Starting phenix.real_space_refine on Mon Dec 11 03:11:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/12_2023/8bc4_15962_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/12_2023/8bc4_15962.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/12_2023/8bc4_15962_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/12_2023/8bc4_15962_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/12_2023/8bc4_15962_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/12_2023/8bc4_15962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/12_2023/8bc4_15962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/12_2023/8bc4_15962_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/12_2023/8bc4_15962_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 10399 2.51 5 N 2679 2.21 5 O 3315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 14": "NH1" <-> "NH2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 104": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "G ARG 14": "NH1" <-> "NH2" Residue "G TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 104": "OE1" <-> "OE2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "H ARG 14": "NH1" <-> "NH2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "I ARG 14": "NH1" <-> "NH2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 104": "OE1" <-> "OE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "I ARG 171": "NH1" <-> "NH2" Residue "I ARG 211": "NH1" <-> "NH2" Residue "J ARG 14": "NH1" <-> "NH2" Residue "J GLU 104": "OE1" <-> "OE2" Residue "J GLU 140": "OE1" <-> "OE2" Residue "J ARG 171": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 16440 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1607 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1602 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1596 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1617 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1615 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 53 Chain: "F" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1613 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 53 Chain: "G" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1604 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "H" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1598 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "I" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1587 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 67 Chain: "J" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1605 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 57 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "I" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "J" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 9.17, per 1000 atoms: 0.56 Number of scatterers: 16440 At special positions: 0 Unit cell: (115.2, 115.2, 86.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 3315 8.00 N 2679 7.00 C 10399 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.72 Conformation dependent library (CDL) restraints added in 3.1 seconds 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 11 sheets defined 49.9% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'A' and resid 39 through 49 Processing helix chain 'A' and resid 69 through 82 removed outlier: 3.516A pdb=" N LYS A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.627A pdb=" N ALA A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 removed outlier: 4.016A pdb=" N GLN A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 137 through 142 removed outlier: 3.625A pdb=" N SER A 142 " --> pdb=" O TRP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 173 through 182 Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 201 through 216 removed outlier: 3.584A pdb=" N ASP A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 39 through 49 Processing helix chain 'B' and resid 75 through 81 Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 119 through 126 removed outlier: 4.145A pdb=" N GLN B 123 " --> pdb=" O SER B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix No H-bonds generated for 'chain 'B' and resid 119 through 126' Processing helix chain 'B' and resid 137 through 142 removed outlier: 3.625A pdb=" N SER B 142 " --> pdb=" O TRP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 158 Processing helix chain 'B' and resid 173 through 182 Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'C' and resid 10 through 19 removed outlier: 3.540A pdb=" N TYR C 15 " --> pdb=" O GLU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 34 No H-bonds generated for 'chain 'C' and resid 31 through 34' Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 69 through 78 Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 118 through 126 removed outlier: 4.082A pdb=" N GLN C 123 " --> pdb=" O SER C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 137 through 142 removed outlier: 3.625A pdb=" N SER C 142 " --> pdb=" O TRP C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 173 through 182 Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'D' and resid 10 through 19 Processing helix chain 'D' and resid 29 through 35 Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 69 through 75 removed outlier: 3.749A pdb=" N GLU D 74 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 75 " --> pdb=" O ASP D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 82 removed outlier: 3.716A pdb=" N LYS D 81 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU D 82 " --> pdb=" O LYS D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 77 through 82' Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 118 through 127 removed outlier: 4.243A pdb=" N GLN D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Proline residue: D 124 - end of helix Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'D' and resid 151 through 158 Processing helix chain 'D' and resid 173 through 182 Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 201 through 216 removed outlier: 3.546A pdb=" N ASP D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 19 Processing helix chain 'E' and resid 29 through 35 Processing helix chain 'E' and resid 39 through 49 removed outlier: 3.779A pdb=" N ALA E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER E 48 " --> pdb=" O ASP E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 81 removed outlier: 3.783A pdb=" N THR E 77 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 79 " --> pdb=" O GLU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 106 Processing helix chain 'E' and resid 118 through 126 removed outlier: 4.022A pdb=" N GLN E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 137 through 142 removed outlier: 3.625A pdb=" N SER E 142 " --> pdb=" O TRP E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 173 through 182 Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 202 through 215 removed outlier: 3.730A pdb=" N GLY E 206 " --> pdb=" O PHE E 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 19 Processing helix chain 'F' and resid 29 through 35 removed outlier: 3.701A pdb=" N MET F 33 " --> pdb=" O PRO F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 49 Processing helix chain 'F' and resid 69 through 82 removed outlier: 3.645A pdb=" N THR F 77 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 105 Processing helix chain 'F' and resid 120 through 127 Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 137 through 142 removed outlier: 3.624A pdb=" N SER F 142 " --> pdb=" O TRP F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 158 Processing helix chain 'F' and resid 173 through 182 Processing helix chain 'F' and resid 191 through 198 Processing helix chain 'F' and resid 201 through 216 Processing helix chain 'G' and resid 10 through 20 Processing helix chain 'G' and resid 39 through 49 Processing helix chain 'G' and resid 69 through 82 removed outlier: 3.653A pdb=" N LEU G 82 " --> pdb=" O LYS G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 105 Processing helix chain 'G' and resid 120 through 123 No H-bonds generated for 'chain 'G' and resid 120 through 123' Processing helix chain 'G' and resid 125 through 127 No H-bonds generated for 'chain 'G' and resid 125 through 127' Processing helix chain 'G' and resid 137 through 142 removed outlier: 3.626A pdb=" N SER G 142 " --> pdb=" O TRP G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 159 Processing helix chain 'G' and resid 173 through 182 Processing helix chain 'G' and resid 191 through 198 Processing helix chain 'G' and resid 201 through 215 Processing helix chain 'H' and resid 10 through 19 Processing helix chain 'H' and resid 29 through 35 Processing helix chain 'H' and resid 39 through 49 Processing helix chain 'H' and resid 69 through 82 removed outlier: 3.591A pdb=" N LYS H 78 " --> pdb=" O GLU H 74 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 105 Processing helix chain 'H' and resid 119 through 127 removed outlier: 4.017A pdb=" N GLN H 123 " --> pdb=" O SER H 119 " (cutoff:3.500A) Proline residue: H 124 - end of helix Processing helix chain 'H' and resid 151 through 158 Processing helix chain 'H' and resid 173 through 182 Processing helix chain 'H' and resid 191 through 198 Processing helix chain 'H' and resid 201 through 216 Processing helix chain 'I' and resid 10 through 19 Processing helix chain 'I' and resid 29 through 35 Processing helix chain 'I' and resid 39 through 49 Processing helix chain 'I' and resid 69 through 81 removed outlier: 3.501A pdb=" N GLU I 74 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR I 77 " --> pdb=" O VAL I 73 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS I 78 " --> pdb=" O GLU I 74 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE I 79 " --> pdb=" O GLU I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 106 Processing helix chain 'I' and resid 119 through 126 removed outlier: 4.017A pdb=" N GLN I 123 " --> pdb=" O SER I 119 " (cutoff:3.500A) Proline residue: I 124 - end of helix No H-bonds generated for 'chain 'I' and resid 119 through 126' Processing helix chain 'I' and resid 137 through 142 removed outlier: 3.974A pdb=" N SER I 142 " --> pdb=" O TRP I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 158 removed outlier: 3.564A pdb=" N VAL I 153 " --> pdb=" O ILE I 149 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS I 157 " --> pdb=" O VAL I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 182 removed outlier: 3.737A pdb=" N ALA I 180 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 198 Processing helix chain 'I' and resid 201 through 214 removed outlier: 3.880A pdb=" N GLY I 206 " --> pdb=" O PHE I 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 19 Processing helix chain 'J' and resid 29 through 35 Processing helix chain 'J' and resid 39 through 49 Processing helix chain 'J' and resid 69 through 81 removed outlier: 3.840A pdb=" N LYS J 78 " --> pdb=" O GLU J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 104 Processing helix chain 'J' and resid 118 through 127 removed outlier: 4.264A pdb=" N GLN J 123 " --> pdb=" O SER J 119 " (cutoff:3.500A) Proline residue: J 124 - end of helix Processing helix chain 'J' and resid 137 through 142 removed outlier: 3.625A pdb=" N SER J 142 " --> pdb=" O TRP J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 158 Processing helix chain 'J' and resid 173 through 182 Processing helix chain 'J' and resid 191 through 198 Processing helix chain 'J' and resid 201 through 215 Processing sheet with id= A, first strand: chain 'A' and resid 2 through 5 Processing sheet with id= B, first strand: chain 'A' and resid 58 through 61 Processing sheet with id= C, first strand: chain 'B' and resid 186 through 189 removed outlier: 6.413A pdb=" N LYS B 2 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N CYS B 189 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 4 " --> pdb=" O CYS B 189 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY B 24 " --> pdb=" O LEU B 5 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 186 through 189 removed outlier: 6.502A pdb=" N LYS C 2 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS C 189 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE C 4 " --> pdb=" O CYS C 189 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY C 24 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR C 27 " --> pdb=" O PRO C 57 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER C 59 " --> pdb=" O THR C 27 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 186 through 189 removed outlier: 6.502A pdb=" N LYS D 2 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS D 189 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE D 4 " --> pdb=" O CYS D 189 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY D 24 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 186 through 189 removed outlier: 6.403A pdb=" N LYS E 2 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N CYS E 189 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE E 4 " --> pdb=" O CYS E 189 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY E 24 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 186 through 189 removed outlier: 6.503A pdb=" N LYS F 2 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS F 189 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE F 4 " --> pdb=" O CYS F 189 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY F 24 " --> pdb=" O LEU F 5 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 186 through 189 removed outlier: 6.501A pdb=" N LYS G 2 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N CYS G 189 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE G 4 " --> pdb=" O CYS G 189 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLY G 24 " --> pdb=" O LEU G 5 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 186 through 189 removed outlier: 6.598A pdb=" N LYS H 2 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N CYS H 189 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE H 4 " --> pdb=" O CYS H 189 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY H 24 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 186 through 189 removed outlier: 6.561A pdb=" N LYS I 2 " --> pdb=" O VAL I 187 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N CYS I 189 " --> pdb=" O LYS I 2 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE I 4 " --> pdb=" O CYS I 189 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY I 24 " --> pdb=" O LEU I 5 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 186 through 189 removed outlier: 6.519A pdb=" N LYS J 2 " --> pdb=" O VAL J 187 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N CYS J 189 " --> pdb=" O LYS J 2 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE J 4 " --> pdb=" O CYS J 189 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLY J 24 " --> pdb=" O LEU J 5 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1890 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: 4.72 Time building geometry restraints manager: 7.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2665 1.30 - 1.43: 4710 1.43 - 1.57: 9094 1.57 - 1.70: 27 1.70 - 1.84: 65 Bond restraints: 16561 Sorted by residual: bond pdb=" O2 QC9 E 301 " pdb=" S13 QC9 E 301 " ideal model delta sigma weight residual 1.510 1.343 0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" O14 QC9 J 301 " pdb=" S13 QC9 J 301 " ideal model delta sigma weight residual 1.510 1.343 0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" O14 QC9 H 301 " pdb=" S13 QC9 H 301 " ideal model delta sigma weight residual 1.510 1.343 0.167 2.00e-02 2.50e+03 6.93e+01 bond pdb=" O2 QC9 C 301 " pdb=" S13 QC9 C 301 " ideal model delta sigma weight residual 1.510 1.344 0.166 2.00e-02 2.50e+03 6.88e+01 bond pdb=" O2 QC9 F 301 " pdb=" S13 QC9 F 301 " ideal model delta sigma weight residual 1.510 1.344 0.166 2.00e-02 2.50e+03 6.88e+01 ... (remaining 16556 not shown) Histogram of bond angle deviations from ideal: 98.24 - 106.43: 579 106.43 - 114.61: 9196 114.61 - 122.79: 9122 122.79 - 130.98: 3673 130.98 - 139.16: 70 Bond angle restraints: 22640 Sorted by residual: angle pdb=" C3 QC9 G 301 " pdb=" C12 QC9 G 301 " pdb=" S13 QC9 G 301 " ideal model delta sigma weight residual 109.47 139.16 -29.69 3.00e+00 1.11e-01 9.79e+01 angle pdb=" C3 QC9 B 301 " pdb=" C12 QC9 B 301 " pdb=" S13 QC9 B 301 " ideal model delta sigma weight residual 109.47 139.10 -29.63 3.00e+00 1.11e-01 9.76e+01 angle pdb=" C3 QC9 H 301 " pdb=" C12 QC9 H 301 " pdb=" S13 QC9 H 301 " ideal model delta sigma weight residual 109.47 139.08 -29.61 3.00e+00 1.11e-01 9.74e+01 angle pdb=" C3 QC9 D 301 " pdb=" C12 QC9 D 301 " pdb=" S13 QC9 D 301 " ideal model delta sigma weight residual 109.47 139.08 -29.61 3.00e+00 1.11e-01 9.74e+01 angle pdb=" C3 QC9 J 301 " pdb=" C12 QC9 J 301 " pdb=" S13 QC9 J 301 " ideal model delta sigma weight residual 109.47 139.07 -29.60 3.00e+00 1.11e-01 9.74e+01 ... (remaining 22635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.19: 9078 33.19 - 66.37: 415 66.37 - 99.56: 42 99.56 - 132.75: 0 132.75 - 165.93: 9 Dihedral angle restraints: 9544 sinusoidal: 3233 harmonic: 6311 Sorted by residual: dihedral pdb=" CD ARG I 171 " pdb=" NE ARG I 171 " pdb=" CZ ARG I 171 " pdb=" NH1 ARG I 171 " ideal model delta sinusoidal sigma weight residual 0.00 85.93 -85.93 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CD ARG G 14 " pdb=" NE ARG G 14 " pdb=" CZ ARG G 14 " pdb=" NH1 ARG G 14 " ideal model delta sinusoidal sigma weight residual 0.00 79.93 -79.93 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CD ARG D 14 " pdb=" NE ARG D 14 " pdb=" CZ ARG D 14 " pdb=" NH1 ARG D 14 " ideal model delta sinusoidal sigma weight residual 0.00 73.27 -73.27 1 1.00e+01 1.00e-02 6.84e+01 ... (remaining 9541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 2232 0.142 - 0.283: 326 0.283 - 0.425: 0 0.425 - 0.566: 9 0.566 - 0.708: 18 Chirality restraints: 2585 Sorted by residual: chirality pdb=" C1 QC9 F 301 " pdb=" C2 QC9 F 301 " pdb=" C4 QC9 F 301 " pdb=" O1 QC9 F 301 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" C1 QC9 J 301 " pdb=" C2 QC9 J 301 " pdb=" C4 QC9 J 301 " pdb=" O1 QC9 J 301 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" C1 QC9 A 301 " pdb=" C2 QC9 A 301 " pdb=" C4 QC9 A 301 " pdb=" O1 QC9 A 301 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 2582 not shown) Planarity restraints: 2926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 14 " 1.099 9.50e-02 1.11e+02 4.93e-01 1.47e+02 pdb=" NE ARG G 14 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG G 14 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG G 14 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG G 14 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 171 " 1.096 9.50e-02 1.11e+02 4.91e-01 1.45e+02 pdb=" NE ARG I 171 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG I 171 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG I 171 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG I 171 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 14 " 1.066 9.50e-02 1.11e+02 4.78e-01 1.38e+02 pdb=" NE ARG D 14 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG D 14 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG D 14 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG D 14 " 0.023 2.00e-02 2.50e+03 ... (remaining 2923 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4504 2.83 - 3.35: 17398 3.35 - 3.86: 30856 3.86 - 4.38: 38555 4.38 - 4.90: 58973 Nonbonded interactions: 150286 Sorted by model distance: nonbonded pdb=" O LEU D 170 " pdb=" O HOH D 401 " model vdw 2.310 2.440 nonbonded pdb=" O LEU E 170 " pdb=" O HOH E 401 " model vdw 2.310 2.440 nonbonded pdb=" O LEU H 170 " pdb=" O HOH H 401 " model vdw 2.311 2.440 nonbonded pdb=" O LEU A 170 " pdb=" O HOH A 401 " model vdw 2.311 2.440 nonbonded pdb=" O LEU C 170 " pdb=" O HOH C 401 " model vdw 2.311 2.440 ... (remaining 150281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 52 or (resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 60 or (resid 61 through 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 71 or (resid 72 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 78 or (resid 79 through 82 and (name N or name CA or name C or name O or name \ CB )) or resid 83 or (resid 84 and (name N or name CA or name C or name O or na \ me CB )) or resid 85 through 93 or (resid 94 and (name N or name CA or name C or \ name O or name CB )) or resid 95 through 103 or (resid 104 through 106 and (nam \ e N or name CA or name C or name O or name CB )) or resid 107 through 138 or (re \ sid 139 and (name N or name CA or name C or name O or name CB )) or resid 140 th \ rough 145 or (resid 146 and (name N or name CA or name C or name O or name CB )) \ or resid 148 or (resid 149 through 151 and (name N or name CA or name C or name \ O or name CB )) or resid 152 through 159 or (resid 160 and (name N or name CA o \ r name C or name O or name CB )) or resid 161 through 163 or (resid 164 and (nam \ e N or name CA or name C or name O or name CB )) or resid 165 through 166 or (re \ sid 167 through 170 and (name N or name CA or name C or name O or name CB )) or \ resid 171 through 173 or (resid 174 and (name N or name CA or name C or name O o \ r name CB )) or resid 175 or (resid 176 through 180 and (name N or name CA or na \ me C or name O or name CB )) or resid 181 through 191 or (resid 192 and (name N \ or name CA or name C or name O or name CB )) or resid 193 through 195 or (resid \ 196 and (name N or name CA or name C or name O or name CB )) or resid 197 throug \ h 210 or (resid 211 and (name N or name CA or name C or name O or name CB )) or \ resid 212 through 217)) selection = (chain 'B' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 52 or (resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 60 or (resid 61 through 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 71 or (resid 72 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 78 or (resid 79 through 82 and (name N or name CA or name C or name O or name \ CB )) or resid 83 or (resid 84 and (name N or name CA or name C or name O or na \ me CB )) or resid 85 through 138 or (resid 139 and (name N or name CA or name C \ or name O or name CB )) or resid 140 through 145 or (resid 146 and (name N or na \ me CA or name C or name O or name CB )) or resid 148 or (resid 149 through 151 a \ nd (name N or name CA or name C or name O or name CB )) or resid 152 through 156 \ or (resid 157 and (name N or name CA or name C or name O or name CB )) or resid \ 158 through 159 or (resid 160 and (name N or name CA or name C or name O or nam \ e CB )) or resid 161 or (resid 162 and (name N or name CA or name C or name O or \ name CB )) or resid 163 through 166 or (resid 167 through 170 and (name N or na \ me CA or name C or name O or name CB )) or resid 171 through 173 or (resid 174 a \ nd (name N or name CA or name C or name O or name CB )) or resid 175 or (resid 1 \ 76 through 180 and (name N or name CA or name C or name O or name CB )) or resid \ 181 through 191 or (resid 192 and (name N or name CA or name C or name O or nam \ e CB )) or resid 193 through 195 or (resid 196 and (name N or name CA or name C \ or name O or name CB )) or resid 197 through 203 or (resid 204 and (name N or na \ me CA or name C or name O or name CB )) or resid 205 through 206 or (resid 207 a \ nd (name N or name CA or name C or name O or name CB )) or resid 208 through 210 \ or (resid 211 and (name N or name CA or name C or name O or name CB )) or resid \ 212 through 217)) selection = (chain 'C' and (resid 1 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 52 or (resid 53 throug \ h 55 and (name N or name CA or name C or name O or name CB )) or resid 56 throug \ h 71 or (resid 72 through 75 and (name N or name CA or name C or name O or name \ CB )) or resid 76 through 78 or (resid 79 through 82 and (name N or name CA or n \ ame C or name O or name CB )) or resid 83 or (resid 84 and (name N or name CA or \ name C or name O or name CB )) or resid 85 through 103 or (resid 104 through 10 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 107 through \ 138 or (resid 139 and (name N or name CA or name C or name O or name CB )) or re \ sid 140 through 145 or (resid 146 and (name N or name CA or name C or name O or \ name CB )) or resid 148 or (resid 149 through 151 and (name N or name CA or name \ C or name O or name CB )) or resid 152 through 159 or (resid 160 and (name N or \ name CA or name C or name O or name CB )) or resid 161 or (resid 162 and (name \ N or name CA or name C or name O or name CB )) or resid 163 or (resid 164 and (n \ ame N or name CA or name C or name O or name CB )) or resid 165 through 166 or ( \ resid 167 through 170 and (name N or name CA or name C or name O or name CB )) o \ r resid 171 through 173 or (resid 174 and (name N or name CA or name C or name O \ or name CB )) or resid 175 or (resid 176 through 180 and (name N or name CA or \ name C or name O or name CB )) or resid 181 through 191 or (resid 192 and (name \ N or name CA or name C or name O or name CB )) or resid 193 through 195 or (resi \ d 196 and (name N or name CA or name C or name O or name CB )) or resid 197 thro \ ugh 203 or (resid 204 and (name N or name CA or name C or name O or name CB )) o \ r resid 205 through 206 or (resid 207 and (name N or name CA or name C or name O \ or name CB )) or resid 208 through 210 or (resid 211 and (name N or name CA or \ name C or name O or name CB )) or resid 212 through 217)) selection = (chain 'D' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 52 or (resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 60 or (resid 61 through 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 71 or (resid 72 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 78 or (resid 79 through 82 and (name N or name CA or name C or name O or name \ CB )) or resid 83 or (resid 84 and (name N or name CA or name C or name O or na \ me CB )) or resid 85 through 93 or (resid 94 and (name N or name CA or name C or \ name O or name CB )) or resid 95 through 103 or (resid 104 through 106 and (nam \ e N or name CA or name C or name O or name CB )) or resid 107 through 138 or (re \ sid 139 and (name N or name CA or name C or name O or name CB )) or resid 140 th \ rough 148 or (resid 149 through 151 and (name N or name CA or name C or name O o \ r name CB )) or resid 152 through 156 or (resid 157 and (name N or name CA or na \ me C or name O or name CB )) or resid 158 through 159 or (resid 160 and (name N \ or name CA or name C or name O or name CB )) or resid 161 or (resid 162 and (nam \ e N or name CA or name C or name O or name CB )) or resid 163 or (resid 164 and \ (name N or name CA or name C or name O or name CB )) or resid 165 through 166 or \ (resid 167 through 170 and (name N or name CA or name C or name O or name CB )) \ or resid 171 through 173 or (resid 174 and (name N or name CA or name C or name \ O or name CB )) or resid 175 through 177 or (resid 178 through 180 and (name N \ or name CA or name C or name O or name CB )) or resid 181 through 186 or (resid \ 187 and (name N or name CA or name C or name O or name CB )) or resid 188 throug \ h 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) or \ resid 193 through 195 or (resid 196 and (name N or name CA or name C or name O o \ r name CB )) or resid 197 through 203 or (resid 204 and (name N or name CA or na \ me C or name O or name CB )) or resid 205 through 206 or (resid 207 and (name N \ or name CA or name C or name O or name CB )) or resid 208 through 210 or (resid \ 211 and (name N or name CA or name C or name O or name CB )) or resid 212 throug \ h 217)) selection = (chain 'E' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 52 \ or (resid 53 through 55 and (name N or name CA or name C or name O or name CB ) \ ) or resid 56 through 60 or (resid 61 through 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 78 or (resid 79 through 82 and (na \ me N or name CA or name C or name O or name CB )) or resid 83 or (resid 84 and ( \ name N or name CA or name C or name O or name CB )) or resid 85 through 93 or (r \ esid 94 and (name N or name CA or name C or name O or name CB )) or resid 95 thr \ ough 103 or (resid 104 through 106 and (name N or name CA or name C or name O or \ name CB )) or resid 107 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB )) or resid 140 through 145 or (resid 146 and (name N o \ r name CA or name C or name O or name CB )) or resid 148 or (resid 149 through 1 \ 51 and (name N or name CA or name C or name O or name CB )) or resid 152 through \ 156 or (resid 157 and (name N or name CA or name C or name O or name CB )) or r \ esid 158 through 159 or (resid 160 and (name N or name CA or name C or name O or \ name CB )) or resid 161 or (resid 162 and (name N or name CA or name C or name \ O or name CB )) or resid 163 or (resid 164 and (name N or name CA or name C or n \ ame O or name CB )) or resid 165 through 166 or (resid 167 through 170 and (name \ N or name CA or name C or name O or name CB )) or resid 171 through 173 or (res \ id 174 and (name N or name CA or name C or name O or name CB )) or resid 175 or \ (resid 176 through 180 and (name N or name CA or name C or name O or name CB )) \ or resid 181 through 186 or (resid 187 and (name N or name CA or name C or name \ O or name CB )) or resid 188 through 191 or (resid 192 and (name N or name CA or \ name C or name O or name CB )) or resid 193 through 195 or (resid 196 and (name \ N or name CA or name C or name O or name CB )) or resid 197 through 203 or (res \ id 204 and (name N or name CA or name C or name O or name CB )) or resid 205 thr \ ough 206 or (resid 207 and (name N or name CA or name C or name O or name CB )) \ or resid 208 through 210 or (resid 211 and (name N or name CA or name C or name \ O or name CB )) or resid 212 through 217)) selection = (chain 'F' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 60 \ or (resid 61 through 63 and (name N or name CA or name C or name O or name CB ) \ ) or resid 64 through 71 or (resid 72 through 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 78 or (resid 79 through 82 and (na \ me N or name CA or name C or name O or name CB )) or resid 83 or (resid 84 and ( \ name N or name CA or name C or name O or name CB )) or resid 85 through 93 or (r \ esid 94 and (name N or name CA or name C or name O or name CB )) or resid 95 thr \ ough 103 or (resid 104 through 106 and (name N or name CA or name C or name O or \ name CB )) or resid 107 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB )) or resid 140 through 145 or (resid 146 and (name N o \ r name CA or name C or name O or name CB )) or resid 148 or (resid 149 through 1 \ 51 and (name N or name CA or name C or name O or name CB )) or resid 152 through \ 156 or (resid 157 and (name N or name CA or name C or name O or name CB )) or r \ esid 158 through 161 or (resid 162 and (name N or name CA or name C or name O or \ name CB )) or resid 163 or (resid 164 and (name N or name CA or name C or name \ O or name CB )) or resid 165 through 166 or (resid 167 through 170 and (name N o \ r name CA or name C or name O or name CB )) or resid 171 through 173 or (resid 1 \ 74 and (name N or name CA or name C or name O or name CB )) or resid 175 or (res \ id 176 through 180 and (name N or name CA or name C or name O or name CB )) or r \ esid 181 through 186 or (resid 187 and (name N or name CA or name C or name O or \ name CB )) or resid 188 through 191 or (resid 192 and (name N or name CA or nam \ e C or name O or name CB )) or resid 193 through 195 or (resid 196 and (name N o \ r name CA or name C or name O or name CB )) or resid 197 through 203 or (resid 2 \ 04 and (name N or name CA or name C or name O or name CB )) or resid 205 through \ 206 or (resid 207 and (name N or name CA or name C or name O or name CB )) or r \ esid 208 through 210 or (resid 211 and (name N or name CA or name C or name O or \ name CB )) or resid 212 through 217)) selection = (chain 'G' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 60 or (resid 61 through 63 and (name N or name CA or name C or name O \ or name CB )) or resid 64 through 71 or (resid 72 through 75 and (name N or nam \ e CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throu \ gh 82 and (name N or name CA or name C or name O or name CB )) or resid 83 or (r \ esid 84 and (name N or name CA or name C or name O or name CB )) or resid 85 thr \ ough 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) or \ resid 95 through 103 or (resid 104 through 106 and (name N or name CA or name C \ or name O or name CB )) or resid 107 through 145 or (resid 146 and (name N or n \ ame CA or name C or name O or name CB )) or resid 148 or (resid 149 through 151 \ and (name N or name CA or name C or name O or name CB )) or resid 152 through 16 \ 1 or (resid 162 and (name N or name CA or name C or name O or name CB )) or resi \ d 163 or (resid 164 and (name N or name CA or name C or name O or name CB )) or \ resid 165 through 166 or (resid 167 through 170 and (name N or name CA or name C \ or name O or name CB )) or resid 171 through 175 or (resid 176 through 180 and \ (name N or name CA or name C or name O or name CB )) or resid 181 through 195 or \ (resid 196 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 7 through 203 or (resid 204 and (name N or name CA or name C or name O or name C \ B )) or resid 205 through 206 or (resid 207 and (name N or name CA or name C or \ name O or name CB )) or resid 208 through 210 or (resid 211 and (name N or name \ CA or name C or name O or name CB )) or resid 212 through 217)) selection = (chain 'H' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 52 or (resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 60 or (resid 61 through 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 71 or (resid 72 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 78 or (resid 79 through 82 and (name N or name CA or name C or name O or name \ CB )) or resid 83 or (resid 84 and (name N or name CA or name C or name O or na \ me CB )) or resid 85 through 93 or (resid 94 and (name N or name CA or name C or \ name O or name CB )) or resid 95 through 103 or (resid 104 through 106 and (nam \ e N or name CA or name C or name O or name CB )) or resid 107 through 138 or (re \ sid 139 and (name N or name CA or name C or name O or name CB )) or resid 140 th \ rough 149 or (resid 150 through 151 and (name N or name CA or name C or name O o \ r name CB )) or resid 152 through 156 or (resid 157 and (name N or name CA or na \ me C or name O or name CB )) or resid 158 through 159 or (resid 160 and (name N \ or name CA or name C or name O or name CB )) or resid 161 through 163 or (resid \ 164 and (name N or name CA or name C or name O or name CB )) or resid 165 throug \ h 166 or (resid 167 through 170 and (name N or name CA or name C or name O or na \ me CB )) or resid 171 through 173 or (resid 174 and (name N or name CA or name C \ or name O or name CB )) or resid 175 through 177 or (resid 178 through 180 and \ (name N or name CA or name C or name O or name CB )) or resid 181 through 191 or \ (resid 192 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 3 through 195 or (resid 196 and (name N or name CA or name C or name O or name C \ B )) or resid 197 through 203 or (resid 204 and (name N or name CA or name C or \ name O or name CB )) or resid 205 through 206 or (resid 207 and (name N or name \ CA or name C or name O or name CB )) or resid 208 through 217)) selection = (chain 'I' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 52 or (resid 53 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 60 or (resid 61 through 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 71 or (resid 72 throu \ gh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 81 or (resid 82 and (name N or name CA or name C or name O or name CB )) or r \ esid 83 or (resid 84 and (name N or name CA or name C or name O or name CB )) or \ resid 85 through 93 or (resid 94 and (name N or name CA or name C or name O or \ name CB )) or resid 95 through 103 or (resid 104 through 106 and (name N or name \ CA or name C or name O or name CB )) or resid 107 through 138 or (resid 139 and \ (name N or name CA or name C or name O or name CB )) or resid 140 through 145 o \ r (resid 146 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 48 or (resid 149 through 151 and (name N or name CA or name C or name O or name \ CB )) or resid 152 through 161 or (resid 162 and (name N or name CA or name C or \ name O or name CB )) or resid 163 or (resid 164 and (name N or name CA or name \ C or name O or name CB )) or resid 165 through 173 or (resid 174 and (name N or \ name CA or name C or name O or name CB )) or resid 175 or (resid 176 through 180 \ and (name N or name CA or name C or name O or name CB )) or resid 181 through 1 \ 86 or (resid 187 and (name N or name CA or name C or name O or name CB )) or res \ id 188 through 191 or (resid 192 and (name N or name CA or name C or name O or n \ ame CB )) or resid 193 through 203 or (resid 204 and (name N or name CA or name \ C or name O or name CB )) or resid 205 through 206 or (resid 207 and (name N or \ name CA or name C or name O or name CB )) or resid 208 through 210 or (resid 211 \ and (name N or name CA or name C or name O or name CB )) or resid 212 through 2 \ 17)) selection = (chain 'J' and (resid 1 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 31 or (resid 32 through 33 \ and (name N or name CA or name C or name O or name CB )) or resid 34 through 39 \ or (resid 40 and (name N or name CA or name C or name O or name CB )) or resid \ 41 through 60 or (resid 61 through 63 and (name N or name CA or name C or name O \ or name CB )) or resid 64 through 71 or (resid 72 through 75 and (name N or nam \ e CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throu \ gh 82 and (name N or name CA or name C or name O or name CB )) or resid 83 throu \ gh 103 or (resid 104 through 106 and (name N or name CA or name C or name O or n \ ame CB )) or resid 107 through 138 or (resid 139 and (name N or name CA or name \ C or name O or name CB )) or resid 140 through 145 or (resid 146 and (name N or \ name CA or name C or name O or name CB )) or resid 148 or (resid 149 through 151 \ and (name N or name CA or name C or name O or name CB )) or resid 152 through 1 \ 59 or (resid 160 and (name N or name CA or name C or name O or name CB )) or res \ id 161 or (resid 162 and (name N or name CA or name C or name O or name CB )) or \ resid 163 or (resid 164 and (name N or name CA or name C or name O or name CB ) \ ) or resid 165 through 166 or (resid 167 through 170 and (name N or name CA or n \ ame C or name O or name CB )) or resid 171 through 173 or (resid 174 and (name N \ or name CA or name C or name O or name CB )) or resid 175 or (resid 176 through \ 180 and (name N or name CA or name C or name O or name CB )) or resid 181 throu \ gh 186 or (resid 187 and (name N or name CA or name C or name O or name CB )) or \ resid 188 through 191 or (resid 192 and (name N or name CA or name C or name O \ or name CB )) or resid 193 through 195 or (resid 196 and (name N or name CA or n \ ame C or name O or name CB )) or resid 197 through 203 or (resid 204 and (name N \ or name CA or name C or name O or name CB )) or resid 205 through 206 or (resid \ 207 and (name N or name CA or name C or name O or name CB )) or resid 208 throu \ gh 210 or (resid 211 and (name N or name CA or name C or name O or name CB )) or \ resid 212 through 217)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.190 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 45.710 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.060 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:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.167 16561 Z= 0.964 Angle : 2.142 29.690 22640 Z= 1.408 Chirality : 0.113 0.708 2585 Planarity : 0.025 0.493 2926 Dihedral : 19.242 165.933 5470 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 10.79 % Allowed : 13.42 % Favored : 75.79 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.13), residues: 2127 helix: -3.32 (0.10), residues: 1283 sheet: -3.05 (0.21), residues: 300 loop : -2.23 (0.21), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 214 HIS 0.009 0.002 HIS E 200 PHE 0.030 0.002 PHE A 103 TYR 0.024 0.003 TYR D 148 ARG 0.011 0.001 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 512 time to evaluate : 1.798 Fit side-chains revert: symmetry clash outliers start: 164 outliers final: 11 residues processed: 595 average time/residue: 1.0640 time to fit residues: 714.9429 Evaluate side-chains 300 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 289 time to evaluate : 1.878 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 2 average time/residue: 0.1908 time to fit residues: 2.9062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 ASN A 150 GLN A 172 ASN A 199 GLN A 200 HIS B 34 ASN B 85 ASN B 120 GLN B 141 ASN B 160 ASN B 172 ASN C 31 HIS C 111 ASN C 123 GLN C 172 ASN C 199 GLN ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN D 123 GLN D 172 ASN D 200 HIS E 65 HIS E 85 ASN E 111 ASN E 120 GLN E 162 ASN E 172 ASN E 200 HIS F 34 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN F 172 ASN F 200 HIS ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN G 111 ASN G 154 ASN G 162 ASN G 175 GLN G 200 HIS H 63 ASN I 63 ASN I 65 HIS I 85 ASN J 123 GLN J 162 ASN J 172 ASN J 200 HIS J 212 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16561 Z= 0.171 Angle : 0.526 5.934 22640 Z= 0.277 Chirality : 0.044 0.136 2585 Planarity : 0.005 0.060 2926 Dihedral : 10.603 142.056 2340 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 3.22 % Allowed : 18.03 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2127 helix: -0.70 (0.13), residues: 1307 sheet: -1.57 (0.25), residues: 300 loop : -1.29 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 214 HIS 0.008 0.002 HIS J 200 PHE 0.024 0.002 PHE C 191 TYR 0.011 0.001 TYR H 205 ARG 0.005 0.001 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 308 time to evaluate : 1.878 Fit side-chains outliers start: 49 outliers final: 16 residues processed: 341 average time/residue: 1.2102 time to fit residues: 461.9818 Evaluate side-chains 281 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 265 time to evaluate : 1.877 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.2111 time to fit residues: 3.6424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 189 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 153 optimal weight: 2.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 85 ASN A 199 GLN B 111 ASN B 141 ASN B 185 HIS B 200 HIS B 208 ASN C 85 ASN C 199 GLN ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN D 199 GLN E 158 ASN F 31 HIS F 63 ASN F 216 ASN G 111 ASN G 154 ASN G 175 GLN H 65 HIS H 85 ASN I 212 ASN J 162 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16561 Z= 0.267 Angle : 0.571 5.872 22640 Z= 0.303 Chirality : 0.047 0.151 2585 Planarity : 0.005 0.040 2926 Dihedral : 10.788 155.686 2340 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 3.68 % Allowed : 17.70 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2127 helix: 0.27 (0.14), residues: 1307 sheet: -1.08 (0.24), residues: 360 loop : -0.79 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 20 HIS 0.008 0.002 HIS H 185 PHE 0.027 0.002 PHE C 191 TYR 0.013 0.002 TYR H 148 ARG 0.007 0.001 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 273 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 27 residues processed: 311 average time/residue: 1.2048 time to fit residues: 420.0388 Evaluate side-chains 278 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 251 time to evaluate : 1.775 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 20 residues processed: 8 average time/residue: 0.6055 time to fit residues: 8.3232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 191 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 181 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 199 GLN C 200 HIS E 158 ASN F 216 ASN G 150 GLN H 172 ASN I 65 HIS J 162 ASN J 199 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16561 Z= 0.191 Angle : 0.489 7.023 22640 Z= 0.257 Chirality : 0.044 0.138 2585 Planarity : 0.004 0.041 2926 Dihedral : 10.492 150.007 2340 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 3.09 % Allowed : 17.43 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.18), residues: 2127 helix: 0.86 (0.14), residues: 1300 sheet: -0.90 (0.24), residues: 360 loop : -0.62 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 20 HIS 0.005 0.001 HIS G 65 PHE 0.026 0.002 PHE C 191 TYR 0.011 0.001 TYR E 205 ARG 0.007 0.001 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 266 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 24 residues processed: 298 average time/residue: 1.2139 time to fit residues: 404.8359 Evaluate side-chains 274 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 250 time to evaluate : 1.801 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 3 average time/residue: 0.8256 time to fit residues: 5.3102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 151 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 111 ASN C 199 GLN E 158 ASN F 63 ASN G 199 GLN J 34 ASN J 162 ASN J 216 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16561 Z= 0.321 Angle : 0.585 7.014 22640 Z= 0.313 Chirality : 0.049 0.213 2585 Planarity : 0.005 0.045 2926 Dihedral : 10.844 168.125 2340 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.68 % Allowed : 17.43 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2127 helix: 0.73 (0.14), residues: 1290 sheet: -0.97 (0.24), residues: 360 loop : -0.77 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 20 HIS 0.007 0.002 HIS H 185 PHE 0.030 0.002 PHE C 191 TYR 0.017 0.002 TYR I 159 ARG 0.007 0.001 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 257 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 29 residues processed: 293 average time/residue: 1.1590 time to fit residues: 381.5098 Evaluate side-chains 275 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 246 time to evaluate : 1.749 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 6 average time/residue: 0.4845 time to fit residues: 5.9648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 203 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS A 199 GLN C 199 GLN F 34 ASN H 200 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16561 Z= 0.301 Angle : 0.566 6.942 22640 Z= 0.303 Chirality : 0.048 0.198 2585 Planarity : 0.005 0.045 2926 Dihedral : 10.822 166.256 2340 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.22 % Allowed : 17.89 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2127 helix: 0.76 (0.14), residues: 1290 sheet: -1.00 (0.24), residues: 360 loop : -0.81 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 214 HIS 0.006 0.002 HIS A 65 PHE 0.031 0.002 PHE C 191 TYR 0.017 0.002 TYR I 159 ARG 0.008 0.001 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 254 time to evaluate : 1.979 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 27 residues processed: 293 average time/residue: 1.1667 time to fit residues: 384.8584 Evaluate side-chains 272 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 245 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 25 residues processed: 3 average time/residue: 0.2719 time to fit residues: 3.7397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 199 GLN D 199 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16561 Z= 0.222 Angle : 0.511 6.479 22640 Z= 0.272 Chirality : 0.046 0.171 2585 Planarity : 0.004 0.044 2926 Dihedral : 10.528 157.226 2340 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.96 % Allowed : 18.29 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.18), residues: 2127 helix: 1.00 (0.14), residues: 1297 sheet: -0.92 (0.24), residues: 360 loop : -0.55 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 214 HIS 0.004 0.001 HIS H 185 PHE 0.027 0.002 PHE C 191 TYR 0.018 0.002 TYR C 15 ARG 0.009 0.001 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 249 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 32 residues processed: 284 average time/residue: 1.2030 time to fit residues: 383.1982 Evaluate side-chains 277 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 245 time to evaluate : 1.792 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 29 residues processed: 5 average time/residue: 0.8897 time to fit residues: 7.4356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 39 optimal weight: 0.4980 chunk 128 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 overall best weight: 2.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16561 Z= 0.226 Angle : 0.513 6.348 22640 Z= 0.273 Chirality : 0.046 0.160 2585 Planarity : 0.004 0.044 2926 Dihedral : 10.546 157.736 2340 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.83 % Allowed : 18.09 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2127 helix: 1.10 (0.14), residues: 1293 sheet: -0.92 (0.25), residues: 360 loop : -0.68 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 20 HIS 0.004 0.001 HIS H 185 PHE 0.028 0.002 PHE C 191 TYR 0.015 0.002 TYR G 205 ARG 0.009 0.001 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 247 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 31 residues processed: 282 average time/residue: 1.1498 time to fit residues: 364.8680 Evaluate side-chains 275 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 244 time to evaluate : 1.702 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 28 residues processed: 4 average time/residue: 0.6365 time to fit residues: 5.5638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 82 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 170 optimal weight: 0.2980 chunk 178 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 199 GLN F 63 ASN J 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16561 Z= 0.170 Angle : 0.473 6.036 22640 Z= 0.250 Chirality : 0.044 0.138 2585 Planarity : 0.004 0.043 2926 Dihedral : 10.270 148.301 2340 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.17 % Allowed : 18.82 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2127 helix: 1.33 (0.14), residues: 1294 sheet: -0.88 (0.25), residues: 366 loop : -0.31 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 20 HIS 0.003 0.001 HIS F 65 PHE 0.025 0.001 PHE C 191 TYR 0.019 0.001 TYR C 15 ARG 0.009 0.001 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 256 time to evaluate : 1.753 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 29 residues processed: 285 average time/residue: 1.1689 time to fit residues: 375.8910 Evaluate side-chains 274 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 245 time to evaluate : 1.729 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 3 average time/residue: 0.2706 time to fit residues: 3.5822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.3993 > 50: distance: 52 - 57: 15.459 distance: 53 - 86: 21.147 distance: 57 - 58: 11.996 distance: 58 - 59: 16.774 distance: 58 - 61: 21.104 distance: 59 - 60: 34.459 distance: 59 - 68: 9.897 distance: 60 - 94: 24.167 distance: 61 - 62: 11.040 distance: 62 - 63: 11.597 distance: 63 - 64: 8.499 distance: 64 - 65: 6.127 distance: 65 - 66: 27.432 distance: 65 - 67: 16.682 distance: 68 - 69: 9.384 distance: 69 - 70: 11.518 distance: 69 - 72: 9.962 distance: 70 - 71: 26.930 distance: 70 - 78: 13.012 distance: 71 - 102: 18.590 distance: 72 - 73: 17.892 distance: 73 - 74: 14.240 distance: 73 - 75: 31.376 distance: 74 - 76: 15.992 distance: 75 - 77: 19.118 distance: 76 - 77: 16.398 distance: 78 - 79: 22.343 distance: 79 - 80: 4.750 distance: 79 - 82: 14.042 distance: 80 - 81: 7.403 distance: 80 - 86: 9.053 distance: 82 - 83: 23.948 distance: 82 - 84: 23.520 distance: 83 - 85: 9.433 distance: 86 - 87: 14.068 distance: 87 - 90: 3.232 distance: 88 - 89: 5.790 distance: 88 - 94: 5.793 distance: 90 - 91: 13.736 distance: 91 - 92: 13.434 distance: 92 - 93: 18.357 distance: 94 - 95: 19.627 distance: 95 - 96: 11.495 distance: 95 - 98: 15.574 distance: 96 - 97: 21.545 distance: 96 - 102: 16.704 distance: 98 - 99: 15.724 distance: 99 - 100: 11.303 distance: 99 - 101: 13.971 distance: 102 - 103: 3.355 distance: 103 - 104: 6.228 distance: 103 - 106: 13.806 distance: 104 - 105: 13.287 distance: 104 - 108: 8.507 distance: 106 - 107: 12.907 distance: 108 - 109: 18.241 distance: 109 - 110: 3.199 distance: 110 - 111: 10.332 distance: 110 - 112: 19.597 distance: 112 - 113: 35.791 distance: 113 - 114: 11.362 distance: 113 - 116: 14.141 distance: 114 - 115: 13.650 distance: 114 - 117: 24.484 distance: 117 - 118: 54.316 distance: 117 - 123: 35.390 distance: 118 - 119: 15.597 distance: 118 - 121: 32.288 distance: 119 - 120: 26.409 distance: 119 - 124: 10.720 distance: 121 - 122: 22.085 distance: 122 - 123: 19.197 distance: 124 - 125: 5.713 distance: 125 - 128: 8.442 distance: 126 - 127: 8.699 distance: 126 - 135: 15.669 distance: 127 - 155: 20.934 distance: 128 - 129: 11.121 distance: 129 - 130: 21.739 distance: 129 - 131: 29.174 distance: 130 - 132: 26.358 distance: 131 - 133: 8.043 distance: 132 - 134: 15.430 distance: 133 - 134: 24.441