : 19.47 % Favored : 77.76 % 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: -1.39 (0.19), residues: 1749 helix: 0.27 (0.34), residues: 231 sheet: -0.36 (0.22), residues: 513 loop : -1.56 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 596 TYR 0.026 0.001 TYR H 54 PHE 0.015 0.001 PHE F 572 TRP 0.025 0.002 TRP E 104 HIS 0.003 0.000 HIS Q 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (14487) covalent geometry : angle 0.66473 / 0.33 (19710) SS BOND : bond 0.00389 / 0.24 ( 21) SS BOND : angle 1.14727 / 0.80 ( 42) hydrogen bonds : bond 0.03403 / 2.17 ( 474) hydrogen bonds : angle 5.42882 / 3.77 ( 1341) link_BETA1-4 : bond 0.00146 / 0.08 ( 6) link_BETA1-4 : angle 2.15565 / 1.25 ( 18) link_NAG-ASN : bond 0.00669 / 0.33 ( 6) link_NAG-ASN : angle 3.12366 / 1.93 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3469.12 seconds wall clock time: 60 minutes 4.10 seconds (3604.10 seconds total)