Starting phenix.real_space_refine on Thu Jul 2 22:22:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rn7_54083/07_2026/9rn7_54083.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rn7_54083/07_2026/9rn7_54083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rn7_54083/07_2026/9rn7_54083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rn7_54083/07_2026/9rn7_54083.map" model { file = "/net/cci-nas-00/data/ceres_data/9rn7_54083/07_2026/9rn7_54083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rn7_54083/07_2026/9rn7_54083.cif" } resolution = 3.1 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= 0.005 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 71 5.16 5 C 6916 2.51 5 N 1626 2.21 5 O 1758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10372 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1189 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 1205 Chain: "B" Number of atoms: 1147 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 147, 1139 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 147, 1139 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1162 Chain: "C" Number of atoms: 1165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 148, 1157 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 148, 1157 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1181 Chain: "D" Number of atoms: 1172 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 148, 1164 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 148, 1164 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1188 Chain: "E" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1382 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 179} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1356 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 3 Chain: "G" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1391 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 179} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1401 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 180} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.90, per 1000 atoms: 0.28 Number of scatterers: 10372 At special positions: 0 Unit cell: (105.446, 104.623, 97.2084, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 71 16.00 O 1758 8.00 N 1626 7.00 C 6916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.04 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.02 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.02 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 506.5 milliseconds 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 5 sheets defined 70.0% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 544 through 568 removed outlier: 3.784A pdb=" N VAL A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 removed outlier: 3.579A pdb=" N LEU A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 649 removed outlier: 3.617A pdb=" N VAL A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 624 " --> pdb=" O GLY A 620 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TRP A 627 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 652 No H-bonds generated for 'chain 'A' and resid 650 through 652' Processing helix chain 'A' and resid 815 through 832 removed outlier: 3.637A pdb=" N LEU A 821 " --> pdb=" O VAL A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 846 Processing helix chain 'B' and resid 537 through 541 removed outlier: 3.864A pdb=" N LEU B 540 " --> pdb=" O PHE B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 568 removed outlier: 3.861A pdb=" N VAL B 552 " --> pdb=" O TRP B 548 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 561 " --> pdb=" O GLY B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 607 Processing helix chain 'B' and resid 619 through 649 removed outlier: 3.507A pdb=" N VAL B 623 " --> pdb=" O SER B 619 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY B 625 " --> pdb=" O ARG B 621 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 631 " --> pdb=" O TRP B 627 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 844 removed outlier: 3.598A pdb=" N PHE B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 826 " --> pdb=" O VAL B 822 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU B 835 " --> pdb=" O VAL B 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 541 removed outlier: 3.664A pdb=" N ASP C 541 " --> pdb=" O SER C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 548 Processing helix chain 'C' and resid 550 through 568 removed outlier: 3.585A pdb=" N ILE C 556 " --> pdb=" O VAL C 552 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 564 " --> pdb=" O VAL C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 606 removed outlier: 3.705A pdb=" N LEU C 599 " --> pdb=" O ILE C 595 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 627 removed outlier: 4.039A pdb=" N VAL C 623 " --> pdb=" O SER C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 648 removed outlier: 3.534A pdb=" N THR C 639 " --> pdb=" O ILE C 635 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 820 Processing helix chain 'C' and resid 820 through 845 removed outlier: 3.608A pdb=" N GLY C 826 " --> pdb=" O VAL C 822 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET C 829 " --> pdb=" O LEU C 825 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 834 " --> pdb=" O LEU C 830 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 835 " --> pdb=" O VAL C 831 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 550 removed outlier: 3.672A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 568 removed outlier: 3.526A pdb=" N VAL D 560 " --> pdb=" O ILE D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 607 removed outlier: 3.505A pdb=" N TRP D 600 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE D 606 " --> pdb=" O SER D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 648 removed outlier: 3.508A pdb=" N VAL D 623 " --> pdb=" O SER D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 815 removed outlier: 3.776A pdb=" N VAL D 814 " --> pdb=" O SER D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 846 removed outlier: 3.581A pdb=" N GLU D 843 " --> pdb=" O LYS D 839 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 30 Processing helix chain 'E' and resid 94 through 105 Processing helix chain 'E' and resid 105 through 127 removed outlier: 3.599A pdb=" N VAL E 112 " --> pdb=" O PRO E 108 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU E 126 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 163 removed outlier: 3.557A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 212 removed outlier: 3.599A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 30 removed outlier: 3.684A pdb=" N GLY F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY F 29 " --> pdb=" O THR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 105 through 128 removed outlier: 3.507A pdb=" N PHE F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 153 removed outlier: 3.664A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 159 removed outlier: 3.505A pdb=" N ALA F 159 " --> pdb=" O VAL F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 212 removed outlier: 3.735A pdb=" N ALA F 212 " --> pdb=" O LEU F 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 30 removed outlier: 3.696A pdb=" N ALA G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL G 28 " --> pdb=" O MET G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 105 Processing helix chain 'G' and resid 105 through 128 removed outlier: 3.597A pdb=" N VAL G 112 " --> pdb=" O PRO G 108 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.512A pdb=" N SER G 137 " --> pdb=" O ASN G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 212 removed outlier: 3.996A pdb=" N ILE G 188 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA G 212 " --> pdb=" O LEU G 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 30 removed outlier: 3.511A pdb=" N THR H 13 " --> pdb=" O GLN H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 100 removed outlier: 3.633A pdb=" N ARG H 99 " --> pdb=" O GLU H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 129 removed outlier: 3.743A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 163 removed outlier: 3.501A pdb=" N ALA H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP H 163 " --> pdb=" O ALA H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 212 Processing sheet with id=AA1, first strand: chain 'E' and resid 57 through 61 Processing sheet with id=AA2, first strand: chain 'E' and resid 65 through 67 Processing sheet with id=AA3, first strand: chain 'F' and resid 35 through 38 removed outlier: 3.735A pdb=" N CYS F 67 " --> pdb=" O HIS F 60 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AA5, first strand: chain 'H' and resid 66 through 68 removed outlier: 3.522A pdb=" N VAL H 57 " --> pdb=" O GLY H 38 " (cutoff:3.500A) 709 hydrogen bonds defined for protein. 2091 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: 1.48 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1720 1.32 - 1.45: 3106 1.45 - 1.58: 5692 1.58 - 1.70: 0 1.70 - 1.83: 110 Bond restraints: 10628 Sorted by residual: bond pdb=" N CYS D 837 " pdb=" CA CYS D 837 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.16e-02 7.43e+03 6.65e+00 bond pdb=" N CYS A 837 " pdb=" CA CYS A 837 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.16e-02 7.43e+03 6.05e+00 bond pdb=" N CYS C 837 " pdb=" CA CYS C 837 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.23e-02 6.61e+03 5.74e+00 bond pdb=" N CYS B 837 " pdb=" CA CYS B 837 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.35e+00 bond pdb=" C1 PLM C1001 " pdb=" O2 PLM C1001 " ideal model delta sigma weight residual 1.249 1.206 0.043 2.00e-02 2.50e+03 4.66e+00 ... (remaining 10623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 13608 1.73 - 3.46: 627 3.46 - 5.19: 90 5.19 - 6.92: 16 6.92 - 8.65: 4 Bond angle restraints: 14345 Sorted by residual: angle pdb=" CA CYS A 837 " pdb=" C CYS A 837 " pdb=" O CYS A 837 " ideal model delta sigma weight residual 121.07 117.50 3.57 1.10e+00 8.26e-01 1.06e+01 angle pdb=" N GLY C 824 " pdb=" CA GLY C 824 " pdb=" C GLY C 824 " ideal model delta sigma weight residual 113.18 105.58 7.60 2.37e+00 1.78e-01 1.03e+01 angle pdb=" N GLY C 604 " pdb=" CA GLY C 604 " pdb=" C GLY C 604 " ideal model delta sigma weight residual 113.18 105.68 7.50 2.37e+00 1.78e-01 1.00e+01 angle pdb=" N TYR C 819 " pdb=" CA TYR C 819 " pdb=" C TYR C 819 " ideal model delta sigma weight residual 112.54 108.69 3.85 1.22e+00 6.72e-01 9.95e+00 angle pdb=" N VAL F 155 " pdb=" CA VAL F 155 " pdb=" C VAL F 155 " ideal model delta sigma weight residual 113.39 108.77 4.62 1.47e+00 4.63e-01 9.88e+00 ... (remaining 14340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.58: 5891 26.58 - 53.15: 145 53.15 - 79.73: 36 79.73 - 106.31: 1 106.31 - 132.89: 5 Dihedral angle restraints: 6078 sinusoidal: 2312 harmonic: 3766 Sorted by residual: dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual -86.00 -30.03 -55.97 1 1.00e+01 1.00e-02 4.23e+01 dihedral pdb=" CA TYR F 176 " pdb=" C TYR F 176 " pdb=" N GLY F 177 " pdb=" CA GLY F 177 " ideal model delta harmonic sigma weight residual -180.00 -152.42 -27.58 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" C21 OLC D1002 " pdb=" C1 OLC D1002 " pdb=" O20 OLC D1002 " pdb=" O19 OLC D1002 " ideal model delta sinusoidal sigma weight residual -1.92 -134.81 132.89 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 6075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1172 0.047 - 0.095: 369 0.095 - 0.142: 62 0.142 - 0.189: 10 0.189 - 0.236: 3 Chirality restraints: 1616 Sorted by residual: chirality pdb=" CA ASP B 541 " pdb=" N ASP B 541 " pdb=" C ASP B 541 " pdb=" CB ASP B 541 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ARG B 567 " pdb=" N ARG B 567 " pdb=" C ARG B 567 " pdb=" CB ARG B 567 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB VAL G 57 " pdb=" CA VAL G 57 " pdb=" CG1 VAL G 57 " pdb=" CG2 VAL G 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.70e-01 ... (remaining 1613 not shown) Planarity restraints: 1729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLC A1003 " 0.066 2.00e-02 2.50e+03 7.64e-02 5.83e+01 pdb=" C11 OLC A1003 " -0.074 2.00e-02 2.50e+03 pdb=" C8 OLC A1003 " -0.078 2.00e-02 2.50e+03 pdb=" C9 OLC A1003 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLC D1002 " -0.059 2.00e-02 2.50e+03 6.86e-02 4.71e+01 pdb=" C11 OLC D1002 " 0.066 2.00e-02 2.50e+03 pdb=" C8 OLC D1002 " 0.070 2.00e-02 2.50e+03 pdb=" C9 OLC D1002 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 573 " 0.023 2.00e-02 2.50e+03 2.37e-02 1.40e+01 pdb=" CG TRP C 573 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP C 573 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP C 573 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 573 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 573 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 573 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 573 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 573 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 573 " 0.001 2.00e-02 2.50e+03 ... (remaining 1726 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1741 2.75 - 3.29: 10272 3.29 - 3.83: 16888 3.83 - 4.36: 21075 4.36 - 4.90: 35748 Nonbonded interactions: 85724 Sorted by model distance: nonbonded pdb=" NZ LYS G 41 " pdb=" O THR G 42 " model vdw 2.216 3.120 nonbonded pdb=" OD2 ASP H 31 " pdb=" NH1 ARG H 65 " model vdw 2.265 3.120 nonbonded pdb=" OH TYR D 555 " pdb=" O LEU D 599 " model vdw 2.265 3.040 nonbonded pdb=" O ILE F 154 " pdb=" OG SER F 158 " model vdw 2.270 3.040 nonbonded pdb=" OE2 GLU B 546 " pdb=" OH TYR G 174 " model vdw 2.302 3.040 ... (remaining 85719 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 532 through 573 or (resid 574 through 588 and (name N or n \ ame CA or name C or name O or name CB )) or resid 589 through 595 or resid 597 t \ hrough 650 or resid 807 through 837 or (resid 838 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 839 through 844)) selection = (chain 'B' and (resid 532 through 595 or resid 597 through 650 or resid 807 thro \ ugh 844)) selection = (chain 'C' and (resid 532 through 573 or (resid 574 through 588 and (name N or n \ ame CA or name C or name O or name CB )) or resid 589 through 595 or resid 597 t \ hrough 650 or resid 807 through 837 or (resid 838 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 839 through 844)) selection = (chain 'D' and (resid 532 or (resid 533 and (name N or name CA or name C or name \ O or name CB )) or resid 534 through 573 or (resid 574 through 588 and (name N \ or name CA or name C or name O or name CB )) or resid 589 through 595 or resid 5 \ 97 through 650 or resid 807 through 837 or (resid 838 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or na \ me CE2 or name CZ )) or resid 839 through 844)) } ncs_group { reference = (chain 'E' and (resid 7 through 40 or (resid 56 and (name N or name CA or name C \ or name O or name CB )) or resid 57 through 161 or resid 173 through 212)) selection = (chain 'F' and (resid 7 through 40 or (resid 56 and (name N or name CA or name C \ or name O or name CB )) or resid 57 through 83 or resid 93 through 161 or resid \ 173 through 212)) selection = (chain 'G' and (resid 7 through 40 or resid 56 through 83 or resid 93 through 16 \ 1 or resid 173 through 212)) selection = (chain 'H' and (resid 7 through 40 or resid 56 through 83 or resid 93 through 16 \ 1 or resid 173 through 212)) } 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=0.50 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: 4.630 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.640 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 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 : 0.007 0.059 10640 Z= 0.324 Angle : 0.826 8.647 14361 Z= 0.462 Chirality : 0.046 0.236 1616 Planarity : 0.011 0.106 1729 Dihedral : 13.031 132.887 3638 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.82 (0.20), residues: 1263 helix: -2.18 (0.15), residues: 909 sheet: -2.35 (0.92), residues: 35 loop : -2.99 (0.29), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.005 ARG B 621 TYR 0.024 0.003 TYR A 571 PHE 0.044 0.003 PHE G 182 TRP 0.062 0.003 TRP C 573 HIS 0.013 0.002 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.32 (10628) covalent geometry : angle 0.82209 / 0.46 (14345) SS BOND : bond 0.00618 / 0.40 ( 8) SS BOND : angle 2.52720 / 1.66 ( 16) hydrogen bonds : bond 0.24009 / 15.74 ( 709) hydrogen bonds : angle 8.71159 / 6.28 ( 2091) Misc. bond : bond 0.00620 / 0.31 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 555 TYR cc_start: 0.9135 (t80) cc_final: 0.8881 (t80) REVERT: E 76 LEU cc_start: 0.7514 (tt) cc_final: 0.7128 (mt) REVERT: F 204 ARG cc_start: 0.7941 (mtt90) cc_final: 0.7733 (mtt90) REVERT: G 174 TYR cc_start: 0.8274 (p90) cc_final: 0.7787 (p90) REVERT: H 11 LEU cc_start: 0.8425 (tp) cc_final: 0.8184 (mt) REVERT: H 99 ARG cc_start: 0.7763 (mtt-85) cc_final: 0.7546 (mtt90) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1111 time to fit residues: 28.6545 Evaluate side-chains 154 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 79 GLN F 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.103496 restraints weight = 25198.853| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.34 r_work: 0.2912 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10640 Z= 0.133 Angle : 0.545 7.537 14361 Z= 0.296 Chirality : 0.038 0.257 1616 Planarity : 0.004 0.039 1729 Dihedral : 7.980 108.011 1540 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.04 % Allowed : 5.57 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.23), residues: 1263 helix: 0.47 (0.17), residues: 918 sheet: -1.73 (1.09), residues: 28 loop : -1.98 (0.30), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 204 TYR 0.013 0.001 TYR F 181 PHE 0.016 0.002 PHE G 107 TRP 0.021 0.001 TRP C 573 HIS 0.010 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (10628) covalent geometry : angle 0.54271 / 0.30 (14345) SS BOND : bond 0.00240 / 0.13 ( 8) SS BOND : angle 1.47328 / 0.86 ( 16) hydrogen bonds : bond 0.04823 / 3.18 ( 709) hydrogen bonds : angle 3.92120 / 2.75 ( 2091) Misc. bond : bond 0.00059 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 76 LEU cc_start: 0.7081 (tt) cc_final: 0.6827 (mp) REVERT: F 58 MET cc_start: 0.7812 (mmm) cc_final: 0.7488 (tpt) REVERT: G 37 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7680 (ttt90) REVERT: H 11 LEU cc_start: 0.8628 (tp) cc_final: 0.8106 (mt) REVERT: H 73 PHE cc_start: 0.6193 (m-80) cc_final: 0.5827 (m-80) REVERT: H 76 LEU cc_start: 0.7933 (mm) cc_final: 0.7416 (mm) outliers start: 11 outliers final: 5 residues processed: 174 average time/residue: 0.1053 time to fit residues: 24.8666 Evaluate side-chains 151 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain C residue 572 GLU Chi-restraints excluded: chain H residue 22 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 95 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 641 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 813 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.124263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.093244 restraints weight = 22777.510| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.32 r_work: 0.2761 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 10640 Z= 0.293 Angle : 0.641 8.212 14361 Z= 0.341 Chirality : 0.043 0.272 1616 Planarity : 0.004 0.043 1729 Dihedral : 8.994 100.679 1540 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.08 % Allowed : 8.02 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.23), residues: 1263 helix: 1.13 (0.17), residues: 919 sheet: -1.83 (1.03), residues: 26 loop : -1.66 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 567 TYR 0.026 0.002 TYR A 571 PHE 0.018 0.002 PHE D 563 TRP 0.023 0.002 TRP C 573 HIS 0.007 0.002 HIS H 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.29 (10628) covalent geometry : angle 0.63867 / 0.34 (14345) SS BOND : bond 0.00431 / 0.28 ( 8) SS BOND : angle 1.69428 / 0.99 ( 16) hydrogen bonds : bond 0.05342 / 3.52 ( 709) hydrogen bonds : angle 3.88307 / 2.72 ( 2091) Misc. bond : bond 0.00081 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: C 572 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: E 73 PHE cc_start: 0.7164 (m-80) cc_final: 0.6564 (m-80) REVERT: G 37 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7807 (ttt90) REVERT: H 11 LEU cc_start: 0.8657 (tp) cc_final: 0.8162 (mt) REVERT: H 76 LEU cc_start: 0.7623 (mm) cc_final: 0.7398 (mm) REVERT: H 99 ARG cc_start: 0.8540 (mtt90) cc_final: 0.8107 (mtp85) REVERT: H 129 LYS cc_start: 0.7765 (mttp) cc_final: 0.7529 (mttt) outliers start: 22 outliers final: 11 residues processed: 170 average time/residue: 0.1040 time to fit residues: 23.6682 Evaluate side-chains 161 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain C residue 572 GLU Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 100 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.122676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.093317 restraints weight = 14703.052| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.92 r_work: 0.2847 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10640 Z= 0.131 Angle : 0.480 8.009 14361 Z= 0.260 Chirality : 0.037 0.244 1616 Planarity : 0.003 0.041 1729 Dihedral : 8.126 97.941 1540 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.08 % Allowed : 9.53 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.64 (0.24), residues: 1263 helix: 2.00 (0.17), residues: 919 sheet: -1.50 (1.01), residues: 26 loop : -1.49 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 204 TYR 0.011 0.001 TYR A 571 PHE 0.011 0.001 PHE D 836 TRP 0.012 0.001 TRP C 573 HIS 0.005 0.001 HIS H 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10628) covalent geometry : angle 0.47790 / 0.26 (14345) SS BOND : bond 0.00195 / 0.12 ( 8) SS BOND : angle 1.27177 / 0.75 ( 16) hydrogen bonds : bond 0.04147 / 2.73 ( 709) hydrogen bonds : angle 3.48277 / 2.44 ( 2091) Misc. bond : bond 0.00027 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: E 10 MET cc_start: 0.8637 (tpp) cc_final: 0.8370 (tpp) REVERT: F 58 MET cc_start: 0.7699 (mmm) cc_final: 0.7401 (tpt) REVERT: G 37 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7840 (ttt90) REVERT: G 74 LYS cc_start: 0.7934 (tppp) cc_final: 0.7649 (tppt) REVERT: H 11 LEU cc_start: 0.8608 (tp) cc_final: 0.8111 (mt) REVERT: H 99 ARG cc_start: 0.8512 (mtt90) cc_final: 0.8015 (mtp85) outliers start: 22 outliers final: 14 residues processed: 157 average time/residue: 0.1235 time to fit residues: 26.2438 Evaluate side-chains 156 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain C residue 572 GLU Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 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 = 0.3343 r_free = 0.3343 target = 0.122809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.090746 restraints weight = 30477.876| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.74 r_work: 0.2758 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10640 Z= 0.134 Angle : 0.473 8.218 14361 Z= 0.255 Chirality : 0.037 0.237 1616 Planarity : 0.003 0.040 1729 Dihedral : 7.822 94.161 1540 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.98 % Allowed : 10.09 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.12 (0.24), residues: 1263 helix: 2.38 (0.17), residues: 920 sheet: -1.44 (1.01), residues: 26 loop : -1.41 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 567 TYR 0.012 0.001 TYR A 571 PHE 0.011 0.001 PHE D 836 TRP 0.010 0.001 TRP C 573 HIS 0.012 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (10628) covalent geometry : angle 0.47062 / 0.25 (14345) SS BOND : bond 0.00182 / 0.11 ( 8) SS BOND : angle 1.35496 / 0.79 ( 16) hydrogen bonds : bond 0.04080 / 2.69 ( 709) hydrogen bonds : angle 3.39898 / 2.38 ( 2091) Misc. bond : bond 0.00029 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: E 10 MET cc_start: 0.8583 (tpp) cc_final: 0.8325 (tpp) REVERT: E 160 ASN cc_start: 0.8378 (m-40) cc_final: 0.8130 (m-40) REVERT: F 58 MET cc_start: 0.7695 (mmm) cc_final: 0.7354 (tpt) REVERT: G 37 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7854 (ttt90) REVERT: H 11 LEU cc_start: 0.8589 (tp) cc_final: 0.8115 (mt) REVERT: H 99 ARG cc_start: 0.8423 (mtt90) cc_final: 0.7918 (mtp85) outliers start: 21 outliers final: 17 residues processed: 153 average time/residue: 0.1148 time to fit residues: 23.5562 Evaluate side-chains 155 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.125710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.094467 restraints weight = 25437.331| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.56 r_work: 0.2812 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10640 Z= 0.115 Angle : 0.452 8.243 14361 Z= 0.244 Chirality : 0.036 0.235 1616 Planarity : 0.003 0.040 1729 Dihedral : 7.505 90.700 1540 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.98 % Allowed : 10.38 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.56 (0.24), residues: 1263 helix: 2.74 (0.17), residues: 920 sheet: -0.82 (1.02), residues: 26 loop : -1.39 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 616 TYR 0.010 0.001 TYR F 181 PHE 0.009 0.001 PHE F 201 TRP 0.009 0.001 TRP F 178 HIS 0.010 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (10628) covalent geometry : angle 0.44929 / 0.24 (14345) SS BOND : bond 0.00155 / 0.10 ( 8) SS BOND : angle 1.54871 / 0.98 ( 16) hydrogen bonds : bond 0.03850 / 2.54 ( 709) hydrogen bonds : angle 3.31546 / 2.31 ( 2091) Misc. bond : bond 0.00020 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: E 10 MET cc_start: 0.8572 (tpp) cc_final: 0.8319 (tpp) REVERT: E 160 ASN cc_start: 0.8373 (m-40) cc_final: 0.8142 (m-40) REVERT: F 56 GLU cc_start: 0.6336 (mm-30) cc_final: 0.6079 (mm-30) REVERT: F 58 MET cc_start: 0.7801 (mmm) cc_final: 0.7439 (tpt) REVERT: H 11 LEU cc_start: 0.8583 (tp) cc_final: 0.8103 (mt) REVERT: H 99 ARG cc_start: 0.8473 (mtt90) cc_final: 0.7959 (mtp85) outliers start: 21 outliers final: 16 residues processed: 153 average time/residue: 0.1276 time to fit residues: 26.3300 Evaluate side-chains 152 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 151 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 chunk 26 optimal weight: 0.0670 chunk 88 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.127266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.095314 restraints weight = 25959.773| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.45 r_work: 0.2843 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10640 Z= 0.106 Angle : 0.443 8.275 14361 Z= 0.237 Chirality : 0.036 0.230 1616 Planarity : 0.003 0.041 1729 Dihedral : 7.268 86.188 1540 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.70 % Allowed : 11.23 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.87 (0.24), residues: 1263 helix: 3.01 (0.17), residues: 918 sheet: -0.50 (1.02), residues: 26 loop : -1.43 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 616 TYR 0.008 0.001 TYR F 181 PHE 0.009 0.001 PHE F 201 TRP 0.008 0.001 TRP F 178 HIS 0.009 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (10628) covalent geometry : angle 0.43981 / 0.24 (14345) SS BOND : bond 0.00169 / 0.11 ( 8) SS BOND : angle 1.55439 / 0.99 ( 16) hydrogen bonds : bond 0.03699 / 2.44 ( 709) hydrogen bonds : angle 3.25435 / 2.27 ( 2091) Misc. bond : bond 0.00015 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: E 10 MET cc_start: 0.8629 (tpp) cc_final: 0.8390 (tpp) REVERT: E 160 ASN cc_start: 0.8317 (m-40) cc_final: 0.8113 (m-40) REVERT: F 56 GLU cc_start: 0.6327 (mm-30) cc_final: 0.6101 (mm-30) REVERT: F 58 MET cc_start: 0.7850 (mmm) cc_final: 0.7454 (tpt) REVERT: G 37 ARG cc_start: 0.8282 (ttm-80) cc_final: 0.8031 (ttm-80) REVERT: H 11 LEU cc_start: 0.8583 (tp) cc_final: 0.8102 (mt) REVERT: H 99 ARG cc_start: 0.8477 (mtt90) cc_final: 0.7989 (mtp85) outliers start: 18 outliers final: 16 residues processed: 149 average time/residue: 0.1135 time to fit residues: 22.9961 Evaluate side-chains 154 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 151 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 39 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.096959 restraints weight = 20751.982| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.26 r_work: 0.2849 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10640 Z= 0.124 Angle : 0.458 8.315 14361 Z= 0.245 Chirality : 0.036 0.234 1616 Planarity : 0.003 0.042 1729 Dihedral : 7.345 81.887 1540 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.70 % Allowed : 11.51 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.97 (0.24), residues: 1263 helix: 3.08 (0.17), residues: 918 sheet: -0.34 (1.03), residues: 26 loop : -1.42 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 616 TYR 0.011 0.001 TYR A 571 PHE 0.010 0.001 PHE H 201 TRP 0.008 0.001 TRP F 178 HIS 0.015 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (10628) covalent geometry : angle 0.45449 / 0.24 (14345) SS BOND : bond 0.00154 / 0.10 ( 8) SS BOND : angle 1.70820 / 1.07 ( 16) hydrogen bonds : bond 0.03876 / 2.56 ( 709) hydrogen bonds : angle 3.29142 / 2.30 ( 2091) Misc. bond : bond 0.00021 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 10 MET cc_start: 0.8620 (tpp) cc_final: 0.8366 (tpp) REVERT: E 160 ASN cc_start: 0.8332 (m-40) cc_final: 0.8122 (m-40) REVERT: F 129 LYS cc_start: 0.8091 (mptt) cc_final: 0.7321 (mmmt) REVERT: G 37 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.8082 (ttm-80) REVERT: H 11 LEU cc_start: 0.8585 (tp) cc_final: 0.8102 (mt) REVERT: H 99 ARG cc_start: 0.8474 (mtt90) cc_final: 0.7978 (mtp85) outliers start: 18 outliers final: 16 residues processed: 148 average time/residue: 0.1280 time to fit residues: 25.5802 Evaluate side-chains 151 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 68 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 9 GLN H 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.097731 restraints weight = 25505.532| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.53 r_work: 0.2819 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10640 Z= 0.120 Angle : 0.453 8.306 14361 Z= 0.242 Chirality : 0.036 0.233 1616 Planarity : 0.003 0.042 1729 Dihedral : 7.259 78.462 1540 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.89 % Allowed : 11.42 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.12 (0.24), residues: 1263 helix: 3.18 (0.16), residues: 918 sheet: 0.01 (1.04), residues: 26 loop : -1.35 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 616 TYR 0.011 0.001 TYR A 571 PHE 0.009 0.001 PHE F 201 TRP 0.008 0.001 TRP F 178 HIS 0.014 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (10628) covalent geometry : angle 0.44934 / 0.24 (14345) SS BOND : bond 0.00108 / 0.07 ( 8) SS BOND : angle 1.78109 / 1.09 ( 16) hydrogen bonds : bond 0.03819 / 2.52 ( 709) hydrogen bonds : angle 3.25823 / 2.28 ( 2091) Misc. bond : bond 0.00018 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 10 MET cc_start: 0.8612 (tpp) cc_final: 0.8354 (tpp) REVERT: E 160 ASN cc_start: 0.8341 (m-40) cc_final: 0.8072 (m-40) REVERT: F 58 MET cc_start: 0.7800 (mmm) cc_final: 0.7458 (tpt) REVERT: F 129 LYS cc_start: 0.8088 (mptt) cc_final: 0.7313 (mmmt) REVERT: G 37 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.8110 (ttm-80) REVERT: H 11 LEU cc_start: 0.8570 (tp) cc_final: 0.8076 (mt) REVERT: H 99 ARG cc_start: 0.8499 (mtt90) cc_final: 0.7988 (mtp85) outliers start: 20 outliers final: 17 residues processed: 149 average time/residue: 0.1299 time to fit residues: 25.8812 Evaluate side-chains 152 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 115 optimal weight: 0.0010 chunk 119 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.097155 restraints weight = 20451.095| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.24 r_work: 0.2847 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10640 Z= 0.133 Angle : 0.468 8.343 14361 Z= 0.250 Chirality : 0.037 0.234 1616 Planarity : 0.003 0.044 1729 Dihedral : 7.345 74.996 1540 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.70 % Allowed : 11.70 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.08 (0.24), residues: 1263 helix: 3.14 (0.16), residues: 918 sheet: -0.71 (0.99), residues: 30 loop : -1.27 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 616 TYR 0.012 0.001 TYR A 571 PHE 0.011 0.001 PHE H 201 TRP 0.008 0.001 TRP F 178 HIS 0.014 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (10628) covalent geometry : angle 0.46386 / 0.25 (14345) SS BOND : bond 0.00181 / 0.10 ( 8) SS BOND : angle 2.00484 / 1.22 ( 16) hydrogen bonds : bond 0.03961 / 2.61 ( 709) hydrogen bonds : angle 3.28970 / 2.30 ( 2091) Misc. bond : bond 0.00020 / 0.01 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 10 MET cc_start: 0.8640 (tpp) cc_final: 0.8377 (tpp) REVERT: E 160 ASN cc_start: 0.8348 (m-40) cc_final: 0.8048 (m-40) REVERT: F 58 MET cc_start: 0.7797 (mmm) cc_final: 0.7464 (tpt) REVERT: F 129 LYS cc_start: 0.8080 (mptt) cc_final: 0.7341 (mmmt) REVERT: G 37 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.8101 (ttm-80) REVERT: H 11 LEU cc_start: 0.8560 (tp) cc_final: 0.8088 (mt) REVERT: H 99 ARG cc_start: 0.8508 (mtt90) cc_final: 0.8004 (mtp85) outliers start: 18 outliers final: 17 residues processed: 147 average time/residue: 0.1302 time to fit residues: 25.5577 Evaluate side-chains 152 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 611 CYS Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 33 optimal weight: 0.0010 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.130847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.100528 restraints weight = 18678.510| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.07 r_work: 0.2896 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10640 Z= 0.111 Angle : 0.447 8.277 14361 Z= 0.239 Chirality : 0.036 0.231 1616 Planarity : 0.003 0.044 1729 Dihedral : 7.149 71.107 1540 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.70 % Allowed : 11.60 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.28 (0.24), residues: 1263 helix: 3.30 (0.16), residues: 918 sheet: 0.18 (1.06), residues: 26 loop : -1.31 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 616 TYR 0.009 0.001 TYR A 571 PHE 0.009 0.001 PHE F 201 TRP 0.008 0.001 TRP F 178 HIS 0.013 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10628) covalent geometry : angle 0.44214 / 0.24 (14345) SS BOND : bond 0.00128 / 0.08 ( 8) SS BOND : angle 1.92459 / 1.15 ( 16) hydrogen bonds : bond 0.03730 / 2.46 ( 709) hydrogen bonds : angle 3.19807 / 2.23 ( 2091) Misc. bond : bond 0.00017 / 0.01 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2925.97 seconds wall clock time: 50 minutes 47.18 seconds (3047.18 seconds total)