Starting phenix.real_space_refine (version: dev) on Wed Feb 22 04:46:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/02_2023/8bc4_15962_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/02_2023/8bc4_15962.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/02_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_15962/02_2023/8bc4_15962_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/02_2023/8bc4_15962_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/02_2023/8bc4_15962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/02_2023/8bc4_15962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/02_2023/8bc4_15962_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc4_15962/02_2023/8bc4_15962_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 9.51, per 1000 atoms: 0.58 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: 6.81 Conformation dependent library (CDL) restraints added in 2.4 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: 1.36 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: 4.57 Time building geometry restraints manager: 7.47 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 - 17.25: 8288 17.25 - 34.49: 789 34.49 - 51.74: 297 51.74 - 68.98: 92 68.98 - 86.23: 42 Dihedral angle restraints: 9508 sinusoidal: 3197 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 9505 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.960 Check model and map are aligned: 0.270 Process input model: 42.850 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 17.932 86.226 5434 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 % 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 *********************** 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 : 1.921 Fit side-chains revert: symmetry clash outliers start: 164 outliers final: 11 residues processed: 595 average time/residue: 1.0693 time to fit residues: 719.0919 Evaluate side-chains 300 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 289 time to evaluate : 1.873 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 2 average time/residue: 0.2221 time to fit residues: 3.3860 ------------------------------------------------------------------------------- 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 200 HIS J 212 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2913 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= 0.172 Angle : 0.530 5.908 22640 Z= 0.278 Chirality : 0.044 0.135 2585 Planarity : 0.005 0.060 2926 Dihedral : 5.747 68.560 2304 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer Outliers : 3.36 % 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: -1.65 (0.16), residues: 2127 helix: -0.69 (0.13), residues: 1307 sheet: -1.57 (0.25), residues: 300 loop : -1.29 (0.24), residues: 520 *********************** 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 362 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 311 time to evaluate : 1.882 Fit side-chains outliers start: 51 outliers final: 18 residues processed: 345 average time/residue: 1.1378 time to fit residues: 440.7285 Evaluate side-chains 285 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 267 time to evaluate : 1.958 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 5 average time/residue: 0.2013 time to fit residues: 4.2370 ------------------------------------------------------------------------------- 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: 5.9990 chunk 52 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 65 optimal weight: 0.0570 chunk 153 optimal weight: 9.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- 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 85 ASN 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 34 ASN J 162 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 16561 Z= 0.318 Angle : 0.611 6.515 22640 Z= 0.324 Chirality : 0.049 0.170 2585 Planarity : 0.005 0.048 2926 Dihedral : 5.967 69.064 2304 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer Outliers : 3.62 % 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: -0.64 (0.17), residues: 2127 helix: 0.17 (0.14), residues: 1307 sheet: -1.13 (0.24), residues: 360 loop : -1.09 (0.27), residues: 460 *********************** 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 319 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 264 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 26 residues processed: 300 average time/residue: 1.2044 time to fit residues: 405.0058 Evaluate side-chains 271 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 245 time to evaluate : 2.002 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 8 average time/residue: 0.6284 time to fit residues: 8.7326 ------------------------------------------------------------------------------- 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: 0.6980 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 191 optimal weight: 0.7980 chunk 202 optimal weight: 0.2980 chunk 100 optimal weight: 8.9990 chunk 181 optimal weight: 0.0770 chunk 54 optimal weight: 6.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 172 ASN J 199 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 16561 Z= 0.120 Angle : 0.433 5.964 22640 Z= 0.226 Chirality : 0.042 0.132 2585 Planarity : 0.004 0.040 2926 Dihedral : 5.316 67.812 2304 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.51 (0.18), residues: 2127 helix: 1.05 (0.14), residues: 1294 sheet: -0.83 (0.25), residues: 366 loop : -0.35 (0.28), residues: 467 *********************** 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 314 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 277 time to evaluate : 2.018 Fit side-chains outliers start: 37 outliers final: 21 residues processed: 304 average time/residue: 1.1630 time to fit residues: 397.3360 Evaluate side-chains 267 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 246 time to evaluate : 2.070 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 5 average time/residue: 0.2208 time to fit residues: 4.4173 ------------------------------------------------------------------------------- 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: 5.9990 chunk 115 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 G 175 GLN J 162 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 16561 Z= 0.278 Angle : 0.558 8.028 22640 Z= 0.296 Chirality : 0.047 0.168 2585 Planarity : 0.004 0.041 2926 Dihedral : 5.735 70.941 2304 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer Outliers : 3.29 % 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: 0.28 (0.18), residues: 2127 helix: 0.93 (0.14), residues: 1293 sheet: -0.92 (0.24), residues: 360 loop : -0.66 (0.28), residues: 474 *********************** 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 305 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 255 time to evaluate : 1.985 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 25 residues processed: 290 average time/residue: 1.1673 time to fit residues: 380.5248 Evaluate side-chains 270 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 245 time to evaluate : 2.106 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 5 average time/residue: 0.5496 time to fit residues: 6.1064 ------------------------------------------------------------------------------- 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: 0.1980 chunk 182 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 203 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 85 ASN C 199 GLN D 185 HIS F 63 ASN G 199 GLN J 216 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 16561 Z= 0.279 Angle : 0.551 6.496 22640 Z= 0.293 Chirality : 0.047 0.160 2585 Planarity : 0.004 0.043 2926 Dihedral : 5.804 70.547 2304 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 3.09 % 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: 0.22 (0.18), residues: 2127 helix: 0.89 (0.14), residues: 1293 sheet: -0.93 (0.24), residues: 360 loop : -0.72 (0.28), residues: 474 *********************** 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 301 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 254 time to evaluate : 1.962 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 28 residues processed: 289 average time/residue: 1.1347 time to fit residues: 370.2031 Evaluate side-chains 270 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 242 time to evaluate : 1.979 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 23 residues processed: 6 average time/residue: 0.4802 time to fit residues: 6.3110 ------------------------------------------------------------------------------- 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: 0.6980 chunk 22 optimal weight: 5.9990 chunk 115 optimal weight: 0.5980 chunk 148 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 93 optimal weight: 0.0980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 H 150 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 16561 Z= 0.128 Angle : 0.437 5.796 22640 Z= 0.229 Chirality : 0.043 0.132 2585 Planarity : 0.004 0.040 2926 Dihedral : 5.181 64.234 2304 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer Outliers : 2.24 % 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: 1.00 (0.18), residues: 2127 helix: 1.45 (0.14), residues: 1294 sheet: -0.76 (0.25), residues: 366 loop : -0.10 (0.29), residues: 467 *********************** 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 302 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 268 time to evaluate : 2.089 Fit side-chains outliers start: 34 outliers final: 21 residues processed: 295 average time/residue: 1.1381 time to fit residues: 378.0256 Evaluate side-chains 274 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 253 time to evaluate : 2.019 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 2 average time/residue: 0.3082 time to fit residues: 3.5781 ------------------------------------------------------------------------------- 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: 9.9990 chunk 80 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 60 optimal weight: 0.2980 chunk 39 optimal weight: 9.9990 chunk 128 optimal weight: 0.0370 chunk 137 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 0.0980 chunk 159 optimal weight: 0.6980 chunk 184 optimal weight: 9.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- 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 H 150 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 16561 Z= 0.135 Angle : 0.439 5.728 22640 Z= 0.229 Chirality : 0.043 0.133 2585 Planarity : 0.004 0.040 2926 Dihedral : 5.017 65.379 2304 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.21 (0.18), residues: 2127 helix: 1.58 (0.14), residues: 1307 sheet: -0.62 (0.25), residues: 366 loop : -0.02 (0.30), residues: 454 *********************** 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 284 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 255 time to evaluate : 1.985 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 23 residues processed: 277 average time/residue: 1.0943 time to fit residues: 342.3456 Evaluate side-chains 266 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 243 time to evaluate : 1.917 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 4 average time/residue: 0.2547 time to fit residues: 4.0459 ------------------------------------------------------------------------------- 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: 5.9990 chunk 176 optimal weight: 9.9990 chunk 188 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 170 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 187 optimal weight: 0.2980 chunk 123 optimal weight: 10.0000 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN B 185 HIS C 199 GLN F 34 ASN G 216 ASN H 200 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 16561 Z= 0.238 Angle : 0.520 5.748 22640 Z= 0.276 Chirality : 0.046 0.206 2585 Planarity : 0.004 0.042 2926 Dihedral : 5.493 67.216 2304 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 1.84 % 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: 0.86 (0.18), residues: 2127 helix: 1.33 (0.14), residues: 1307 sheet: -0.71 (0.25), residues: 360 loop : -0.29 (0.29), residues: 460 *********************** 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 277 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 249 time to evaluate : 1.815 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 25 residues processed: 271 average time/residue: 1.1227 time to fit residues: 344.9839 Evaluate side-chains 265 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 240 time to evaluate : 1.938 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 22 residues processed: 5 average time/residue: 0.5525 time to fit residues: 5.9438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 192 optimal weight: 0.0870 chunk 166 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.0964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN C 85 ASN C 199 GLN G 216 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 16561 Z= 0.205 Angle : 0.496 5.765 22640 Z= 0.263 Chirality : 0.045 0.175 2585 Planarity : 0.004 0.042 2926 Dihedral : 5.440 68.612 2304 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 1.78 % 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: 0.92 (0.18), residues: 2127 helix: 1.41 (0.14), residues: 1294 sheet: -0.71 (0.25), residues: 360 loop : -0.29 (0.28), residues: 473 ********************** REFINEMENT MACRO_CYCLE 10 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 269 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 242 time to evaluate : 1.984 Fit side-chains outliers start: 27 outliers final: 24 residues processed: 264 average time/residue: 1.1281 time to fit residues: 336.8669 Evaluate side-chains 263 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 239 time to evaluate : 2.033 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 23 residues processed: 3 average time/residue: 0.2404 time to fit residues: 3.7798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 153 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 G 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.141193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132391 restraints weight = 20216.042| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 0.92 r_work: 0.3484 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4389 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= 0.203 Angle : 0.497 5.754 22640 Z= 0.263 Chirality : 0.045 0.172 2585 Planarity : 0.004 0.042 2926 Dihedral : 5.434 68.022 2304 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 1.97 % 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: 0.90 (0.18), residues: 2127 helix: 1.40 (0.14), residues: 1297 sheet: -0.72 (0.25), residues: 360 loop : -0.34 (0.28), residues: 470 =============================================================================== Job complete usr+sys time: 6236.37 seconds wall clock time: 110 minutes 52.32 seconds (6652.32 seconds total)