Starting phenix.real_space_refine on Thu Mar 14 15:38:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbj_9791/03_2024/6jbj_9791_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbj_9791/03_2024/6jbj_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_9791/03_2024/6jbj_9791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbj_9791/03_2024/6jbj_9791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbj_9791/03_2024/6jbj_9791_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jbj_9791/03_2024/6jbj_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-dev-5265/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: 5.28, 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: 3.45 Conformation dependent library (CDL) restraints added in 1.7 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: 1.90 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: 2.28 Time building geometry restraints manager: 3.74 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: 0.330 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: 2.240 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.200 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.970 ------------------------------------------------------------------------------- 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 : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9050 (mt) cc_final: 0.8779 (mt) REVERT: A 55 PHE cc_start: 0.7354 (t80) cc_final: 0.6893 (m-10) REVERT: A 68 TYR cc_start: 0.7741 (m-80) cc_final: 0.7426 (m-10) REVERT: A 217 LYS cc_start: 0.8455 (tttt) cc_final: 0.8248 (tttp) REVERT: A 247 MET cc_start: 0.7616 (mmt) cc_final: 0.7366 (mmt) REVERT: A 465 PHE cc_start: 0.9099 (m-80) cc_final: 0.8878 (m-10) REVERT: A 567 GLN cc_start: 0.7960 (mp10) cc_final: 0.7664 (pm20) REVERT: B 55 PHE cc_start: 0.7394 (t80) cc_final: 0.6830 (m-10) REVERT: B 315 PHE cc_start: 0.7541 (t80) cc_final: 0.7050 (t80) REVERT: B 388 LEU cc_start: 0.8653 (mt) cc_final: 0.8401 (mt) REVERT: B 422 ASN cc_start: 0.8214 (t0) cc_final: 0.7305 (m-40) REVERT: B 465 PHE cc_start: 0.9070 (m-80) cc_final: 0.8856 (m-10) REVERT: B 495 ARG cc_start: 0.8205 (ttt180) cc_final: 0.7997 (ttt90) REVERT: B 517 ASP cc_start: 0.7162 (m-30) cc_final: 0.6952 (m-30) REVERT: B 518 TRP cc_start: 0.7900 (m-10) cc_final: 0.7395 (m-10) REVERT: B 567 GLN cc_start: 0.7880 (mp10) cc_final: 0.7636 (pm20) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2090 time to fit residues: 79.6985 Evaluate side-chains 201 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.7980 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN B 228 GLN B 254 GLN B 549 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9368 Z= 0.203 Angle : 0.665 8.185 12702 Z= 0.340 Chirality : 0.041 0.140 1448 Planarity : 0.005 0.061 1580 Dihedral : 10.047 76.300 1310 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.47 % Allowed : 20.36 % Favored : 77.17 % 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: -4.44 (0.19), residues: 1122 helix: -2.61 (0.15), residues: 716 sheet: None (None), residues: 0 loop : -3.36 (0.25), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 111 HIS 0.004 0.001 HIS B 342 PHE 0.023 0.002 PHE B 451 TYR 0.015 0.001 TYR A 319 ARG 0.006 0.000 ARG A 152 *********************** 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 269 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 244 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7506 (tm-30) cc_final: 0.6871 (tm-30) REVERT: A 51 LEU cc_start: 0.9076 (mt) cc_final: 0.8865 (mt) REVERT: A 52 LEU cc_start: 0.9351 (tp) cc_final: 0.8978 (tp) REVERT: A 55 PHE cc_start: 0.7524 (t80) cc_final: 0.7094 (m-10) REVERT: A 84 PHE cc_start: 0.7885 (t80) cc_final: 0.7594 (t80) REVERT: A 217 LYS cc_start: 0.8587 (tttt) cc_final: 0.8339 (tttp) REVERT: A 234 GLU cc_start: 0.8673 (tp30) cc_final: 0.8248 (mm-30) REVERT: A 247 MET cc_start: 0.7768 (mmt) cc_final: 0.7521 (mmt) REVERT: A 312 LYS cc_start: 0.8265 (tmmt) cc_final: 0.7851 (ptmm) REVERT: B 51 LEU cc_start: 0.9040 (mt) cc_final: 0.8677 (mp) REVERT: B 55 PHE cc_start: 0.7563 (t80) cc_final: 0.6877 (m-10) REVERT: B 68 TYR cc_start: 0.7581 (m-10) cc_final: 0.7313 (m-10) REVERT: B 230 ARG cc_start: 0.8644 (ttp80) cc_final: 0.8028 (ttp80) REVERT: B 312 LYS cc_start: 0.8254 (tmmt) cc_final: 0.7877 (ptmm) REVERT: B 422 ASN cc_start: 0.8167 (t0) cc_final: 0.7436 (m110) outliers start: 25 outliers final: 11 residues processed: 256 average time/residue: 0.2151 time to fit residues: 75.4113 Evaluate side-chains 212 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 201 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 585 PHE 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: 5.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.0670 overall best weight: 1.6124 ------------------------------------------------------------------------------- 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 ** B 66 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9368 Z= 0.242 Angle : 0.643 7.683 12702 Z= 0.328 Chirality : 0.042 0.188 1448 Planarity : 0.004 0.045 1580 Dihedral : 8.949 65.511 1310 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 3.06 % Allowed : 23.62 % Favored : 73.32 % 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: -3.61 (0.21), residues: 1122 helix: -1.82 (0.17), residues: 722 sheet: None (None), residues: 0 loop : -3.33 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 598 HIS 0.002 0.001 HIS B 226 PHE 0.016 0.002 PHE A 222 TYR 0.013 0.001 TYR A 319 ARG 0.005 0.000 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 260 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 229 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7592 (tm-30) cc_final: 0.6766 (tm-30) REVERT: A 42 MET cc_start: 0.8645 (ttm) cc_final: 0.8329 (ttm) REVERT: A 47 LEU cc_start: 0.9181 (tt) cc_final: 0.8979 (tp) REVERT: A 52 LEU cc_start: 0.9370 (tp) cc_final: 0.9057 (tp) REVERT: A 55 PHE cc_start: 0.7610 (t80) cc_final: 0.6924 (m-10) REVERT: A 84 PHE cc_start: 0.7929 (t80) cc_final: 0.7686 (t80) REVERT: A 85 LEU cc_start: 0.9207 (tp) cc_final: 0.8956 (tt) REVERT: A 217 LYS cc_start: 0.8621 (tttt) cc_final: 0.8399 (tttp) REVERT: A 247 MET cc_start: 0.7830 (mmt) cc_final: 0.7561 (mmt) REVERT: A 268 LEU cc_start: 0.9361 (tt) cc_final: 0.9093 (tp) REVERT: A 312 LYS cc_start: 0.8335 (tmmt) cc_final: 0.7947 (ptmt) REVERT: A 502 LEU cc_start: 0.9151 (pt) cc_final: 0.8844 (pp) REVERT: B 51 LEU cc_start: 0.8992 (mt) cc_final: 0.8672 (mp) REVERT: B 55 PHE cc_start: 0.7623 (t80) cc_final: 0.6926 (m-10) REVERT: B 68 TYR cc_start: 0.7713 (m-10) cc_final: 0.7479 (m-10) REVERT: B 85 LEU cc_start: 0.9217 (tp) cc_final: 0.9006 (tt) REVERT: B 312 LYS cc_start: 0.8322 (tmmt) cc_final: 0.7910 (ptmm) REVERT: B 422 ASN cc_start: 0.8165 (t0) cc_final: 0.7478 (m110) REVERT: B 502 LEU cc_start: 0.9114 (pt) cc_final: 0.8773 (pp) outliers start: 31 outliers final: 19 residues processed: 246 average time/residue: 0.1809 time to fit residues: 63.3525 Evaluate side-chains 227 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 208 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 105 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9368 Z= 0.249 Angle : 0.619 7.798 12702 Z= 0.317 Chirality : 0.042 0.171 1448 Planarity : 0.004 0.034 1580 Dihedral : 7.962 67.624 1310 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.35 % Allowed : 23.42 % Favored : 72.23 % 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: -3.15 (0.22), residues: 1122 helix: -1.36 (0.18), residues: 722 sheet: -0.53 (1.19), residues: 20 loop : -3.52 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 598 HIS 0.003 0.001 HIS A 226 PHE 0.014 0.001 PHE A 222 TYR 0.015 0.001 TYR A 271 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 265 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 221 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7080 (tm-30) REVERT: A 55 PHE cc_start: 0.7608 (t80) cc_final: 0.6938 (m-10) REVERT: A 84 PHE cc_start: 0.7852 (t80) cc_final: 0.7621 (t80) REVERT: A 85 LEU cc_start: 0.9209 (tp) cc_final: 0.8977 (tt) REVERT: A 165 ILE cc_start: 0.8935 (tp) cc_final: 0.8706 (tp) REVERT: A 217 LYS cc_start: 0.8567 (tttt) cc_final: 0.8344 (tttp) REVERT: A 247 MET cc_start: 0.7722 (mmt) cc_final: 0.7459 (mmt) REVERT: A 268 LEU cc_start: 0.9385 (tt) cc_final: 0.9115 (tp) REVERT: A 312 LYS cc_start: 0.8276 (tmmt) cc_final: 0.7912 (ptmm) REVERT: A 388 LEU cc_start: 0.8583 (mt) cc_final: 0.8362 (mt) REVERT: A 502 LEU cc_start: 0.9238 (pt) cc_final: 0.8907 (pp) REVERT: B 55 PHE cc_start: 0.7630 (t80) cc_final: 0.6908 (m-10) REVERT: B 68 TYR cc_start: 0.7829 (m-10) cc_final: 0.7545 (m-10) REVERT: B 85 LEU cc_start: 0.9229 (tp) cc_final: 0.9022 (tt) REVERT: B 312 LYS cc_start: 0.8271 (tmmt) cc_final: 0.7816 (ptmt) REVERT: B 319 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7705 (t80) REVERT: B 502 LEU cc_start: 0.9219 (pt) cc_final: 0.8878 (pp) outliers start: 44 outliers final: 22 residues processed: 248 average time/residue: 0.1904 time to fit residues: 67.3318 Evaluate side-chains 225 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 319 TYR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 0.0470 chunk 36 optimal weight: 9.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- 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** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8108 moved from start: 0.2984 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= 0.175 Angle : 0.595 6.921 12702 Z= 0.302 Chirality : 0.040 0.177 1448 Planarity : 0.003 0.037 1580 Dihedral : 6.923 66.806 1310 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.56 % Allowed : 24.80 % Favored : 71.64 % 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: -2.75 (0.23), residues: 1122 helix: -0.98 (0.18), residues: 728 sheet: -0.72 (1.18), residues: 20 loop : -3.50 (0.25), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 598 HIS 0.003 0.001 HIS B 226 PHE 0.018 0.001 PHE A 324 TYR 0.011 0.001 TYR A 476 ARG 0.002 0.000 ARG B 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 261 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 225 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7829 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 55 PHE cc_start: 0.7589 (t80) cc_final: 0.6915 (m-10) REVERT: A 68 TYR cc_start: 0.7885 (m-10) cc_final: 0.7593 (m-10) REVERT: A 85 LEU cc_start: 0.9218 (tp) cc_final: 0.8988 (tt) REVERT: A 165 ILE cc_start: 0.8907 (tp) cc_final: 0.8700 (tp) REVERT: A 217 LYS cc_start: 0.8476 (tttt) cc_final: 0.8267 (tttp) REVERT: A 247 MET cc_start: 0.7802 (mmt) cc_final: 0.7539 (mmt) REVERT: A 312 LYS cc_start: 0.8158 (tmmt) cc_final: 0.7741 (ptmm) REVERT: A 502 LEU cc_start: 0.9215 (pt) cc_final: 0.8879 (pp) REVERT: A 529 MET cc_start: 0.8347 (mtt) cc_final: 0.7856 (mtt) REVERT: A 567 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7168 (mt0) REVERT: B 55 PHE cc_start: 0.7603 (t80) cc_final: 0.6890 (m-10) REVERT: B 68 TYR cc_start: 0.7779 (m-10) cc_final: 0.7549 (m-10) REVERT: B 85 LEU cc_start: 0.9234 (tp) cc_final: 0.9020 (tt) REVERT: B 312 LYS cc_start: 0.8255 (tmmt) cc_final: 0.7790 (ptmt) REVERT: B 319 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7670 (t80) REVERT: B 330 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8224 (pp) REVERT: B 567 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7154 (mt0) outliers start: 36 outliers final: 20 residues processed: 243 average time/residue: 0.1710 time to fit residues: 60.1970 Evaluate side-chains 225 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 201 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 319 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 228 GLN B 38 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3082 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= 0.224 Angle : 0.613 7.409 12702 Z= 0.312 Chirality : 0.042 0.177 1448 Planarity : 0.004 0.040 1580 Dihedral : 6.554 64.913 1310 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.55 % Allowed : 24.41 % Favored : 71.05 % 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: -2.50 (0.23), residues: 1122 helix: -0.74 (0.19), residues: 732 sheet: -1.39 (1.04), residues: 20 loop : -3.49 (0.26), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 598 HIS 0.003 0.001 HIS A 226 PHE 0.011 0.001 PHE A 324 TYR 0.010 0.001 TYR B 476 ARG 0.004 0.000 ARG A 15 *********************** 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 257 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 211 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 55 PHE cc_start: 0.7584 (t80) cc_final: 0.6918 (m-10) REVERT: A 68 TYR cc_start: 0.7944 (m-10) cc_final: 0.7630 (m-10) REVERT: A 83 THR cc_start: 0.8443 (t) cc_final: 0.8206 (t) REVERT: A 85 LEU cc_start: 0.9232 (tp) cc_final: 0.8977 (tt) REVERT: A 108 TYR cc_start: 0.9125 (OUTLIER) cc_final: 0.8555 (t80) REVERT: A 165 ILE cc_start: 0.8875 (tp) cc_final: 0.8660 (tp) REVERT: A 217 LYS cc_start: 0.8497 (tttt) cc_final: 0.8277 (tttp) REVERT: A 227 MET cc_start: 0.7998 (ptp) cc_final: 0.7633 (ptp) REVERT: A 247 MET cc_start: 0.7738 (mmt) cc_final: 0.7501 (mmt) REVERT: A 268 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9037 (tt) REVERT: A 312 LYS cc_start: 0.8126 (tmmt) cc_final: 0.7708 (ptmm) REVERT: A 319 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.7683 (t80) REVERT: A 502 LEU cc_start: 0.9268 (pt) cc_final: 0.8983 (pp) REVERT: A 567 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7147 (mt0) REVERT: B 55 PHE cc_start: 0.7613 (t80) cc_final: 0.6899 (m-10) REVERT: B 68 TYR cc_start: 0.7859 (m-10) cc_final: 0.7550 (m-10) REVERT: B 85 LEU cc_start: 0.9243 (tp) cc_final: 0.9035 (tt) REVERT: B 312 LYS cc_start: 0.8212 (tmmt) cc_final: 0.7772 (ptmt) REVERT: B 319 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7621 (t80) REVERT: B 330 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8283 (pp) REVERT: B 502 LEU cc_start: 0.9220 (pt) cc_final: 0.8895 (pp) REVERT: B 567 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7135 (mt0) outliers start: 46 outliers final: 32 residues processed: 239 average time/residue: 0.1756 time to fit residues: 60.5979 Evaluate side-chains 231 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 319 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 0.0870 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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** ** 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: 0.8105 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9368 Z= 0.177 Angle : 0.606 7.667 12702 Z= 0.305 Chirality : 0.040 0.167 1448 Planarity : 0.003 0.041 1580 Dihedral : 6.286 62.919 1310 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.46 % Allowed : 26.28 % Favored : 70.26 % 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: -2.27 (0.24), residues: 1122 helix: -0.54 (0.19), residues: 732 sheet: -1.49 (1.04), residues: 20 loop : -3.44 (0.26), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 598 HIS 0.003 0.001 HIS B 226 PHE 0.013 0.001 PHE A 324 TYR 0.009 0.001 TYR B 476 ARG 0.007 0.000 ARG B 15 *********************** 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 246 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 211 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7557 (tm-30) REVERT: A 55 PHE cc_start: 0.7589 (t80) cc_final: 0.6954 (m-10) REVERT: A 68 TYR cc_start: 0.7895 (m-10) cc_final: 0.7601 (m-10) REVERT: A 83 THR cc_start: 0.8414 (t) cc_final: 0.8168 (t) REVERT: A 85 LEU cc_start: 0.9216 (tp) cc_final: 0.8960 (tt) REVERT: A 136 ARG cc_start: 0.8282 (mmt-90) cc_final: 0.7507 (mpt180) REVERT: A 165 ILE cc_start: 0.8841 (tp) cc_final: 0.8632 (tp) REVERT: A 217 LYS cc_start: 0.8494 (tttt) cc_final: 0.8292 (tttp) REVERT: A 247 MET cc_start: 0.7704 (mmt) cc_final: 0.7490 (mmt) REVERT: A 260 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8861 (mt0) REVERT: A 312 LYS cc_start: 0.8133 (tmmt) cc_final: 0.7709 (ptmm) REVERT: A 319 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7548 (t80) REVERT: A 502 LEU cc_start: 0.9241 (pt) cc_final: 0.8937 (pp) REVERT: A 529 MET cc_start: 0.8341 (mtt) cc_final: 0.7906 (mtt) REVERT: A 567 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7081 (mt0) REVERT: B 55 PHE cc_start: 0.7605 (t80) cc_final: 0.6891 (m-10) REVERT: B 68 TYR cc_start: 0.7867 (m-10) cc_final: 0.7644 (m-10) REVERT: B 83 THR cc_start: 0.8327 (t) cc_final: 0.8093 (t) REVERT: B 85 LEU cc_start: 0.9238 (tp) cc_final: 0.9014 (tt) REVERT: B 293 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7424 (tt) REVERT: B 312 LYS cc_start: 0.8184 (tmmt) cc_final: 0.7751 (ptmt) REVERT: B 319 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7459 (t80) REVERT: B 502 LEU cc_start: 0.9202 (pt) cc_final: 0.8856 (pp) REVERT: B 567 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7068 (mt0) outliers start: 35 outliers final: 26 residues processed: 234 average time/residue: 0.1780 time to fit residues: 60.8416 Evaluate side-chains 234 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 202 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 319 TYR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 0.0170 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** 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: 0.8086 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9368 Z= 0.168 Angle : 0.607 11.547 12702 Z= 0.305 Chirality : 0.040 0.233 1448 Planarity : 0.003 0.039 1580 Dihedral : 6.200 64.875 1310 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 4.15 % Allowed : 26.48 % Favored : 69.37 % 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: -2.07 (0.24), residues: 1122 helix: -0.40 (0.19), residues: 738 sheet: -1.44 (1.06), residues: 20 loop : -3.38 (0.26), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 598 HIS 0.002 0.000 HIS A 226 PHE 0.019 0.001 PHE B 84 TYR 0.007 0.001 TYR A 476 ARG 0.004 0.000 ARG B 15 *********************** 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 257 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 215 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7585 (t80) cc_final: 0.6907 (m-10) REVERT: A 68 TYR cc_start: 0.7888 (m-10) cc_final: 0.7607 (m-10) REVERT: A 83 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8113 (t) REVERT: A 85 LEU cc_start: 0.9229 (tp) cc_final: 0.8974 (tt) REVERT: A 136 ARG cc_start: 0.8288 (mmt-90) cc_final: 0.7692 (mpt180) REVERT: A 165 ILE cc_start: 0.8852 (tp) cc_final: 0.8640 (tp) REVERT: A 234 GLU cc_start: 0.8601 (tp30) cc_final: 0.8373 (tp30) REVERT: A 247 MET cc_start: 0.7666 (mmt) cc_final: 0.7460 (mmt) REVERT: A 260 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8821 (mt0) REVERT: A 268 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9072 (tt) REVERT: A 280 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8453 (tt) REVERT: A 312 LYS cc_start: 0.8197 (tmmt) cc_final: 0.7768 (ptmm) REVERT: A 319 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.7446 (t80) REVERT: A 502 LEU cc_start: 0.9256 (pt) cc_final: 0.8957 (pp) REVERT: A 529 MET cc_start: 0.8261 (mtt) cc_final: 0.7823 (mtt) REVERT: A 561 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8114 (tm-30) REVERT: A 567 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6993 (mt0) REVERT: B 55 PHE cc_start: 0.7595 (t80) cc_final: 0.6888 (m-10) REVERT: B 68 TYR cc_start: 0.7832 (m-10) cc_final: 0.7609 (m-10) REVERT: B 83 THR cc_start: 0.8328 (t) cc_final: 0.8039 (t) REVERT: B 85 LEU cc_start: 0.9251 (tp) cc_final: 0.9015 (tt) REVERT: B 136 ARG cc_start: 0.8299 (mmt-90) cc_final: 0.7700 (mpt180) REVERT: B 293 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7387 (tt) REVERT: B 319 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7442 (t80) REVERT: B 502 LEU cc_start: 0.9206 (pt) cc_final: 0.8884 (pp) REVERT: B 561 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8144 (tm-30) REVERT: B 567 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7067 (mt0) outliers start: 42 outliers final: 25 residues processed: 244 average time/residue: 0.1773 time to fit residues: 62.8590 Evaluate side-chains 233 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 199 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 319 TYR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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** ** 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: 0.8120 moved from start: 0.3466 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= 0.221 Angle : 0.625 7.968 12702 Z= 0.315 Chirality : 0.041 0.190 1448 Planarity : 0.003 0.039 1580 Dihedral : 6.171 65.404 1310 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.95 % Allowed : 26.88 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.24), residues: 1122 helix: -0.27 (0.19), residues: 732 sheet: -1.45 (1.11), residues: 20 loop : -3.27 (0.25), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 269 HIS 0.005 0.001 HIS B 226 PHE 0.019 0.001 PHE A 84 TYR 0.019 0.001 TYR A 544 ARG 0.004 0.000 ARG B 15 *********************** 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 246 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 206 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7601 (t80) cc_final: 0.6972 (m-10) REVERT: A 68 TYR cc_start: 0.7935 (m-10) cc_final: 0.7644 (m-10) REVERT: A 85 LEU cc_start: 0.9220 (tp) cc_final: 0.8972 (tt) REVERT: A 108 TYR cc_start: 0.9176 (OUTLIER) cc_final: 0.8611 (t80) REVERT: A 136 ARG cc_start: 0.8288 (mmt-90) cc_final: 0.7688 (mpt180) REVERT: A 165 ILE cc_start: 0.8840 (tp) cc_final: 0.8621 (tp) REVERT: A 260 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8854 (mt0) REVERT: A 268 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9089 (tt) REVERT: A 280 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8472 (tt) REVERT: A 319 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7480 (t80) REVERT: A 502 LEU cc_start: 0.9274 (pt) cc_final: 0.8963 (pp) REVERT: A 561 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 567 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7024 (mt0) REVERT: B 55 PHE cc_start: 0.7614 (t80) cc_final: 0.6897 (m-10) REVERT: B 68 TYR cc_start: 0.7883 (m-10) cc_final: 0.7614 (m-10) REVERT: B 85 LEU cc_start: 0.9238 (tp) cc_final: 0.8996 (tt) REVERT: B 136 ARG cc_start: 0.8311 (mmt-90) cc_final: 0.7716 (mpt180) REVERT: B 280 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8526 (tt) REVERT: B 293 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7414 (tt) REVERT: B 319 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7413 (t80) REVERT: B 502 LEU cc_start: 0.9241 (pt) cc_final: 0.8875 (pp) REVERT: B 529 MET cc_start: 0.8366 (mtt) cc_final: 0.7852 (mtt) REVERT: B 567 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7064 (mt0) outliers start: 40 outliers final: 28 residues processed: 231 average time/residue: 0.1764 time to fit residues: 59.8828 Evaluate side-chains 235 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 197 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 319 TYR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.0470 chunk 54 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 overall best weight: 0.7678 ------------------------------------------------------------------------------- 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 415 GLN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** 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: 0.8085 moved from start: 0.3596 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= 0.179 Angle : 0.634 9.514 12702 Z= 0.318 Chirality : 0.041 0.195 1448 Planarity : 0.003 0.039 1580 Dihedral : 6.122 68.383 1310 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.56 % Allowed : 27.57 % Favored : 68.87 % 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: -1.76 (0.24), residues: 1122 helix: -0.16 (0.19), residues: 734 sheet: -1.55 (1.07), residues: 20 loop : -3.21 (0.26), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 598 HIS 0.003 0.001 HIS A 120 PHE 0.014 0.001 PHE B 224 TYR 0.015 0.001 TYR A 544 ARG 0.004 0.000 ARG B 15 ********************** 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 247 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 211 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7589 (t80) cc_final: 0.6968 (m-10) REVERT: A 85 LEU cc_start: 0.9218 (tp) cc_final: 0.8964 (tt) REVERT: A 136 ARG cc_start: 0.8293 (mmt-90) cc_final: 0.7541 (mpt180) REVERT: A 165 ILE cc_start: 0.8871 (tp) cc_final: 0.8668 (tp) REVERT: A 280 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8446 (tt) REVERT: A 319 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7380 (t80) REVERT: A 502 LEU cc_start: 0.9259 (pt) cc_final: 0.8940 (pp) REVERT: A 529 MET cc_start: 0.8337 (mtt) cc_final: 0.7821 (mtt) REVERT: A 561 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8187 (tm-30) REVERT: A 564 ARG cc_start: 0.8211 (mmt180) cc_final: 0.7812 (mmt180) REVERT: A 567 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7056 (mt0) REVERT: B 55 PHE cc_start: 0.7605 (t80) cc_final: 0.6895 (m-10) REVERT: B 68 TYR cc_start: 0.7869 (m-10) cc_final: 0.7580 (m-10) REVERT: B 85 LEU cc_start: 0.9230 (tp) cc_final: 0.8969 (tt) REVERT: B 136 ARG cc_start: 0.8289 (mmt-90) cc_final: 0.7691 (mpt180) REVERT: B 234 GLU cc_start: 0.8605 (tp30) cc_final: 0.8371 (tp30) REVERT: B 280 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8468 (tt) REVERT: B 293 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7380 (tt) REVERT: B 319 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7360 (t80) REVERT: B 502 LEU cc_start: 0.9213 (pt) cc_final: 0.8902 (pp) REVERT: B 529 MET cc_start: 0.8394 (mtt) cc_final: 0.7892 (mtt) REVERT: B 561 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8151 (tm-30) REVERT: B 567 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7093 (mt0) outliers start: 36 outliers final: 26 residues processed: 234 average time/residue: 0.1676 time to fit residues: 57.6843 Evaluate side-chains 238 residues out of total 1012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 205 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 319 TYR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 574 ILE 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: 0.6980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 91 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 215 GLN A 260 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.107545 restraints weight = 14424.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.111089 restraints weight = 6904.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.113252 restraints weight = 4387.436| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9368 Z= 0.172 Angle : 0.625 7.977 12702 Z= 0.311 Chirality : 0.041 0.192 1448 Planarity : 0.003 0.038 1580 Dihedral : 6.062 69.615 1310 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.66 % Allowed : 27.37 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.24), residues: 1122 helix: -0.07 (0.19), residues: 742 sheet: -1.48 (1.10), residues: 20 loop : -3.26 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 111 HIS 0.007 0.001 HIS A 226 PHE 0.020 0.001 PHE B 84 TYR 0.015 0.001 TYR B 544 ARG 0.004 0.000 ARG A 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1998.46 seconds wall clock time: 36 minutes 59.58 seconds (2219.58 seconds total)