Starting phenix.real_space_refine on Wed Feb 4 11:58:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rn7_54083/02_2026/9rn7_54083.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rn7_54083/02_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_54083/02_2026/9rn7_54083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rn7_54083/02_2026/9rn7_54083.map" model { file = "/net/cci-nas-00/data/ceres_data/9rn7_54083/02_2026/9rn7_54083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rn7_54083/02_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-2.0-5952/lib/python3.9/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, 43 Unusual residues: {' CA': 1, 'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 3.59, per 1000 atoms: 0.35 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: 0.97 Conformation dependent library (CDL) restraints added in 658.5 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: 0.30 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: 1.69 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 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: 4.260 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.620 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 covalent geometry : bond 0.00743 (10628) covalent geometry : angle 0.82209 (14345) SS BOND : bond 0.00618 ( 8) SS BOND : angle 2.52720 ( 16) hydrogen bonds : bond 0.24009 ( 709) hydrogen bonds : angle 8.71159 ( 2091) Misc. bond : bond 0.00620 ( 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 : 0.378 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: 0.1394 time to fit residues: 35.5016 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 : 0.418 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 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 covalent geometry : bond 0.00284 (10628) covalent geometry : angle 0.54271 (14345) SS BOND : bond 0.00240 ( 8) SS BOND : angle 1.47328 ( 16) hydrogen bonds : bond 0.04823 ( 709) hydrogen bonds : angle 3.92120 ( 2091) Misc. bond : bond 0.00059 ( 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 : 0.475 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: 0.1262 time to fit residues: 29.3688 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 : 0.366 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 | |-----------------------------------------------------------------------------| r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 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 covalent geometry : bond 0.00712 (10628) covalent geometry : angle 0.63867 (14345) SS BOND : bond 0.00431 ( 8) SS BOND : angle 1.69428 ( 16) hydrogen bonds : bond 0.05342 ( 709) hydrogen bonds : angle 3.88307 ( 2091) Misc. bond : bond 0.00081 ( 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 : 0.347 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: 0.1173 time to fit residues: 26.6533 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 : 0.374 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 | |-----------------------------------------------------------------------------| r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 covalent geometry : bond 0.00298 (10628) covalent geometry : angle 0.47790 (14345) SS BOND : bond 0.00195 ( 8) SS BOND : angle 1.27177 ( 16) hydrogen bonds : bond 0.04147 ( 709) hydrogen bonds : angle 3.48277 ( 2091) Misc. bond : bond 0.00027 ( 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 : 0.233 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: 0.1157 time to fit residues: 24.4151 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 : 0.478 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 | |-----------------------------------------------------------------------------| r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 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 covalent geometry : bond 0.00309 (10628) covalent geometry : angle 0.47062 (14345) SS BOND : bond 0.00182 ( 8) SS BOND : angle 1.35496 ( 16) hydrogen bonds : bond 0.04080 ( 709) hydrogen bonds : angle 3.39898 ( 2091) Misc. bond : bond 0.00029 ( 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 : 0.309 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: 0.1115 time to fit residues: 22.6286 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 : 0.292 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 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 covalent geometry : bond 0.00256 (10628) covalent geometry : angle 0.44929 (14345) SS BOND : bond 0.00155 ( 8) SS BOND : angle 1.54871 ( 16) hydrogen bonds : bond 0.03850 ( 709) hydrogen bonds : angle 3.31546 ( 2091) Misc. bond : bond 0.00020 ( 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 : 0.329 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: G 74 LYS cc_start: 0.7523 (tppt) cc_final: 0.7125 (mmtp) 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: 0.1286 time to fit residues: 26.3213 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 : 0.320 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.125506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.092893 restraints weight = 26157.455| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.54 r_work: 0.2840 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3214 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= 0.105 Angle : 0.441 8.260 14361 Z= 0.236 Chirality : 0.036 0.229 1616 Planarity : 0.003 0.041 1729 Dihedral : 7.233 85.512 1540 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: 2.91 (0.24), residues: 1263 helix: 3.03 (0.17), residues: 918 sheet: -0.46 (1.02), residues: 26 loop : -1.41 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 616 TYR 0.008 0.001 TYR A 555 PHE 0.009 0.001 PHE F 201 TRP 0.008 0.001 TRP F 178 HIS 0.008 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00230 (10628) covalent geometry : angle 0.43800 (14345) SS BOND : bond 0.00163 ( 8) SS BOND : angle 1.56330 ( 16) hydrogen bonds : bond 0.03681 ( 709) hydrogen bonds : angle 3.24452 ( 2091) Misc. bond : bond 0.00014 ( 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 160 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: E 10 MET cc_start: 0.8607 (tpp) cc_final: 0.8378 (tpp) REVERT: F 58 MET cc_start: 0.7729 (mmm) cc_final: 0.7329 (tpt) REVERT: G 74 LYS cc_start: 0.7281 (tppt) cc_final: 0.6939 (mmtp) REVERT: H 11 LEU cc_start: 0.8555 (tp) cc_final: 0.8093 (mt) REVERT: H 99 ARG cc_start: 0.8348 (mtt90) cc_final: 0.7862 (mtp85) outliers start: 18 outliers final: 16 residues processed: 152 average time/residue: 0.1173 time to fit residues: 23.7340 Evaluate side-chains 156 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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: 0.6980 chunk 122 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3374 r_free = 0.3374 target = 0.125351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.093427 restraints weight = 21166.760| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.32 r_work: 0.2849 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 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 = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3248 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= 0.112 Angle : 0.446 8.286 14361 Z= 0.239 Chirality : 0.036 0.233 1616 Planarity : 0.003 0.041 1729 Dihedral : 7.204 80.181 1540 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.79 % Allowed : 11.32 % Favored : 86.89 % 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: 3.09 (0.24), residues: 1263 helix: 3.17 (0.17), residues: 918 sheet: -0.28 (1.03), residues: 26 loop : -1.36 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.015 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00252 (10628) covalent geometry : angle 0.44292 (14345) SS BOND : bond 0.00108 ( 8) SS BOND : angle 1.62329 ( 16) hydrogen bonds : bond 0.03742 ( 709) hydrogen bonds : angle 3.24437 ( 2091) Misc. bond : bond 0.00017 ( 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: 19 poor density : 136 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: E 10 MET cc_start: 0.8601 (tpp) cc_final: 0.8358 (tpp) REVERT: F 58 MET cc_start: 0.7816 (mmm) cc_final: 0.7398 (tpt) REVERT: F 129 LYS cc_start: 0.8081 (mptt) cc_final: 0.7300 (mmmt) REVERT: G 37 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.8083 (ttm-80) REVERT: G 74 LYS cc_start: 0.7371 (tppt) cc_final: 0.7018 (mmtp) REVERT: H 11 LEU cc_start: 0.8573 (tp) cc_final: 0.8068 (mt) REVERT: H 99 ARG cc_start: 0.8456 (mtt90) cc_final: 0.7944 (mtp85) outliers start: 19 outliers final: 17 residues processed: 148 average time/residue: 0.1260 time to fit residues: 24.6716 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 : 0.231 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 19 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 115 optimal weight: 0.4980 chunk 109 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.129860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.097445 restraints weight = 25586.582| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.49 r_work: 0.2840 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10640 Z= 0.115 Angle : 0.448 8.294 14361 Z= 0.240 Chirality : 0.036 0.232 1616 Planarity : 0.003 0.042 1729 Dihedral : 7.168 74.639 1540 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.79 % Allowed : 11.60 % 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: 3.20 (0.24), residues: 1263 helix: 3.24 (0.16), residues: 917 sheet: -0.07 (1.01), residues: 26 loop : -1.30 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 616 TYR 0.010 0.001 TYR A 571 PHE 0.013 0.001 PHE E 127 TRP 0.008 0.001 TRP F 178 HIS 0.014 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00260 (10628) covalent geometry : angle 0.44406 (14345) SS BOND : bond 0.00126 ( 8) SS BOND : angle 1.76629 ( 16) hydrogen bonds : bond 0.03771 ( 709) hydrogen bonds : angle 3.22227 ( 2091) Misc. bond : bond 0.00017 ( 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 158 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: E 10 MET cc_start: 0.8634 (tpp) cc_final: 0.8378 (tpp) REVERT: E 64 TRP cc_start: 0.9122 (m100) cc_final: 0.8861 (m100) REVERT: F 129 LYS cc_start: 0.8080 (mptt) cc_final: 0.7319 (mmmt) REVERT: G 37 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.8091 (ttm-80) REVERT: G 74 LYS cc_start: 0.7445 (tppt) cc_final: 0.7001 (mmtp) REVERT: H 11 LEU cc_start: 0.8548 (tp) cc_final: 0.8093 (mt) REVERT: H 99 ARG cc_start: 0.8538 (mtt90) cc_final: 0.8039 (mtp85) outliers start: 19 outliers final: 16 residues processed: 151 average time/residue: 0.1360 time to fit residues: 27.0865 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 : 0.390 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.0170 chunk 61 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.125073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.093485 restraints weight = 20869.980| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.28 r_work: 0.2841 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 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 = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3297 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= 0.122 Angle : 0.456 8.311 14361 Z= 0.244 Chirality : 0.036 0.233 1616 Planarity : 0.003 0.043 1729 Dihedral : 7.205 70.449 1540 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: 3.21 (0.24), residues: 1263 helix: 3.23 (0.16), residues: 918 sheet: 0.26 (1.07), residues: 26 loop : -1.28 (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 0.014 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00280 (10628) covalent geometry : angle 0.45165 (14345) SS BOND : bond 0.00128 ( 8) SS BOND : angle 1.92559 ( 16) hydrogen bonds : bond 0.03840 ( 709) hydrogen bonds : angle 3.23293 ( 2091) Misc. bond : bond 0.00018 ( 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 155 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: E 10 MET cc_start: 0.8622 (tpp) cc_final: 0.8364 (tpp) REVERT: F 58 MET cc_start: 0.7768 (mmm) cc_final: 0.7432 (tpt) REVERT: F 129 LYS cc_start: 0.8075 (mptt) cc_final: 0.7327 (mmmt) REVERT: G 37 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.8069 (ttm-80) REVERT: G 74 LYS cc_start: 0.7472 (tppt) cc_final: 0.7045 (mmtp) REVERT: H 11 LEU cc_start: 0.8552 (tp) cc_final: 0.8075 (mt) REVERT: H 99 ARG cc_start: 0.8509 (mtt90) cc_final: 0.7995 (mtp85) outliers start: 18 outliers final: 17 residues processed: 148 average time/residue: 0.1182 time to fit residues: 23.3893 Evaluate side-chains 153 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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: 0.0980 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 25 optimal weight: 0.0000 chunk 36 optimal weight: 0.0980 chunk 125 optimal weight: 2.9990 overall best weight: 0.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN H 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.134216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.104133 restraints weight = 18655.220| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.06 r_work: 0.2923 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10640 Z= 0.089 Angle : 0.419 8.177 14361 Z= 0.224 Chirality : 0.035 0.228 1616 Planarity : 0.003 0.043 1729 Dihedral : 6.791 63.426 1540 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.42 % Allowed : 11.79 % 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: 3.60 (0.24), residues: 1263 helix: 3.55 (0.16), residues: 917 sheet: 0.28 (1.07), residues: 26 loop : -1.21 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 616 TYR 0.007 0.001 TYR B 555 PHE 0.009 0.001 PHE F 201 TRP 0.008 0.001 TRP G 178 HIS 0.014 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00179 (10628) covalent geometry : angle 0.41573 (14345) SS BOND : bond 0.00116 ( 8) SS BOND : angle 1.68687 ( 16) hydrogen bonds : bond 0.03346 ( 709) hydrogen bonds : angle 3.05667 ( 2091) Misc. bond : bond 0.00013 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2856.19 seconds wall clock time: 49 minutes 25.60 seconds (2965.60 seconds total)