Starting phenix.real_space_refine on Mon Apr 8 19:32:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2024/8dbn_27291_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2024/8dbn_27291.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2024/8dbn_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_2024/8dbn_27291_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2024/8dbn_27291_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2024/8dbn_27291.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2024/8dbn_27291.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2024/8dbn_27291_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbn_27291/04_2024/8dbn_27291_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.347 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-dev-5288/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: 7.65, per 1000 atoms: 0.54 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: 5.56 Conformation dependent library (CDL) restraints added in 2.6 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: 2.76 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: 4.15 Time building geometry restraints manager: 5.93 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: 1.610 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: 7.230 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 39.760 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.760 ------------------------------------------------------------------------------- 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 % Allowed : 14.66 % Favored : 82.10 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP F 162 HIS 0.007 0.001 HIS C 12 PHE 0.013 0.001 PHE B 138 TYR 0.007 0.002 TYR E 54 ARG 0.008 0.001 ARG D 214 *********************** 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 : 1.598 Fit side-chains REVERT: A 222 MET cc_start: 0.5355 (ptp) cc_final: 0.5067 (ptt) REVERT: B 191 LEU cc_start: 0.7012 (tt) cc_final: 0.6491 (mm) REVERT: B 222 MET cc_start: 0.5242 (ptp) cc_final: 0.5035 (ptt) REVERT: E 191 LEU cc_start: 0.7304 (tt) cc_final: 0.7060 (mm) REVERT: F 191 LEU cc_start: 0.7166 (tt) cc_final: 0.6964 (mm) REVERT: F 222 MET cc_start: 0.4920 (ptp) cc_final: 0.4640 (ptt) REVERT: F 261 ILE cc_start: 0.6313 (mt) cc_final: 0.6027 (mt) outliers start: 50 outliers final: 0 residues processed: 341 average time/residue: 1.1406 time to fit residues: 430.1923 Evaluate side-chains 219 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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: 0.5980 chunk 75 optimal weight: 0.0370 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 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: 0.8860 ------------------------------------------------------------------------------- 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: 0.6056 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14436 Z= 0.228 Angle : 1.435 47.732 19566 Z= 0.531 Chirality : 0.047 0.172 2274 Planarity : 0.005 0.076 2478 Dihedral : 16.858 142.371 2106 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.02 % Allowed : 17.32 % Favored : 78.66 % 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: 0.69 (0.19), residues: 1812 helix: 1.47 (0.20), residues: 690 sheet: -0.40 (0.25), residues: 414 loop : 0.15 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 162 HIS 0.007 0.002 HIS E 130 PHE 0.011 0.002 PHE D 7 TYR 0.010 0.002 TYR B 245 ARG 0.007 0.001 ARG F 184 *********************** 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 303 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 241 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.6144 (mtp) cc_final: 0.5540 (mtt) REVERT: A 96 ARG cc_start: 0.6728 (mtp180) cc_final: 0.6462 (mtp180) REVERT: B 115 MET cc_start: 0.5896 (mtp) cc_final: 0.5679 (mtp) REVERT: B 191 LEU cc_start: 0.7350 (tt) cc_final: 0.6989 (mp) REVERT: C 29 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.6237 (mttm) REVERT: C 68 MET cc_start: 0.6327 (mmt) cc_final: 0.5945 (mtt) REVERT: C 73 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.6212 (ttm) REVERT: C 176 LYS cc_start: 0.6288 (mptt) cc_final: 0.5838 (tptm) REVERT: C 237 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6043 (mm) REVERT: E 176 LYS cc_start: 0.6213 (mptt) cc_final: 0.5844 (tptm) REVERT: E 191 LEU cc_start: 0.7336 (tp) cc_final: 0.6907 (mm) REVERT: F 102 LYS cc_start: 0.7057 (mtpp) cc_final: 0.6813 (tttp) outliers start: 62 outliers final: 22 residues processed: 279 average time/residue: 1.1367 time to fit residues: 351.3210 Evaluate side-chains 222 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 284 CYS 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: 2.9990 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 176 optimal weight: 0.3980 chunk 145 optimal weight: 0.0060 chunk 162 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- 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** A 97 GLN A 135 GLN A 231 HIS ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN C 135 GLN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN E 135 GLN F 135 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.4530 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= 0.205 Angle : 1.364 47.129 19566 Z= 0.502 Chirality : 0.046 0.154 2274 Planarity : 0.004 0.027 2478 Dihedral : 13.162 87.233 2106 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.57 % Allowed : 19.65 % Favored : 76.78 % 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: 0.46 (0.20), residues: 1812 helix: 1.35 (0.20), residues: 684 sheet: -0.27 (0.24), residues: 480 loop : -0.19 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 162 HIS 0.006 0.002 HIS C 250 PHE 0.010 0.002 PHE C 138 TYR 0.010 0.001 TYR B 245 ARG 0.009 0.001 ARG C 96 *********************** 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 272 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 217 time to evaluate : 1.578 Fit side-chains revert: symmetry clash REVERT: B 191 LEU cc_start: 0.7313 (tt) cc_final: 0.7043 (mp) REVERT: B 301 ARG cc_start: 0.5960 (ttm110) cc_final: 0.5741 (ttp-110) REVERT: C 73 MET cc_start: 0.6471 (OUTLIER) cc_final: 0.6261 (ttm) REVERT: C 176 LYS cc_start: 0.6303 (mptt) cc_final: 0.5914 (tptm) REVERT: C 237 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6345 (mm) REVERT: E 129 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7152 (mt) REVERT: E 176 LYS cc_start: 0.6352 (mptt) cc_final: 0.5888 (tptm) REVERT: E 191 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6900 (mm) REVERT: F 102 LYS cc_start: 0.7060 (mtpp) cc_final: 0.6854 (tttp) outliers start: 55 outliers final: 24 residues processed: 250 average time/residue: 1.1791 time to fit residues: 326.5746 Evaluate side-chains 219 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 191 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 195 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 164 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** B 135 GLN C 97 GLN C 133 GLN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14436 Z= 0.300 Angle : 1.401 46.474 19566 Z= 0.530 Chirality : 0.048 0.158 2274 Planarity : 0.004 0.049 2478 Dihedral : 13.619 89.197 2106 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.73 % Allowed : 19.78 % Favored : 75.49 % 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: -0.07 (0.19), residues: 1812 helix: 0.79 (0.20), residues: 678 sheet: -0.59 (0.25), residues: 450 loop : -0.33 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 162 HIS 0.006 0.002 HIS E 130 PHE 0.009 0.002 PHE D 138 TYR 0.009 0.002 TYR B 245 ARG 0.012 0.001 ARG C 96 *********************** 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 285 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 212 time to evaluate : 1.550 Fit side-chains REVERT: A 129 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7152 (mt) REVERT: A 191 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6755 (mm) REVERT: B 191 LEU cc_start: 0.7387 (tt) cc_final: 0.7150 (mp) REVERT: C 73 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.6282 (ttm) REVERT: C 139 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.6818 (m-30) REVERT: C 237 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6823 (mm) REVERT: D 252 ILE cc_start: 0.6510 (OUTLIER) cc_final: 0.5924 (mt) REVERT: E 129 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7267 (mt) REVERT: E 176 LYS cc_start: 0.6639 (mptt) cc_final: 0.5915 (tptt) REVERT: E 191 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6963 (mm) REVERT: F 102 LYS cc_start: 0.7072 (mtpp) cc_final: 0.6855 (tttp) outliers start: 73 outliers final: 30 residues processed: 251 average time/residue: 1.1861 time to fit residues: 328.9729 Evaluate side-chains 229 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 191 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 194 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.0980 chunk 98 optimal weight: 6.9990 chunk 2 optimal weight: 0.0470 chunk 129 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 D 97 GLN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.5470 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= 0.177 Angle : 1.354 46.891 19566 Z= 0.495 Chirality : 0.046 0.148 2274 Planarity : 0.003 0.037 2478 Dihedral : 11.976 83.598 2106 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.50 % Allowed : 21.01 % Favored : 75.49 % 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: 0.13 (0.20), residues: 1812 helix: 1.10 (0.21), residues: 690 sheet: -0.54 (0.24), residues: 498 loop : -0.34 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 154 HIS 0.003 0.001 HIS B 304 PHE 0.010 0.001 PHE A 138 TYR 0.005 0.001 TYR B 245 ARG 0.010 0.001 ARG B 301 *********************** 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 250 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 196 time to evaluate : 1.557 Fit side-chains REVERT: A 129 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7141 (mt) REVERT: A 176 LYS cc_start: 0.6654 (mptt) cc_final: 0.6083 (tptt) REVERT: A 191 LEU cc_start: 0.7257 (tp) cc_final: 0.7013 (mt) REVERT: A 221 ASP cc_start: 0.6881 (p0) cc_final: 0.6593 (p0) REVERT: C 73 MET cc_start: 0.6538 (OUTLIER) cc_final: 0.6286 (ttm) REVERT: C 237 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6486 (mm) REVERT: D 191 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7344 (mm) REVERT: D 247 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7439 (mm) REVERT: E 176 LYS cc_start: 0.6207 (mptt) cc_final: 0.5934 (tptm) REVERT: E 191 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6868 (mm) outliers start: 54 outliers final: 28 residues processed: 226 average time/residue: 1.1964 time to fit residues: 298.7416 Evaluate side-chains 210 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 195 GLU 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: 0.5980 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** B 133 GLN ** 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** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14436 Z= 0.192 Angle : 1.358 46.833 19566 Z= 0.498 Chirality : 0.046 0.145 2274 Planarity : 0.003 0.033 2478 Dihedral : 11.645 88.735 2106 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.83 % Allowed : 21.60 % Favored : 74.58 % 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: 0.33 (0.20), residues: 1812 helix: 1.16 (0.21), residues: 690 sheet: -0.38 (0.25), residues: 450 loop : -0.16 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 154 HIS 0.004 0.001 HIS C 250 PHE 0.009 0.001 PHE B 266 TYR 0.006 0.001 TYR B 245 ARG 0.008 0.001 ARG B 96 *********************** 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 : 1.534 Fit side-chains revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7133 (mt) REVERT: A 221 ASP cc_start: 0.6823 (p0) cc_final: 0.6533 (p0) REVERT: C 73 MET cc_start: 0.6508 (OUTLIER) cc_final: 0.6261 (ttm) REVERT: C 237 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6455 (mm) REVERT: D 68 MET cc_start: 0.5817 (mtp) cc_final: 0.5475 (mtt) REVERT: D 247 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7452 (mm) REVERT: E 176 LYS cc_start: 0.6384 (mptt) cc_final: 0.5911 (tptt) REVERT: E 191 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6852 (mm) outliers start: 59 outliers final: 34 residues processed: 224 average time/residue: 1.2405 time to fit residues: 306.3044 Evaluate side-chains 215 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 176 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 195 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 98 optimal weight: 0.0980 chunk 146 optimal weight: 0.3980 chunk 97 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** A 133 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN E 38 GLN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.5702 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= 0.172 Angle : 1.353 46.916 19566 Z= 0.493 Chirality : 0.045 0.157 2274 Planarity : 0.003 0.051 2478 Dihedral : 11.099 82.518 2106 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.44 % Allowed : 22.18 % Favored : 74.38 % 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: 0.33 (0.20), residues: 1812 helix: 1.29 (0.21), residues: 690 sheet: -0.39 (0.24), residues: 498 loop : -0.30 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.003 0.001 HIS C 304 PHE 0.011 0.001 PHE E 35 TYR 0.010 0.001 TYR C 94 ARG 0.010 0.001 ARG C 301 *********************** 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: 53 poor density : 185 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7125 (mt) REVERT: A 191 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6661 (mm) REVERT: B 46 GLU cc_start: 0.5390 (tp30) cc_final: 0.4460 (tm-30) REVERT: C 73 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.6250 (ttm) REVERT: C 237 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6320 (mm) REVERT: C 301 ARG cc_start: 0.5906 (ttm110) cc_final: 0.5652 (ttm-80) REVERT: D 68 MET cc_start: 0.5797 (mtp) cc_final: 0.5482 (mtt) REVERT: D 247 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7445 (mm) REVERT: E 176 LYS cc_start: 0.6181 (mptt) cc_final: 0.5900 (tptm) REVERT: E 235 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7380 (tmtm) outliers start: 53 outliers final: 30 residues processed: 214 average time/residue: 1.1877 time to fit residues: 281.8245 Evaluate side-chains 210 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 195 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.5980 chunk 69 optimal weight: 0.3980 chunk 103 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 136 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14436 Z= 0.201 Angle : 1.365 46.777 19566 Z= 0.502 Chirality : 0.046 0.145 2274 Planarity : 0.004 0.039 2478 Dihedral : 11.472 83.593 2106 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.63 % Allowed : 22.50 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1812 helix: 1.21 (0.21), residues: 690 sheet: -0.34 (0.25), residues: 444 loop : -0.16 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 154 HIS 0.004 0.001 HIS B 130 PHE 0.012 0.001 PHE B 266 TYR 0.006 0.001 TYR B 245 ARG 0.009 0.001 ARG C 301 *********************** 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 238 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 182 time to evaluate : 1.583 Fit side-chains revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7159 (mt) REVERT: A 191 LEU cc_start: 0.7272 (tp) cc_final: 0.6660 (mm) REVERT: B 46 GLU cc_start: 0.5434 (tp30) cc_final: 0.4531 (tm-30) REVERT: C 73 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.6251 (ttm) REVERT: C 237 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6463 (mm) REVERT: D 68 MET cc_start: 0.5838 (mtp) cc_final: 0.5547 (mtt) REVERT: D 247 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7470 (mm) REVERT: E 176 LYS cc_start: 0.6393 (mptt) cc_final: 0.5950 (tptm) REVERT: E 235 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7335 (tmtm) outliers start: 56 outliers final: 37 residues processed: 215 average time/residue: 1.1790 time to fit residues: 280.8591 Evaluate side-chains 214 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 102 LYS Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 166 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14436 Z= 0.213 Angle : 1.368 46.780 19566 Z= 0.505 Chirality : 0.046 0.146 2274 Planarity : 0.004 0.037 2478 Dihedral : 11.714 86.287 2106 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.24 % Allowed : 22.70 % Favored : 74.06 % 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: 0.16 (0.20), residues: 1812 helix: 1.15 (0.21), residues: 690 sheet: -0.43 (0.24), residues: 480 loop : -0.45 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 154 HIS 0.004 0.001 HIS B 130 PHE 0.009 0.001 PHE D 138 TYR 0.007 0.001 TYR B 245 ARG 0.008 0.001 ARG E 96 *********************** 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 234 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 184 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7173 (mt) REVERT: A 191 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6719 (mm) REVERT: A 221 ASP cc_start: 0.6916 (p0) cc_final: 0.6550 (p0) REVERT: C 73 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.6276 (ttm) REVERT: C 237 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6516 (mm) REVERT: D 68 MET cc_start: 0.5797 (mtp) cc_final: 0.5477 (mtt) REVERT: D 247 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7488 (mm) REVERT: E 176 LYS cc_start: 0.6298 (mptt) cc_final: 0.5817 (tptm) REVERT: E 235 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7395 (tmtm) REVERT: F 129 LEU cc_start: 0.7559 (mm) cc_final: 0.7207 (mt) outliers start: 50 outliers final: 34 residues processed: 212 average time/residue: 1.2285 time to fit residues: 287.7332 Evaluate side-chains 221 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 181 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 102 LYS Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 166 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 0.0770 chunk 118 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- 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** ** B 133 GLN ** 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 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14436 Z= 0.257 Angle : 1.386 46.702 19566 Z= 0.519 Chirality : 0.048 0.152 2274 Planarity : 0.004 0.035 2478 Dihedral : 12.156 80.979 2106 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.11 % Allowed : 22.96 % Favored : 73.93 % 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: 0.06 (0.20), residues: 1812 helix: 0.93 (0.20), residues: 690 sheet: -0.52 (0.25), residues: 444 loop : -0.30 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 154 HIS 0.005 0.001 HIS E 130 PHE 0.009 0.002 PHE D 138 TYR 0.008 0.001 TYR B 245 ARG 0.012 0.001 ARG B 96 ********************** 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 235 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 187 time to evaluate : 1.469 Fit side-chains revert: symmetry clash REVERT: A 191 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6783 (mm) REVERT: A 221 ASP cc_start: 0.6953 (p0) cc_final: 0.6595 (p0) REVERT: C 73 MET cc_start: 0.6516 (OUTLIER) cc_final: 0.6270 (ttm) REVERT: C 164 ASN cc_start: 0.7194 (OUTLIER) cc_final: 0.6916 (m110) REVERT: C 237 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6759 (mm) REVERT: D 68 MET cc_start: 0.5828 (mtp) cc_final: 0.5497 (mtt) REVERT: D 247 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7479 (mm) REVERT: E 176 LYS cc_start: 0.6362 (mptt) cc_final: 0.5840 (tptt) REVERT: E 235 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7397 (tmtm) outliers start: 48 outliers final: 34 residues processed: 215 average time/residue: 1.2711 time to fit residues: 300.9473 Evaluate side-chains 221 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 181 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 102 LYS Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 146 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** ** B 133 GLN ** 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** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6010 r_free = 0.6010 target = 0.374856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5926 r_free = 0.5926 target = 0.355298 restraints weight = 12351.748| |-----------------------------------------------------------------------------| r_work (start): 0.5935 rms_B_bonded: 0.96 r_work: 0.5878 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.5781 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.5781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.6084 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= 0.177 Angle : 1.357 46.971 19566 Z= 0.497 Chirality : 0.046 0.144 2274 Planarity : 0.003 0.037 2478 Dihedral : 11.264 89.126 2106 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.66 % Allowed : 23.67 % Favored : 73.67 % 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: 0.19 (0.20), residues: 1812 helix: 1.16 (0.21), residues: 690 sheet: -0.50 (0.25), residues: 480 loop : -0.34 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 154 HIS 0.003 0.001 HIS F 304 PHE 0.010 0.001 PHE D 138 TYR 0.005 0.001 TYR F 94 ARG 0.008 0.001 ARG C 301 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5489.99 seconds wall clock time: 99 minutes 22.25 seconds (5962.25 seconds total)