Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 06:48:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2023/8dbn_27291_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2023/8dbn_27291.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2023/8dbn_27291_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2023/8dbn_27291_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2023/8dbn_27291_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2023/8dbn_27291.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2023/8dbn_27291.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2023/8dbn_27291_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2023/8dbn_27291_updated.pdb" } resolution = 2.4 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= 0.347 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 12 5.21 5 S 102 5.16 5 C 8826 2.51 5 N 2514 2.21 5 O 2766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 26": "OE1" <-> "OE2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E ARG 196": "NH1" <-> "NH2" Residue "E GLU 201": "OE1" <-> "OE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F ARG 196": "NH1" <-> "NH2" Residue "F GLU 201": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14244 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2327 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 8, 'TRANS': 295} Chain: "B" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2327 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 8, 'TRANS': 295} Chain: "C" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2327 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 8, 'TRANS': 295} Chain: "D" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2327 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 8, 'TRANS': 295} Chain: "E" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2327 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 8, 'TRANS': 295} Chain: "F" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2327 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 8, 'TRANS': 295} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.57, per 1000 atoms: 0.53 Number of scatterers: 14244 At special positions: 0 Unit cell: (121.569, 128.185, 75.257, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 24 15.00 Mg 12 11.99 O 2766 8.00 N 2514 7.00 C 8826 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=0, symmetry=0 Time building additional restraints: 5.99 Conformation dependent library (CDL) restraints added in 2.0 seconds 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3456 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 18 sheets defined 36.5% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 255 through 262 removed outlier: 4.553A pdb=" N ILE A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.708A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 63 through 79 Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS B 176 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 255 through 262 removed outlier: 4.553A pdb=" N ILE B 258 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.707A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 108 through 119 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 255 through 262 removed outlier: 4.553A pdb=" N ILE C 258 " --> pdb=" O GLY C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.708A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 304 Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 63 through 79 Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 148 through 158 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 255 through 262 removed outlier: 4.552A pdb=" N ILE D 258 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 283 removed outlier: 3.708A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 304 Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 148 through 158 Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS E 176 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 255 through 262 removed outlier: 4.553A pdb=" N ILE E 258 " --> pdb=" O GLY E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 283 removed outlier: 3.708A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 304 Processing helix chain 'F' and resid 13 through 22 Processing helix chain 'F' and resid 63 through 79 Processing helix chain 'F' and resid 108 through 119 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 162 through 164 No H-bonds generated for 'chain 'F' and resid 162 through 164' Processing helix chain 'F' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS F 176 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 Processing helix chain 'F' and resid 255 through 262 removed outlier: 4.553A pdb=" N ILE F 258 " --> pdb=" O GLY F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 283 removed outlier: 3.708A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 304 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP A 52 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE A 7 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR A 54 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG A 84 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE A 55 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR A 86 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS A 123 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE A 89 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 125 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR A 126 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP A 143 " --> pdb=" O THR A 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 30 through 34 Processing sheet with id= C, first strand: chain 'A' and resid 287 through 290 removed outlier: 7.885A pdb=" N GLN A 288 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 269 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE A 290 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 271 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL A 244 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 269 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA A 246 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL A 271 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU A 248 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA A 216 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 218 " --> pdb=" O ILE A 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR A 166 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL A 219 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL A 168 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP A 188 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER A 169 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA A 190 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP B 52 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE B 7 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR B 54 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG B 84 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE B 55 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR B 86 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS B 123 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE B 89 " --> pdb=" O HIS B 123 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE B 125 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR B 126 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP B 143 " --> pdb=" O THR B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 30 through 34 Processing sheet with id= F, first strand: chain 'B' and resid 287 through 290 removed outlier: 7.885A pdb=" N GLN B 288 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 269 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE B 290 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 271 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL B 244 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B 269 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA B 246 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL B 271 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 248 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA B 216 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU B 218 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR B 166 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL B 219 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL B 168 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP B 188 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N SER B 169 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA B 190 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.279A pdb=" N ASP C 52 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE C 7 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR C 54 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG C 84 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE C 55 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR C 86 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS C 123 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE C 89 " --> pdb=" O HIS C 123 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE C 125 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR C 126 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP C 143 " --> pdb=" O THR C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 30 through 34 Processing sheet with id= I, first strand: chain 'C' and resid 287 through 290 removed outlier: 7.885A pdb=" N GLN C 288 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL C 269 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE C 290 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 271 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL C 244 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL C 269 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA C 246 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N VAL C 271 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU C 248 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 216 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE C 247 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU C 218 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR C 166 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL C 219 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL C 168 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP C 188 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N SER C 169 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA C 190 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP D 52 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE D 7 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR D 54 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG D 84 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE D 55 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR D 86 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS D 123 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE D 89 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE D 125 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR D 126 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP D 143 " --> pdb=" O THR D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 30 through 34 Processing sheet with id= L, first strand: chain 'D' and resid 287 through 290 removed outlier: 7.886A pdb=" N GLN D 288 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL D 269 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE D 290 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL D 271 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL D 244 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL D 269 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA D 246 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL D 271 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU D 248 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA D 216 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE D 247 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU D 218 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR D 166 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL D 219 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL D 168 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP D 188 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N SER D 169 " --> pdb=" O ASP D 188 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA D 190 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP E 52 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE E 7 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR E 54 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG E 84 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE E 55 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR E 86 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS E 123 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE E 89 " --> pdb=" O HIS E 123 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE E 125 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR E 126 " --> pdb=" O PRO E 141 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP E 143 " --> pdb=" O THR E 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 30 through 34 Processing sheet with id= O, first strand: chain 'E' and resid 287 through 290 removed outlier: 7.885A pdb=" N GLN E 288 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL E 269 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE E 290 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL E 271 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL E 244 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E 269 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA E 246 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL E 271 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU E 248 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA E 216 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE E 247 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU E 218 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR E 166 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL E 219 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL E 168 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP E 188 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER E 169 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA E 190 " --> pdb=" O SER E 169 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP F 52 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE F 7 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR F 54 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG F 84 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE F 55 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR F 86 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS F 123 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE F 89 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE F 125 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR F 126 " --> pdb=" O PRO F 141 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP F 143 " --> pdb=" O THR F 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 30 through 34 Processing sheet with id= R, first strand: chain 'F' and resid 287 through 290 removed outlier: 7.885A pdb=" N GLN F 288 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL F 269 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE F 290 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL F 271 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL F 244 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL F 269 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA F 246 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL F 271 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU F 248 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA F 216 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE F 247 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU F 218 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR F 166 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL F 219 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL F 168 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP F 188 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER F 169 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA F 190 " --> pdb=" O SER F 169 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1062 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: 3.93 Time building geometry restraints manager: 6.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4770 1.34 - 1.46: 2065 1.46 - 1.57: 7415 1.57 - 1.69: 36 1.69 - 1.81: 150 Bond restraints: 14436 Sorted by residual: bond pdb=" C3' ATP D 401 " pdb=" C4' ATP D 401 " ideal model delta sigma weight residual 1.305 1.530 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C3' ATP F 401 " pdb=" C4' ATP F 401 " ideal model delta sigma weight residual 1.305 1.529 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C3' ATP C 401 " pdb=" C4' ATP C 401 " ideal model delta sigma weight residual 1.305 1.529 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C3' ATP A 401 " pdb=" C4' ATP A 401 " ideal model delta sigma weight residual 1.305 1.529 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C3' ATP B 401 " pdb=" C4' ATP B 401 " ideal model delta sigma weight residual 1.305 1.529 -0.224 2.00e-02 2.50e+03 1.25e+02 ... (remaining 14431 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.76: 287 105.76 - 112.83: 8272 112.83 - 119.91: 4528 119.91 - 126.98: 6316 126.98 - 134.06: 163 Bond angle restraints: 19566 Sorted by residual: angle pdb=" C1' ATP F 401 " pdb=" N9 ATP F 401 " pdb=" C8 ATP F 401 " ideal model delta sigma weight residual 92.72 126.89 -34.17 3.00e+00 1.11e-01 1.30e+02 angle pdb=" C1' ATP A 401 " pdb=" N9 ATP A 401 " pdb=" C8 ATP A 401 " ideal model delta sigma weight residual 92.72 126.84 -34.12 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C1' ATP D 401 " pdb=" N9 ATP D 401 " pdb=" C8 ATP D 401 " ideal model delta sigma weight residual 92.72 126.83 -34.11 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C1' ATP E 401 " pdb=" N9 ATP E 401 " pdb=" C8 ATP E 401 " ideal model delta sigma weight residual 92.72 126.83 -34.11 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C1' ATP C 401 " pdb=" N9 ATP C 401 " pdb=" C8 ATP C 401 " ideal model delta sigma weight residual 92.72 126.82 -34.10 3.00e+00 1.11e-01 1.29e+02 ... (remaining 19561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.90: 8307 26.90 - 53.79: 460 53.79 - 80.69: 113 80.69 - 107.58: 12 107.58 - 134.48: 18 Dihedral angle restraints: 8910 sinusoidal: 3612 harmonic: 5298 Sorted by residual: dihedral pdb=" O2A ATP D 401 " pdb=" O3A ATP D 401 " pdb=" PA ATP D 401 " pdb=" PB ATP D 401 " ideal model delta sinusoidal sigma weight residual 27.44 161.92 -134.48 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" O2A ATP C 401 " pdb=" O3A ATP C 401 " pdb=" PA ATP C 401 " pdb=" PB ATP C 401 " ideal model delta sinusoidal sigma weight residual 27.44 161.91 -134.47 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" O2A ATP F 401 " pdb=" O3A ATP F 401 " pdb=" PA ATP F 401 " pdb=" PB ATP F 401 " ideal model delta sinusoidal sigma weight residual 27.44 161.91 -134.47 1 3.00e+01 1.11e-03 1.81e+01 ... (remaining 8907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1810 0.066 - 0.131: 429 0.131 - 0.196: 29 0.196 - 0.262: 0 0.262 - 0.327: 6 Chirality restraints: 2274 Sorted by residual: chirality pdb=" CA ILE C 290 " pdb=" N ILE C 290 " pdb=" C ILE C 290 " pdb=" CB ILE C 290 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ILE F 290 " pdb=" N ILE F 290 " pdb=" C ILE F 290 " pdb=" CB ILE F 290 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA ILE A 290 " pdb=" N ILE A 290 " pdb=" C ILE A 290 " pdb=" CB ILE A 290 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 2271 not shown) Planarity restraints: 2478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 HSX A 402 " 0.274 2.00e-02 2.50e+03 6.78e-01 1.03e+04 pdb=" C2 HSX A 402 " 0.852 2.00e-02 2.50e+03 pdb=" C3 HSX A 402 " -0.039 2.00e-02 2.50e+03 pdb=" C4 HSX A 402 " -0.321 2.00e-02 2.50e+03 pdb=" C5 HSX A 402 " 0.562 2.00e-02 2.50e+03 pdb=" O1 HSX A 402 " -0.780 2.00e-02 2.50e+03 pdb=" O2 HSX A 402 " 0.857 2.00e-02 2.50e+03 pdb=" O3 HSX A 402 " -1.241 2.00e-02 2.50e+03 pdb=" O4 HSX A 402 " -0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX E 402 " -0.274 2.00e-02 2.50e+03 6.78e-01 1.03e+04 pdb=" C2 HSX E 402 " -0.851 2.00e-02 2.50e+03 pdb=" C3 HSX E 402 " 0.038 2.00e-02 2.50e+03 pdb=" C4 HSX E 402 " 0.320 2.00e-02 2.50e+03 pdb=" C5 HSX E 402 " -0.562 2.00e-02 2.50e+03 pdb=" O1 HSX E 402 " 0.780 2.00e-02 2.50e+03 pdb=" O2 HSX E 402 " -0.857 2.00e-02 2.50e+03 pdb=" O3 HSX E 402 " 1.241 2.00e-02 2.50e+03 pdb=" O4 HSX E 402 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX F 402 " 0.273 2.00e-02 2.50e+03 6.77e-01 1.03e+04 pdb=" C2 HSX F 402 " 0.851 2.00e-02 2.50e+03 pdb=" C3 HSX F 402 " -0.038 2.00e-02 2.50e+03 pdb=" C4 HSX F 402 " -0.320 2.00e-02 2.50e+03 pdb=" C5 HSX F 402 " 0.562 2.00e-02 2.50e+03 pdb=" O1 HSX F 402 " -0.780 2.00e-02 2.50e+03 pdb=" O2 HSX F 402 " 0.858 2.00e-02 2.50e+03 pdb=" O3 HSX F 402 " -1.241 2.00e-02 2.50e+03 pdb=" O4 HSX F 402 " -0.164 2.00e-02 2.50e+03 ... (remaining 2475 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 771 2.72 - 3.27: 14580 3.27 - 3.81: 25916 3.81 - 4.36: 31229 4.36 - 4.90: 51664 Nonbonded interactions: 124160 Sorted by model distance: nonbonded pdb=" NE2 HIS B 130 " pdb="MG MG B 403 " model vdw 2.177 2.250 nonbonded pdb=" NE2 HIS D 130 " pdb="MG MG D 403 " model vdw 2.178 2.250 nonbonded pdb=" NE2 HIS E 130 " pdb="MG MG E 403 " model vdw 2.178 2.250 nonbonded pdb=" NE2 HIS A 130 " pdb="MG MG A 403 " model vdw 2.178 2.250 nonbonded pdb=" NE2 HIS F 130 " pdb="MG MG F 403 " model vdw 2.178 2.250 ... (remaining 124155 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 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: 8.030 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 37.420 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5607 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 : 0.012 0.225 14436 Z= 0.782 Angle : 1.139 34.166 19566 Z= 0.504 Chirality : 0.054 0.327 2274 Planarity : 0.043 0.678 2478 Dihedral : 18.878 134.476 5454 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 3.24 % 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: 0.86 (0.20), residues: 1812 helix: 1.95 (0.20), residues: 690 sheet: -0.38 (0.24), residues: 450 loop : -0.08 (0.21), residues: 672 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 304 time to evaluate : 1.643 Fit side-chains outliers start: 50 outliers final: 0 residues processed: 341 average time/residue: 1.1390 time to fit residues: 429.7336 Evaluate side-chains 219 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.612 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 75 optimal weight: 0.0370 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 HIS F 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 14436 Z= 0.251 Angle : 1.374 45.890 19566 Z= 0.513 Chirality : 0.047 0.163 2274 Planarity : 0.004 0.034 2478 Dihedral : 16.771 137.814 2106 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 4.28 % 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: 0.63 (0.20), residues: 1812 helix: 1.50 (0.20), residues: 690 sheet: -0.36 (0.24), residues: 444 loop : -0.00 (0.22), residues: 678 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 238 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 19 residues processed: 276 average time/residue: 1.1155 time to fit residues: 342.6163 Evaluate side-chains 221 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 202 time to evaluate : 1.635 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 0.4544 time to fit residues: 4.5799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 135 GLN A 231 HIS ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN C 97 GLN C 135 GLN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 GLN E 231 HIS F 135 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 14436 Z= 0.352 Angle : 1.361 46.084 19566 Z= 0.530 Chirality : 0.050 0.193 2274 Planarity : 0.005 0.037 2478 Dihedral : 15.964 120.782 2106 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 4.15 % 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: -0.29 (0.19), residues: 1812 helix: 0.51 (0.19), residues: 678 sheet: -0.63 (0.24), residues: 450 loop : -0.38 (0.23), residues: 684 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 225 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 24 residues processed: 266 average time/residue: 1.2130 time to fit residues: 355.6337 Evaluate side-chains 220 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 1.511 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 14 residues processed: 10 average time/residue: 0.1842 time to fit residues: 5.1561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 109 optimal weight: 0.4980 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 14436 Z= 0.183 Angle : 1.286 46.984 19566 Z= 0.475 Chirality : 0.046 0.150 2274 Planarity : 0.004 0.033 2478 Dihedral : 13.203 95.500 2106 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 3.63 % 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: 0.02 (0.20), residues: 1812 helix: 0.94 (0.20), residues: 690 sheet: -0.55 (0.24), residues: 492 loop : -0.36 (0.24), residues: 630 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 205 time to evaluate : 1.810 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 25 residues processed: 242 average time/residue: 1.1616 time to fit residues: 311.6290 Evaluate side-chains 205 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 1.651 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 16 residues processed: 9 average time/residue: 0.1751 time to fit residues: 4.9018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 2 optimal weight: 0.0050 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 156 optimal weight: 0.0270 chunk 43 optimal weight: 3.9990 overall best weight: 0.5452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN D 97 GLN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 14436 Z= 0.169 Angle : 1.279 46.929 19566 Z= 0.470 Chirality : 0.045 0.147 2274 Planarity : 0.003 0.029 2478 Dihedral : 12.204 88.371 2106 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 3.18 % 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: 0.21 (0.20), residues: 1812 helix: 1.16 (0.20), residues: 690 sheet: -0.46 (0.24), residues: 492 loop : -0.31 (0.24), residues: 630 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 190 time to evaluate : 1.804 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 27 residues processed: 224 average time/residue: 1.2321 time to fit residues: 310.0955 Evaluate side-chains 197 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.817 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 6 average time/residue: 0.2030 time to fit residues: 4.4938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 0.0030 chunk 91 optimal weight: 3.9990 overall best weight: 1.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 14436 Z= 0.283 Angle : 1.323 46.632 19566 Z= 0.503 Chirality : 0.048 0.153 2274 Planarity : 0.004 0.038 2478 Dihedral : 13.146 87.346 2106 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 3.83 % 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: -0.11 (0.20), residues: 1812 helix: 0.85 (0.20), residues: 678 sheet: -0.67 (0.25), residues: 450 loop : -0.41 (0.23), residues: 684 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 190 time to evaluate : 1.677 Fit side-chains outliers start: 59 outliers final: 39 residues processed: 225 average time/residue: 1.1691 time to fit residues: 291.3697 Evaluate side-chains 220 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 181 time to evaluate : 1.736 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 23 residues processed: 16 average time/residue: 0.4087 time to fit residues: 10.8358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 14436 Z= 0.241 Angle : 1.309 46.690 19566 Z= 0.493 Chirality : 0.047 0.152 2274 Planarity : 0.004 0.049 2478 Dihedral : 12.318 83.578 2106 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 3.18 % 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: -0.29 (0.20), residues: 1812 helix: 0.88 (0.20), residues: 678 sheet: -0.86 (0.24), residues: 498 loop : -0.61 (0.24), residues: 636 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 189 time to evaluate : 1.699 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 29 residues processed: 221 average time/residue: 1.1645 time to fit residues: 285.4051 Evaluate side-chains 212 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 183 time to evaluate : 1.637 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 8 average time/residue: 0.3260 time to fit residues: 5.9253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 14436 Z= 0.220 Angle : 1.302 46.768 19566 Z= 0.488 Chirality : 0.047 0.147 2274 Planarity : 0.004 0.048 2478 Dihedral : 11.947 87.463 2106 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 3.05 % 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: -0.25 (0.20), residues: 1812 helix: 0.86 (0.20), residues: 690 sheet: -0.83 (0.24), residues: 486 loop : -0.57 (0.24), residues: 636 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 189 time to evaluate : 1.601 Fit side-chains outliers start: 47 outliers final: 29 residues processed: 220 average time/residue: 1.0955 time to fit residues: 268.4802 Evaluate side-chains 208 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 179 time to evaluate : 1.684 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 8 average time/residue: 0.2019 time to fit residues: 4.9414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.0770 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 14436 Z= 0.257 Angle : 1.318 46.710 19566 Z= 0.500 Chirality : 0.048 0.152 2274 Planarity : 0.004 0.045 2478 Dihedral : 12.249 87.745 2106 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 2.72 % 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: -0.38 (0.20), residues: 1812 helix: 0.84 (0.20), residues: 678 sheet: -1.02 (0.24), residues: 492 loop : -0.59 (0.24), residues: 642 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 186 time to evaluate : 1.582 Fit side-chains outliers start: 42 outliers final: 31 residues processed: 212 average time/residue: 1.1884 time to fit residues: 279.4482 Evaluate side-chains 208 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 1.612 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 21 residues processed: 10 average time/residue: 0.5713 time to fit residues: 9.2582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 14436 Z= 0.276 Angle : 1.325 46.696 19566 Z= 0.506 Chirality : 0.048 0.154 2274 Planarity : 0.004 0.046 2478 Dihedral : 12.448 85.804 2106 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 2.53 % 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: -0.50 (0.20), residues: 1812 helix: 0.72 (0.20), residues: 678 sheet: -1.04 (0.24), residues: 480 loop : -0.70 (0.23), residues: 654 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 183 time to evaluate : 1.706 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 30 residues processed: 211 average time/residue: 1.2026 time to fit residues: 281.4234 Evaluate side-chains 211 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 181 time to evaluate : 1.762 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 23 residues processed: 7 average time/residue: 0.3834 time to fit residues: 5.7170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5984 r_free = 0.5984 target = 0.369535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.5900 r_free = 0.5900 target = 0.350562 restraints weight = 12251.681| |-----------------------------------------------------------------------------| r_work (start): 0.5904 rms_B_bonded: 0.97 r_work: 0.5845 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.5743 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.5743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 14436 Z= 0.220 Angle : 1.304 46.825 19566 Z= 0.491 Chirality : 0.047 0.153 2274 Planarity : 0.004 0.046 2478 Dihedral : 11.904 88.160 2106 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.29 (0.20), residues: 1812 helix: 0.80 (0.21), residues: 690 sheet: -0.90 (0.25), residues: 480 loop : -0.50 (0.24), residues: 642 =============================================================================== Job complete usr+sys time: 5406.59 seconds wall clock time: 96 minutes 57.24 seconds (5817.24 seconds total)