Starting phenix.real_space_refine on Fri Dec 8 21:14:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbj_9791/12_2023/6jbj_9791_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbj_9791/12_2023/6jbj_9791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbj_9791/12_2023/6jbj_9791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbj_9791/12_2023/6jbj_9791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbj_9791/12_2023/6jbj_9791_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbj_9791/12_2023/6jbj_9791_neut_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 40 5.16 5 C 5914 2.51 5 N 1534 2.21 5 O 1672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 23": "NH1" <-> "NH2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A ARG 127": "NH1" <-> "NH2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 248": "NH1" <-> "NH2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 329": "OD1" <-> "OD2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 495": "NH1" <-> "NH2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A ASP 517": "OD1" <-> "OD2" Residue "A TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B ARG 127": "NH1" <-> "NH2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 137": "OD1" <-> "OD2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B ASP 278": "OD1" <-> "OD2" Residue "B TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 329": "OD1" <-> "OD2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ASP 400": "OD1" <-> "OD2" Residue "B PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 495": "NH1" <-> "NH2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B ASP 517": "OD1" <-> "OD2" Residue "B TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 557": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9166 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4552 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 19, 'TRANS': 545} Chain breaks: 1 Chain: "B" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4552 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 19, 'TRANS': 545} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.35, per 1000 atoms: 0.58 Number of scatterers: 9166 At special positions: 0 Unit cell: (75.92, 73.84, 130, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 6 15.00 O 1672 8.00 N 1534 7.00 C 5914 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: 3.59 Conformation dependent library (CDL) restraints added in 1.9 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 4 sheets defined 57.8% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.743A pdb=" N ILE A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 60 removed outlier: 3.936A pdb=" N THR A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 46 " --> pdb=" O MET A 42 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 52 " --> pdb=" O CYS A 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.929A pdb=" N TYR A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY A 69 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 71 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 123 removed outlier: 3.877A pdb=" N THR A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 134 removed outlier: 3.786A pdb=" N ASN A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 158 removed outlier: 3.736A pdb=" N ASP A 149 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.565A pdb=" N LEU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 removed outlier: 4.039A pdb=" N PHE A 191 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY A 192 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 195 " --> pdb=" O GLY A 192 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 196 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 198 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 199 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL A 200 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 230 removed outlier: 3.905A pdb=" N HIS A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 218 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.664A pdb=" N PHE A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 294 removed outlier: 4.281A pdb=" N MET A 247 " --> pdb=" O HIS A 243 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 251 " --> pdb=" O MET A 247 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TRP A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.608A pdb=" N PHE A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N CYS A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 329 No H-bonds generated for 'chain 'A' and resid 326 through 329' Processing helix chain 'A' and resid 331 through 355 removed outlier: 3.778A pdb=" N VAL A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN A 346 " --> pdb=" O HIS A 342 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 434 removed outlier: 4.071A pdb=" N LEU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 485 No H-bonds generated for 'chain 'A' and resid 482 through 485' Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.896A pdb=" N GLU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.790A pdb=" N ALA A 507 " --> pdb=" O ASN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 539 removed outlier: 3.858A pdb=" N GLN A 530 " --> pdb=" O PRO A 526 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG A 531 " --> pdb=" O GLY A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 569 removed outlier: 3.545A pdb=" N ILE A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'B' and resid 19 through 31 removed outlier: 3.743A pdb=" N ILE B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL B 30 " --> pdb=" O GLN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 60 removed outlier: 3.936A pdb=" N THR B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 46 " --> pdb=" O MET B 42 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B 52 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 71 removed outlier: 3.929A pdb=" N TYR B 68 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY B 69 " --> pdb=" O GLN B 66 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 71 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 123 removed outlier: 3.877A pdb=" N THR B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 134 removed outlier: 3.786A pdb=" N ASN B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.736A pdb=" N ASP B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.565A pdb=" N LEU B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 removed outlier: 4.039A pdb=" N PHE B 191 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY B 192 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 195 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B 196 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR B 198 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 199 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL B 200 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 230 removed outlier: 3.905A pdb=" N HIS B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 218 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 239 removed outlier: 3.664A pdb=" N PHE B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 294 removed outlier: 4.281A pdb=" N MET B 247 " --> pdb=" O HIS B 243 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B 251 " --> pdb=" O MET B 247 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 259 " --> pdb=" O ARG B 255 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 262 " --> pdb=" O GLN B 258 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TRP B 269 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.608A pdb=" N PHE B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N CYS B 323 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 329 No H-bonds generated for 'chain 'B' and resid 326 through 329' Processing helix chain 'B' and resid 331 through 355 removed outlier: 3.778A pdb=" N VAL B 337 " --> pdb=" O THR B 333 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN B 346 " --> pdb=" O HIS B 342 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU B 349 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET B 354 " --> pdb=" O THR B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 434 removed outlier: 4.070A pdb=" N LEU B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 485 No H-bonds generated for 'chain 'B' and resid 482 through 485' Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.896A pdb=" N GLU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.790A pdb=" N ALA B 507 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 539 removed outlier: 3.858A pdb=" N GLN B 530 " --> pdb=" O PRO B 526 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 531 " --> pdb=" O GLY B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 569 removed outlier: 3.545A pdb=" N ILE B 565 " --> pdb=" O GLU B 561 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 584 No H-bonds generated for 'chain 'B' and resid 582 through 584' Processing sheet with id= A, first strand: chain 'A' and resid 444 through 447 Processing sheet with id= B, first strand: chain 'A' and resid 456 through 458 removed outlier: 6.865A pdb=" N TYR A 544 " --> pdb=" O LEU A 457 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 444 through 447 Processing sheet with id= D, first strand: chain 'B' and resid 456 through 458 removed outlier: 6.865A pdb=" N TYR B 544 " --> pdb=" O LEU B 457 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 363 hydrogen bonds defined for protein. 1029 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: 2.55 Time building geometry restraints manager: 3.85 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: 2872 1.34 - 1.46: 1899 1.46 - 1.57: 4521 1.57 - 1.69: 10 1.69 - 1.81: 66 Bond restraints: 9368 Sorted by residual: bond pdb=" C SER B 302 " pdb=" N PRO B 303 " ideal model delta sigma weight residual 1.336 1.376 -0.040 9.80e-03 1.04e+04 1.64e+01 bond pdb=" C SER A 302 " pdb=" N PRO A 303 " ideal model delta sigma weight residual 1.336 1.375 -0.039 9.80e-03 1.04e+04 1.62e+01 bond pdb=" C LEU B 524 " pdb=" N SER B 525 " ideal model delta sigma weight residual 1.333 1.281 0.052 1.39e-02 5.18e+03 1.41e+01 bond pdb=" C LEU A 524 " pdb=" N SER A 525 " ideal model delta sigma weight residual 1.333 1.281 0.052 1.39e-02 5.18e+03 1.39e+01 bond pdb=" N PHE A 387 " pdb=" CA PHE A 387 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.29e-02 6.01e+03 6.45e+00 ... (remaining 9363 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.88: 258 106.88 - 113.68: 5198 113.68 - 120.47: 4056 120.47 - 127.27: 3082 127.27 - 134.07: 108 Bond angle restraints: 12702 Sorted by residual: angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 132.60 7.27 1.00e+00 1.00e+00 5.28e+01 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 132.63 7.24 1.00e+00 1.00e+00 5.25e+01 angle pdb=" C SER B 307 " pdb=" N THR B 308 " pdb=" CA THR B 308 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C SER A 307 " pdb=" N THR A 308 " pdb=" CA THR A 308 " ideal model delta sigma weight residual 121.54 131.37 -9.83 1.91e+00 2.74e-01 2.65e+01 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 132.53 4.30 1.00e+00 1.00e+00 1.85e+01 ... (remaining 12697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 4813 17.67 - 35.33: 600 35.33 - 53.00: 135 53.00 - 70.66: 40 70.66 - 88.33: 10 Dihedral angle restraints: 5598 sinusoidal: 2316 harmonic: 3282 Sorted by residual: dihedral pdb=" CA MET A 227 " pdb=" C MET A 227 " pdb=" N GLN A 228 " pdb=" CA GLN A 228 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA MET B 227 " pdb=" C MET B 227 " pdb=" N GLN B 228 " pdb=" CA GLN B 228 " ideal model delta harmonic sigma weight residual 180.00 157.15 22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ILE A 475 " pdb=" C ILE A 475 " pdb=" N TYR A 476 " pdb=" CA TYR A 476 " ideal model delta harmonic sigma weight residual 180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 5595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1017 0.057 - 0.114: 360 0.114 - 0.171: 49 0.171 - 0.228: 18 0.228 - 0.285: 4 Chirality restraints: 1448 Sorted by residual: chirality pdb=" CB ILE A 574 " pdb=" CA ILE A 574 " pdb=" CG1 ILE A 574 " pdb=" CG2 ILE A 574 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE B 574 " pdb=" CA ILE B 574 " pdb=" CG1 ILE B 574 " pdb=" CG2 ILE B 574 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE A 419 " pdb=" CA ILE A 419 " pdb=" CG1 ILE A 419 " pdb=" CG2 ILE A 419 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1445 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 167 " -0.055 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 168 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 167 " 0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO B 168 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 168 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 168 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 291 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO A 292 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.038 5.00e-02 4.00e+02 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1345 2.75 - 3.28: 9168 3.28 - 3.82: 16026 3.82 - 4.36: 19675 4.36 - 4.90: 31892 Nonbonded interactions: 78106 Sorted by model distance: nonbonded pdb=" O THR B 423 " pdb=" O1B ATP B 701 " model vdw 2.206 3.040 nonbonded pdb=" O THR A 423 " pdb=" O1B ATP A 701 " model vdw 2.206 3.040 nonbonded pdb=" O ILE A 291 " pdb=" OG SER A 295 " model vdw 2.312 2.440 nonbonded pdb=" O ILE B 291 " pdb=" OG SER B 295 " model vdw 2.312 2.440 nonbonded pdb=" OH TYR A 108 " pdb=" OE1 GLN B 260 " model vdw 2.316 2.440 ... (remaining 78101 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' } 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 group one per residue 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: 0.320 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: 2.310 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.930 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 0.008 0.053 9368 Z= 0.500 Angle : 1.036 11.308 12702 Z= 0.555 Chirality : 0.059 0.285 1448 Planarity : 0.007 0.082 1580 Dihedral : 16.772 88.329 3490 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.19 (0.15), residues: 1122 helix: -4.17 (0.09), residues: 720 sheet: None (None), residues: 0 loop : -3.61 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 520 HIS 0.004 0.001 HIS A 118 PHE 0.032 0.003 PHE A 324 TYR 0.021 0.003 TYR B 319 ARG 0.002 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2202 time to fit residues: 83.9961 Evaluate side-chains 196 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN A 228 GLN A 549 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN B 201 ASN B 228 GLN B 422 ASN B 549 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9368 Z= 0.252 Angle : 0.694 8.173 12702 Z= 0.360 Chirality : 0.042 0.147 1448 Planarity : 0.005 0.060 1580 Dihedral : 10.124 78.386 1310 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.57 % Allowed : 20.95 % Favored : 76.48 % 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: -4.48 (0.19), residues: 1122 helix: -2.64 (0.15), residues: 716 sheet: None (None), residues: 0 loop : -3.37 (0.25), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 111 HIS 0.003 0.001 HIS B 342 PHE 0.021 0.002 PHE B 451 TYR 0.015 0.002 TYR A 319 ARG 0.003 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 233 time to evaluate : 1.088 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 248 average time/residue: 0.2081 time to fit residues: 71.4468 Evaluate side-chains 207 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 196 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0887 time to fit residues: 3.2323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 overall best weight: 4.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN A 177 GLN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 549 GLN ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN B 549 GLN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 9368 Z= 0.564 Angle : 0.814 7.376 12702 Z= 0.422 Chirality : 0.049 0.189 1448 Planarity : 0.005 0.047 1580 Dihedral : 9.655 71.381 1310 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 5.93 % Allowed : 22.83 % Favored : 71.25 % 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: -3.95 (0.21), residues: 1122 helix: -2.12 (0.16), residues: 744 sheet: None (None), residues: 0 loop : -3.43 (0.27), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 269 HIS 0.005 0.001 HIS A 226 PHE 0.020 0.003 PHE A 222 TYR 0.019 0.002 TYR B 68 ARG 0.005 0.001 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 204 time to evaluate : 1.107 Fit side-chains outliers start: 60 outliers final: 30 residues processed: 240 average time/residue: 0.1854 time to fit residues: 64.7184 Evaluate side-chains 214 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.0879 time to fit residues: 6.3289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 GLN ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN B 177 GLN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9368 Z= 0.201 Angle : 0.661 9.095 12702 Z= 0.331 Chirality : 0.042 0.161 1448 Planarity : 0.004 0.042 1580 Dihedral : 8.186 76.949 1310 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.96 % Allowed : 25.59 % Favored : 71.44 % 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: -3.34 (0.22), residues: 1122 helix: -1.55 (0.17), residues: 730 sheet: -0.89 (1.01), residues: 30 loop : -3.55 (0.26), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 598 HIS 0.003 0.001 HIS B 226 PHE 0.025 0.001 PHE B 324 TYR 0.012 0.001 TYR B 476 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 222 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 9 residues processed: 240 average time/residue: 0.1952 time to fit residues: 66.5639 Evaluate side-chains 200 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 191 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0898 time to fit residues: 2.9216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9368 Z= 0.214 Angle : 0.656 10.070 12702 Z= 0.326 Chirality : 0.042 0.164 1448 Planarity : 0.004 0.042 1580 Dihedral : 7.281 77.026 1310 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.67 % Allowed : 26.09 % Favored : 71.25 % 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: -2.86 (0.23), residues: 1122 helix: -1.17 (0.18), residues: 732 sheet: -0.26 (1.31), residues: 20 loop : -3.36 (0.27), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 598 HIS 0.005 0.001 HIS A 226 PHE 0.016 0.001 PHE A 84 TYR 0.012 0.001 TYR B 476 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 207 time to evaluate : 1.109 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 221 average time/residue: 0.2008 time to fit residues: 63.1537 Evaluate side-chains 202 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 187 time to evaluate : 1.164 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0910 time to fit residues: 4.0205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9368 Z= 0.369 Angle : 0.716 9.325 12702 Z= 0.362 Chirality : 0.045 0.260 1448 Planarity : 0.004 0.036 1580 Dihedral : 7.046 77.809 1310 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 1.88 % Allowed : 27.96 % Favored : 70.16 % 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: -2.81 (0.23), residues: 1122 helix: -0.98 (0.18), residues: 728 sheet: -1.16 (1.14), residues: 20 loop : -3.62 (0.26), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 598 HIS 0.004 0.001 HIS A 226 PHE 0.016 0.002 PHE A 324 TYR 0.016 0.002 TYR A 476 ARG 0.003 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 210 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 220 average time/residue: 0.2029 time to fit residues: 64.7609 Evaluate side-chains 197 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 188 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0946 time to fit residues: 3.0397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 260 GLN A 415 GLN A 549 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN B 177 GLN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9368 Z= 0.199 Angle : 0.664 8.658 12702 Z= 0.332 Chirality : 0.042 0.226 1448 Planarity : 0.004 0.040 1580 Dihedral : 6.716 74.158 1310 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.38 % Allowed : 28.95 % Favored : 69.66 % 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: -2.54 (0.23), residues: 1122 helix: -0.84 (0.19), residues: 738 sheet: -1.13 (1.13), residues: 20 loop : -3.39 (0.27), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 598 HIS 0.004 0.001 HIS A 226 PHE 0.017 0.001 PHE B 324 TYR 0.013 0.001 TYR B 476 ARG 0.006 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 213 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 219 average time/residue: 0.1898 time to fit residues: 60.4648 Evaluate side-chains 196 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0996 time to fit residues: 2.9802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 73 optimal weight: 0.1980 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9368 Z= 0.190 Angle : 0.678 12.056 12702 Z= 0.334 Chirality : 0.041 0.215 1448 Planarity : 0.004 0.038 1580 Dihedral : 6.430 68.251 1310 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.58 % Allowed : 28.85 % Favored : 69.57 % 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: -2.32 (0.23), residues: 1122 helix: -0.68 (0.19), residues: 728 sheet: -1.02 (1.15), residues: 20 loop : -3.24 (0.26), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 35 HIS 0.003 0.001 HIS B 226 PHE 0.017 0.001 PHE A 84 TYR 0.010 0.001 TYR A 476 ARG 0.002 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 215 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 227 average time/residue: 0.1875 time to fit residues: 62.6030 Evaluate side-chains 202 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1020 time to fit residues: 3.2091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9368 Z= 0.197 Angle : 0.672 9.647 12702 Z= 0.331 Chirality : 0.042 0.225 1448 Planarity : 0.004 0.040 1580 Dihedral : 6.331 64.745 1310 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.59 % Allowed : 29.84 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.23 (0.23), residues: 1122 helix: -0.60 (0.19), residues: 728 sheet: -1.17 (1.12), residues: 20 loop : -3.22 (0.26), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 35 HIS 0.004 0.001 HIS A 226 PHE 0.020 0.001 PHE B 84 TYR 0.013 0.001 TYR A 544 ARG 0.004 0.000 ARG B 564 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 209 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 211 average time/residue: 0.1923 time to fit residues: 58.8158 Evaluate side-chains 194 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 189 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0940 time to fit residues: 2.3817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 73 optimal weight: 0.1980 chunk 111 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9368 Z= 0.220 Angle : 0.697 10.787 12702 Z= 0.340 Chirality : 0.042 0.207 1448 Planarity : 0.004 0.039 1580 Dihedral : 6.300 62.184 1310 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.49 % Allowed : 30.63 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.15 (0.23), residues: 1122 helix: -0.53 (0.19), residues: 732 sheet: -1.37 (1.07), residues: 20 loop : -3.20 (0.26), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 598 HIS 0.004 0.001 HIS A 226 PHE 0.016 0.001 PHE A 573 TYR 0.011 0.001 TYR B 68 ARG 0.008 0.000 ARG B 564 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 202 time to evaluate : 1.129 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 204 average time/residue: 0.1799 time to fit residues: 54.2722 Evaluate side-chains 188 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0920 time to fit residues: 1.9097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 0.0370 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 GLN ** 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 = 0.3574 r_free = 0.3574 target = 0.130517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.104106 restraints weight = 14608.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.107475 restraints weight = 6978.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.109497 restraints weight = 4442.872| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9368 Z= 0.222 Angle : 0.705 10.028 12702 Z= 0.344 Chirality : 0.043 0.364 1448 Planarity : 0.004 0.039 1580 Dihedral : 6.264 59.756 1310 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.89 % Allowed : 31.13 % Favored : 67.98 % 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: -2.08 (0.23), residues: 1122 helix: -0.47 (0.19), residues: 732 sheet: -1.45 (1.06), residues: 20 loop : -3.19 (0.26), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 598 HIS 0.003 0.001 HIS A 120 PHE 0.020 0.001 PHE B 84 TYR 0.017 0.001 TYR B 544 ARG 0.007 0.000 ARG B 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1961.77 seconds wall clock time: 36 minutes 37.62 seconds (2197.62 seconds total)