Starting phenix.real_space_refine on Fri Jul 19 18:46:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/07_2024/8jol_36459_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/07_2024/8jol_36459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/07_2024/8jol_36459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/07_2024/8jol_36459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/07_2024/8jol_36459_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/07_2024/8jol_36459_neut.cif" } resolution = 3.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5388 2.51 5 N 1439 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B ARG 436": "NH1" <-> "NH2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B GLU 486": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8513 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4039 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 481} Chain breaks: 2 Chain: "B" Number of atoms: 3965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3965 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 3 Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 445 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 1, 'TRANS': 88} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 162 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.19, per 1000 atoms: 0.61 Number of scatterers: 8513 At special positions: 0 Unit cell: (95.04, 114.84, 137.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 6 15.00 Mg 2 11.99 O 1620 8.00 N 1439 7.00 C 5388 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: 3.54 Conformation dependent library (CDL) restraints added in 1.5 seconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 65.5% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.630A pdb=" N LEU A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 18 removed outlier: 3.563A pdb=" N LEU A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.758A pdb=" N ALA A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 49 through 65 removed outlier: 3.557A pdb=" N ARG A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 65 " --> pdb=" O TYR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 78 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.620A pdb=" N ALA A 84 " --> pdb=" O GLN A 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 164 through 173 removed outlier: 3.523A pdb=" N ILE A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 4.023A pdb=" N PHE A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 240 removed outlier: 3.692A pdb=" N ALA A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.653A pdb=" N ALA A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 281 removed outlier: 3.915A pdb=" N ILE A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 305 removed outlier: 3.648A pdb=" N TYR A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 327 removed outlier: 4.885A pdb=" N VAL A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'A' and resid 344 through 355 Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.891A pdb=" N ALA A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.738A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 428 through 440 Processing helix chain 'A' and resid 458 through 468 removed outlier: 3.654A pdb=" N PHE A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 485 removed outlier: 3.768A pdb=" N ALA A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.851A pdb=" N LEU A 535 " --> pdb=" O PHE A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 removed outlier: 3.938A pdb=" N SER A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 removed outlier: 3.630A pdb=" N LEU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.560A pdb=" N LEU B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS B 19 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 33 removed outlier: 3.773A pdb=" N ALA B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 46 Processing helix chain 'B' and resid 49 through 65 removed outlier: 3.553A pdb=" N ARG B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 65 " --> pdb=" O TYR B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 78 removed outlier: 3.656A pdb=" N ILE B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 96 removed outlier: 3.618A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B 86 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 94 " --> pdb=" O TYR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 removed outlier: 3.891A pdb=" N MET B 114 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 164 through 173 removed outlier: 3.507A pdb=" N ILE B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 4.015A pdb=" N PHE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 208 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 242 removed outlier: 3.929A pdb=" N ASP B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 4.189A pdb=" N ILE B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 281 removed outlier: 4.001A pdb=" N ILE B 277 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 305 removed outlier: 3.591A pdb=" N TYR B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 327 removed outlier: 4.890A pdb=" N VAL B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.791A pdb=" N GLU B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 373 through 384 removed outlier: 3.891A pdb=" N ALA B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 395 Processing helix chain 'B' and resid 396 through 399 Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 428 through 440 Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 469 through 484 removed outlier: 3.793A pdb=" N ALA B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.850A pdb=" N LEU B 535 " --> pdb=" O PHE B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 removed outlier: 3.925A pdb=" N SER B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 13 Processing helix chain 'C' and resid 13 through 18 removed outlier: 3.750A pdb=" N PHE C 17 " --> pdb=" O ASN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 33 removed outlier: 3.773A pdb=" N ILE C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 46 Processing helix chain 'C' and resid 49 through 64 removed outlier: 3.552A pdb=" N LYS C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 80 through 92 removed outlier: 3.617A pdb=" N LEU C 84 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Proline residue: C 90 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 7.093A pdb=" N THR A 245 " --> pdb=" O ARG A 267 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU A 269 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE A 247 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR A 271 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE A 249 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE A 153 " --> pdb=" O CYS A 268 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL A 270 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 155 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR A 272 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU A 157 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE A 154 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE A 288 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE A 156 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 290 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N HIS A 158 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 405 through 406 Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 191 removed outlier: 6.820A pdb=" N THR B 245 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU B 269 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE B 247 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR B 271 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE B 249 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 272 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 159 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE B 154 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE B 288 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE B 156 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 290 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N HIS B 158 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 405 through 406 399 hydrogen bonds defined for protein. 1128 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: 2.18 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2514 1.33 - 1.46: 1796 1.46 - 1.59: 4252 1.59 - 1.72: 6 1.72 - 1.85: 92 Bond restraints: 8660 Sorted by residual: bond pdb=" C4 ATP A 602 " pdb=" C5 ATP A 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 8.95e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.480 -0.092 1.00e-02 1.00e+04 8.53e+01 bond pdb=" C5 ATP A 602 " pdb=" C6 ATP A 602 " ideal model delta sigma weight residual 1.409 1.492 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C5 ATP B 602 " pdb=" N7 ATP B 602 " ideal model delta sigma weight residual 1.387 1.332 0.055 1.00e-02 1.00e+04 3.01e+01 bond pdb=" C8 ATP A 602 " pdb=" N7 ATP A 602 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.09e+01 ... (remaining 8655 not shown) Histogram of bond angle deviations from ideal: 96.59 - 104.55: 161 104.55 - 112.51: 4239 112.51 - 120.47: 3971 120.47 - 128.43: 3308 128.43 - 136.39: 52 Bond angle restraints: 11731 Sorted by residual: angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 114.14 25.73 1.00e+00 1.00e+00 6.62e+02 angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 119.12 17.71 1.00e+00 1.00e+00 3.14e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 122.83 17.04 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PA ATP A 602 " pdb=" O3A ATP A 602 " pdb=" PB ATP A 602 " ideal model delta sigma weight residual 136.83 121.64 15.19 1.00e+00 1.00e+00 2.31e+02 angle pdb=" N3 ATP B 602 " pdb=" C4 ATP B 602 " pdb=" N9 ATP B 602 " ideal model delta sigma weight residual 127.04 136.39 -9.35 1.15e+00 7.59e-01 6.64e+01 ... (remaining 11726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 4606 17.39 - 34.79: 480 34.79 - 52.18: 162 52.18 - 69.58: 78 69.58 - 86.97: 13 Dihedral angle restraints: 5339 sinusoidal: 2140 harmonic: 3199 Sorted by residual: dihedral pdb=" CA ASP B 216 " pdb=" C ASP B 216 " pdb=" N LEU B 217 " pdb=" CA LEU B 217 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ASP A 216 " pdb=" C ASP A 216 " pdb=" N LEU A 217 " pdb=" CA LEU A 217 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA CYS A 268 " pdb=" C CYS A 268 " pdb=" N LEU A 269 " pdb=" CA LEU A 269 " ideal model delta harmonic sigma weight residual 180.00 158.55 21.45 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 5336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 960 0.070 - 0.140: 301 0.140 - 0.210: 76 0.210 - 0.279: 19 0.279 - 0.349: 4 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CA PHE A 532 " pdb=" N PHE A 532 " pdb=" C PHE A 532 " pdb=" CB PHE A 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA LYS A 212 " pdb=" N LYS A 212 " pdb=" C LYS A 212 " pdb=" CB LYS A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA PHE B 532 " pdb=" N PHE B 532 " pdb=" C PHE B 532 " pdb=" CB PHE B 532 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 1357 not shown) Planarity restraints: 1502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 87 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.22e+00 pdb=" C VAL C 87 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL C 87 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU C 88 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 253 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C VAL A 253 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL A 253 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN A 254 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 220 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO B 221 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 221 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 221 " -0.032 5.00e-02 4.00e+02 ... (remaining 1499 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1343 2.75 - 3.29: 9096 3.29 - 3.83: 14060 3.83 - 4.36: 18222 4.36 - 4.90: 27779 Nonbonded interactions: 70500 Sorted by model distance: nonbonded pdb=" O1B ATP A 602 " pdb=" O2G ATP A 602 " model vdw 2.214 3.040 nonbonded pdb=" O ARG A 259 " pdb=" N GLN A 262 " model vdw 2.275 2.520 nonbonded pdb=" O4' ATP A 602 " pdb=" O5' ATP A 602 " model vdw 2.319 2.432 nonbonded pdb=" OG SER B 166 " pdb="MG MG B 601 " model vdw 2.341 2.170 nonbonded pdb=" O LEU B 120 " pdb=" N ASN B 123 " model vdw 2.349 2.520 ... (remaining 70495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 98 or resid 106 through 416 or resid 426 through \ 543 or resid 601 through 602)) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.810 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 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 : 0.009 0.095 8660 Z= 0.604 Angle : 1.462 25.735 11731 Z= 1.023 Chirality : 0.074 0.349 1360 Planarity : 0.005 0.060 1502 Dihedral : 18.200 86.969 3243 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 35.79 Ramachandran Plot: Outliers : 0.84 % Allowed : 12.32 % Favored : 86.83 % Rotamer: Outliers : 16.43 % Allowed : 15.21 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.77 (0.21), residues: 1071 helix: -3.29 (0.15), residues: 632 sheet: -2.60 (0.61), residues: 60 loop : -2.63 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP B 189 HIS 0.003 0.001 HIS B 225 PHE 0.018 0.003 PHE A 156 TYR 0.022 0.004 TYR B 184 ARG 0.003 0.001 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 215 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8962 (m) cc_final: 0.8522 (p) REVERT: A 47 MET cc_start: 0.6707 (mmm) cc_final: 0.6151 (mmm) REVERT: A 123 ASN cc_start: 0.8269 (m110) cc_final: 0.7650 (t0) REVERT: A 128 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7943 (tpp) REVERT: A 144 LEU cc_start: 0.8740 (mt) cc_final: 0.8503 (mt) REVERT: A 185 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7666 (t0) REVERT: A 205 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8843 (m) REVERT: A 206 ASP cc_start: 0.8609 (m-30) cc_final: 0.8231 (m-30) REVERT: A 218 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8387 (pt) REVERT: A 228 SER cc_start: 0.9145 (m) cc_final: 0.8888 (t) REVERT: A 233 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7569 (ttp-170) REVERT: A 286 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7454 (mm-30) REVERT: A 290 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7993 (t) REVERT: A 443 LEU cc_start: 0.9052 (mt) cc_final: 0.8667 (mp) REVERT: B 45 SER cc_start: 0.4096 (OUTLIER) cc_final: 0.3860 (p) REVERT: B 128 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7837 (OUTLIER) REVERT: B 185 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8356 (m-30) REVERT: B 190 LEU cc_start: 0.8856 (mt) cc_final: 0.8474 (mt) REVERT: B 218 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7944 (pt) REVERT: B 361 VAL cc_start: 0.8410 (t) cc_final: 0.7470 (p) REVERT: B 382 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7187 (t) outliers start: 149 outliers final: 10 residues processed: 317 average time/residue: 0.9137 time to fit residues: 312.7639 Evaluate side-chains 148 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 542 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 219 ASN A 329 ASN A 461 HIS A 471 GLN A 482 GLN A 534 GLN B 34 ASN B 64 GLN B 76 ASN B 113 GLN B 244 ASN B 482 GLN B 534 GLN B 536 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8660 Z= 0.239 Angle : 0.788 12.326 11731 Z= 0.391 Chirality : 0.044 0.191 1360 Planarity : 0.006 0.057 1502 Dihedral : 11.337 80.523 1269 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 7.61 % Allowed : 24.48 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.29 (0.24), residues: 1071 helix: -1.32 (0.18), residues: 673 sheet: -2.16 (0.56), residues: 58 loop : -1.43 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 410 HIS 0.008 0.002 HIS A 40 PHE 0.020 0.002 PHE B 220 TYR 0.019 0.002 TYR A 77 ARG 0.011 0.001 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 116 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6931 (tpt-90) REVERT: A 11 SER cc_start: 0.9014 (m) cc_final: 0.8710 (p) REVERT: A 63 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8328 (mmt-90) REVERT: A 202 ASP cc_start: 0.9176 (m-30) cc_final: 0.8669 (m-30) REVERT: A 206 ASP cc_start: 0.8455 (m-30) cc_final: 0.8156 (m-30) REVERT: A 218 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8562 (pt) REVERT: A 360 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8807 (mt) REVERT: A 361 VAL cc_start: 0.9442 (OUTLIER) cc_final: 0.8947 (t) REVERT: A 364 GLU cc_start: 0.8331 (pm20) cc_final: 0.8102 (pm20) REVERT: A 486 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: B 123 ASN cc_start: 0.9100 (t0) cc_final: 0.8792 (t0) REVERT: B 185 ASP cc_start: 0.9060 (m-30) cc_final: 0.8618 (m-30) REVERT: B 364 GLU cc_start: 0.7874 (pm20) cc_final: 0.7488 (pm20) REVERT: B 533 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.6778 (ppp) outliers start: 69 outliers final: 19 residues processed: 170 average time/residue: 0.9834 time to fit residues: 181.0740 Evaluate side-chains 123 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 533 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 97 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 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 40 HIS A 244 ASN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.7076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8660 Z= 0.204 Angle : 0.682 10.433 11731 Z= 0.337 Chirality : 0.041 0.141 1360 Planarity : 0.005 0.055 1502 Dihedral : 9.525 82.124 1236 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.51 % Allowed : 24.59 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.26), residues: 1071 helix: 0.01 (0.20), residues: 671 sheet: -1.41 (0.61), residues: 58 loop : -0.99 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 189 HIS 0.002 0.001 HIS B 82 PHE 0.016 0.001 PHE B 220 TYR 0.015 0.001 TYR A 77 ARG 0.005 0.001 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 96 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8937 (m) cc_final: 0.8715 (p) REVERT: A 47 MET cc_start: 0.7966 (mmm) cc_final: 0.6115 (mmm) REVERT: A 206 ASP cc_start: 0.8718 (m-30) cc_final: 0.8463 (m-30) REVERT: A 307 MET cc_start: 0.8528 (tpp) cc_final: 0.7959 (tpt) REVERT: A 361 VAL cc_start: 0.9454 (OUTLIER) cc_final: 0.9014 (t) REVERT: A 364 GLU cc_start: 0.8251 (pm20) cc_final: 0.7996 (pm20) REVERT: A 486 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: B 114 MET cc_start: 0.8040 (mpt) cc_final: 0.7806 (mpt) REVERT: B 185 ASP cc_start: 0.9102 (m-30) cc_final: 0.8687 (m-30) REVERT: B 224 GLU cc_start: 0.9247 (mp0) cc_final: 0.8710 (pm20) REVERT: B 225 HIS cc_start: 0.9271 (m-70) cc_final: 0.8925 (m-70) REVERT: B 307 MET cc_start: 0.6539 (tpt) cc_final: 0.5752 (tpp) REVERT: B 338 LYS cc_start: 0.6445 (mptp) cc_final: 0.5682 (mmtt) REVERT: B 383 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8682 (mm-30) REVERT: B 413 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7180 (m) REVERT: B 432 ASP cc_start: 0.8614 (m-30) cc_final: 0.8381 (t0) outliers start: 50 outliers final: 16 residues processed: 135 average time/residue: 0.9629 time to fit residues: 141.8292 Evaluate side-chains 108 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 473 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 7.9990 chunk 73 optimal weight: 0.0970 chunk 50 optimal weight: 0.0470 chunk 10 optimal weight: 0.0970 chunk 46 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 28 optimal weight: 0.1980 overall best weight: 1.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS B 64 GLN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.8398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8660 Z= 0.211 Angle : 0.667 8.977 11731 Z= 0.329 Chirality : 0.041 0.138 1360 Planarity : 0.005 0.056 1502 Dihedral : 9.364 79.689 1232 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.73 % Allowed : 23.37 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1071 helix: 0.59 (0.21), residues: 672 sheet: -0.75 (0.61), residues: 58 loop : -0.70 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 410 HIS 0.003 0.001 HIS B 82 PHE 0.017 0.001 PHE A 220 TYR 0.012 0.001 TYR A 77 ARG 0.006 0.001 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 87 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9256 (mp) cc_final: 0.8954 (mm) REVERT: A 147 MET cc_start: 0.8756 (mtp) cc_final: 0.8434 (ptm) REVERT: A 206 ASP cc_start: 0.8761 (m-30) cc_final: 0.8474 (m-30) REVERT: A 209 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9142 (mm) REVERT: A 307 MET cc_start: 0.8787 (tpp) cc_final: 0.8472 (tpp) REVERT: A 360 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8975 (mt) REVERT: A 361 VAL cc_start: 0.9417 (OUTLIER) cc_final: 0.8934 (t) REVERT: A 364 GLU cc_start: 0.8199 (pm20) cc_final: 0.7965 (pm20) REVERT: A 486 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7568 (tm-30) REVERT: B 114 MET cc_start: 0.8280 (mpt) cc_final: 0.8056 (mpp) REVERT: B 185 ASP cc_start: 0.9163 (m-30) cc_final: 0.8717 (m-30) REVERT: B 224 GLU cc_start: 0.9252 (mp0) cc_final: 0.8603 (pm20) REVERT: B 316 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8184 (pp20) REVERT: B 372 LYS cc_start: 0.9000 (tppp) cc_final: 0.8623 (tppp) REVERT: B 383 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8704 (mm-30) outliers start: 52 outliers final: 15 residues processed: 127 average time/residue: 0.9785 time to fit residues: 134.3032 Evaluate side-chains 94 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 459 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN B 40 HIS B 158 HIS ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.9526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8660 Z= 0.217 Angle : 0.657 10.174 11731 Z= 0.322 Chirality : 0.041 0.156 1360 Planarity : 0.005 0.059 1502 Dihedral : 9.323 86.310 1232 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.41 % Allowed : 25.36 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1071 helix: 0.85 (0.21), residues: 675 sheet: -0.51 (0.65), residues: 56 loop : -0.91 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 189 HIS 0.004 0.001 HIS B 225 PHE 0.017 0.001 PHE B 337 TYR 0.013 0.001 TYR B 369 ARG 0.006 0.001 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 70 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.8964 (mtp) cc_final: 0.8574 (ptp) REVERT: A 206 ASP cc_start: 0.8817 (m-30) cc_final: 0.8522 (m-30) REVERT: A 360 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9004 (mt) REVERT: A 361 VAL cc_start: 0.9424 (OUTLIER) cc_final: 0.8974 (t) REVERT: A 364 GLU cc_start: 0.8110 (pm20) cc_final: 0.7880 (pm20) REVERT: A 486 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: B 114 MET cc_start: 0.8416 (mpt) cc_final: 0.8167 (mpp) REVERT: B 147 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8515 (mtp) REVERT: B 185 ASP cc_start: 0.9232 (m-30) cc_final: 0.8769 (m-30) REVERT: B 316 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8427 (pp20) REVERT: B 338 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.5943 (mmtt) REVERT: B 372 LYS cc_start: 0.9089 (tppp) cc_final: 0.8838 (tppp) REVERT: B 376 MET cc_start: 0.9242 (mmm) cc_final: 0.8802 (mpp) REVERT: B 399 MET cc_start: 0.9327 (tpp) cc_final: 0.9068 (mmm) REVERT: B 435 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8618 (mppt) outliers start: 40 outliers final: 11 residues processed: 101 average time/residue: 1.0014 time to fit residues: 109.4056 Evaluate side-chains 88 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 435 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.9916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8660 Z= 0.194 Angle : 0.627 11.827 11731 Z= 0.304 Chirality : 0.040 0.198 1360 Planarity : 0.004 0.056 1502 Dihedral : 9.115 88.149 1228 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.75 % Allowed : 25.91 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1071 helix: 1.10 (0.21), residues: 669 sheet: -0.24 (0.66), residues: 56 loop : -0.87 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 189 HIS 0.004 0.001 HIS B 82 PHE 0.018 0.001 PHE A 204 TYR 0.010 0.001 TYR B 135 ARG 0.003 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 73 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8811 (mmp) cc_final: 0.8610 (mmp) REVERT: A 147 MET cc_start: 0.8982 (mtp) cc_final: 0.8682 (ptp) REVERT: A 206 ASP cc_start: 0.8815 (m-30) cc_final: 0.8506 (m-30) REVERT: A 307 MET cc_start: 0.8830 (tpp) cc_final: 0.8312 (tpt) REVERT: A 360 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8997 (mt) REVERT: A 361 VAL cc_start: 0.9390 (OUTLIER) cc_final: 0.8942 (t) REVERT: A 364 GLU cc_start: 0.8170 (pm20) cc_final: 0.7951 (pm20) REVERT: A 399 MET cc_start: 0.8961 (mmm) cc_final: 0.8754 (mpp) REVERT: A 486 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7456 (tm-30) REVERT: B 47 MET cc_start: 0.7869 (ptt) cc_final: 0.6900 (ppp) REVERT: B 114 MET cc_start: 0.8475 (mpt) cc_final: 0.8200 (mpp) REVERT: B 147 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8688 (mtp) REVERT: B 185 ASP cc_start: 0.9257 (m-30) cc_final: 0.8775 (m-30) REVERT: B 316 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8502 (pp20) REVERT: B 376 MET cc_start: 0.9267 (mmm) cc_final: 0.8985 (mpp) REVERT: B 383 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8344 (mp0) REVERT: B 399 MET cc_start: 0.9353 (tpp) cc_final: 0.8778 (mmm) REVERT: B 435 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8522 (mtmt) outliers start: 34 outliers final: 15 residues processed: 97 average time/residue: 1.0196 time to fit residues: 107.0289 Evaluate side-chains 91 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 435 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN B 40 HIS ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 1.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 8660 Z= 0.323 Angle : 0.728 13.395 11731 Z= 0.352 Chirality : 0.042 0.186 1360 Planarity : 0.005 0.057 1502 Dihedral : 9.385 89.851 1228 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.07 % Allowed : 25.58 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1071 helix: 0.93 (0.21), residues: 684 sheet: 0.04 (0.68), residues: 56 loop : -1.00 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 410 HIS 0.011 0.001 HIS B 40 PHE 0.024 0.002 PHE A 220 TYR 0.016 0.001 TYR B 369 ARG 0.005 0.001 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 70 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8903 (m-30) cc_final: 0.8588 (m-30) REVERT: A 316 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8352 (pm20) REVERT: A 360 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9135 (mt) REVERT: A 361 VAL cc_start: 0.9425 (OUTLIER) cc_final: 0.8983 (t) REVERT: A 364 GLU cc_start: 0.8266 (pm20) cc_final: 0.8042 (pm20) REVERT: A 486 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: A 533 MET cc_start: 0.8607 (ppp) cc_final: 0.8252 (ppp) REVERT: B 114 MET cc_start: 0.8774 (mpt) cc_final: 0.8561 (mpp) REVERT: B 142 LYS cc_start: 0.9473 (OUTLIER) cc_final: 0.9261 (tmmm) REVERT: B 185 ASP cc_start: 0.9282 (m-30) cc_final: 0.8779 (m-30) REVERT: B 316 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8561 (pp20) REVERT: B 338 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7741 (mmtt) REVERT: B 376 MET cc_start: 0.9387 (mmm) cc_final: 0.9100 (mpp) REVERT: B 383 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8521 (mp0) REVERT: B 435 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8421 (mtmt) REVERT: B 459 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8886 (tt) outliers start: 46 outliers final: 11 residues processed: 103 average time/residue: 1.0672 time to fit residues: 118.3904 Evaluate side-chains 88 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 68 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 459 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 262 GLN A 283 GLN B 254 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 1.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8660 Z= 0.187 Angle : 0.652 11.198 11731 Z= 0.307 Chirality : 0.040 0.196 1360 Planarity : 0.004 0.056 1502 Dihedral : 9.146 89.280 1228 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.43 % Allowed : 27.45 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1071 helix: 1.18 (0.21), residues: 677 sheet: 0.09 (0.69), residues: 56 loop : -0.78 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 189 HIS 0.004 0.001 HIS B 82 PHE 0.017 0.001 PHE A 204 TYR 0.010 0.001 TYR B 135 ARG 0.005 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 69 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8077 (pp20) REVERT: A 206 ASP cc_start: 0.8841 (m-30) cc_final: 0.8522 (m-30) REVERT: A 316 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8425 (pm20) REVERT: A 360 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9035 (mt) REVERT: A 361 VAL cc_start: 0.9351 (OUTLIER) cc_final: 0.8953 (t) REVERT: A 364 GLU cc_start: 0.8132 (pm20) cc_final: 0.7912 (pm20) REVERT: A 399 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8966 (mmm) REVERT: A 486 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: A 533 MET cc_start: 0.8458 (ppp) cc_final: 0.8006 (ppp) REVERT: B 47 MET cc_start: 0.7804 (ptt) cc_final: 0.6891 (ppp) REVERT: B 114 MET cc_start: 0.8827 (mpt) cc_final: 0.8594 (mpp) REVERT: B 185 ASP cc_start: 0.9218 (m-30) cc_final: 0.8740 (m-30) REVERT: B 348 MET cc_start: 0.8985 (ptp) cc_final: 0.8682 (ptp) REVERT: B 376 MET cc_start: 0.9285 (mmm) cc_final: 0.8974 (mpp) REVERT: B 383 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8556 (mp0) REVERT: B 435 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8447 (mtmm) outliers start: 22 outliers final: 12 residues processed: 84 average time/residue: 1.1069 time to fit residues: 100.3267 Evaluate side-chains 85 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 435 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 1.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8660 Z= 0.195 Angle : 0.681 15.046 11731 Z= 0.319 Chirality : 0.041 0.242 1360 Planarity : 0.004 0.055 1502 Dihedral : 9.023 89.619 1228 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.43 % Allowed : 27.89 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.27), residues: 1071 helix: 1.19 (0.21), residues: 678 sheet: 0.09 (0.70), residues: 56 loop : -0.61 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 189 HIS 0.005 0.001 HIS B 82 PHE 0.035 0.001 PHE A 539 TYR 0.010 0.001 TYR B 369 ARG 0.005 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 65 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8092 (pp20) REVERT: A 206 ASP cc_start: 0.8860 (m-30) cc_final: 0.8522 (m-30) REVERT: A 307 MET cc_start: 0.8991 (mmm) cc_final: 0.8304 (tpt) REVERT: A 316 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: A 360 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9054 (mt) REVERT: A 361 VAL cc_start: 0.9359 (OUTLIER) cc_final: 0.8947 (t) REVERT: A 364 GLU cc_start: 0.8114 (pm20) cc_final: 0.7876 (pm20) REVERT: A 399 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.8708 (mmm) REVERT: A 486 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7324 (tm-30) REVERT: A 533 MET cc_start: 0.8411 (ppp) cc_final: 0.8095 (ppp) REVERT: B 47 MET cc_start: 0.7786 (ptt) cc_final: 0.6837 (ppp) REVERT: B 114 MET cc_start: 0.8768 (mpt) cc_final: 0.8559 (mpp) REVERT: B 142 LYS cc_start: 0.9535 (OUTLIER) cc_final: 0.9320 (tmmm) REVERT: B 185 ASP cc_start: 0.9221 (m-30) cc_final: 0.8747 (m-30) REVERT: B 316 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8610 (pp20) REVERT: B 376 MET cc_start: 0.9317 (mmm) cc_final: 0.9053 (mpp) REVERT: B 383 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8524 (mp0) REVERT: B 435 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8403 (mtmm) outliers start: 22 outliers final: 11 residues processed: 83 average time/residue: 1.1199 time to fit residues: 99.9812 Evaluate side-chains 85 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 65 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 435 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 30.0000 chunk 62 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 1.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8660 Z= 0.308 Angle : 0.746 14.625 11731 Z= 0.352 Chirality : 0.043 0.203 1360 Planarity : 0.005 0.056 1502 Dihedral : 9.186 86.690 1228 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.54 % Allowed : 28.00 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1071 helix: 1.12 (0.21), residues: 675 sheet: 0.19 (0.70), residues: 56 loop : -0.62 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 189 HIS 0.005 0.001 HIS B 82 PHE 0.031 0.002 PHE A 539 TYR 0.017 0.001 TYR B 369 ARG 0.003 0.001 ARG A 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 66 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8158 (pp20) REVERT: A 206 ASP cc_start: 0.8911 (m-30) cc_final: 0.8586 (m-30) REVERT: A 316 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: A 360 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9130 (mt) REVERT: A 361 VAL cc_start: 0.9393 (OUTLIER) cc_final: 0.8969 (t) REVERT: A 364 GLU cc_start: 0.8184 (pm20) cc_final: 0.7932 (pm20) REVERT: A 376 MET cc_start: 0.9148 (mpm) cc_final: 0.8939 (mpp) REVERT: A 486 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: A 533 MET cc_start: 0.8549 (ppp) cc_final: 0.8169 (ppp) REVERT: B 47 MET cc_start: 0.7971 (ptt) cc_final: 0.7705 (ppp) REVERT: B 142 LYS cc_start: 0.9516 (OUTLIER) cc_final: 0.9296 (tmmm) REVERT: B 185 ASP cc_start: 0.9233 (m-30) cc_final: 0.8756 (m-30) REVERT: B 376 MET cc_start: 0.9355 (mmm) cc_final: 0.9115 (mpp) REVERT: B 435 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8421 (mtmm) outliers start: 23 outliers final: 9 residues processed: 85 average time/residue: 1.1635 time to fit residues: 106.1423 Evaluate side-chains 78 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 435 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 85 optimal weight: 0.4980 chunk 35 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.060637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.045339 restraints weight = 35647.812| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 4.52 r_work: 0.2728 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 1.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8660 Z= 0.182 Angle : 0.712 16.033 11731 Z= 0.331 Chirality : 0.041 0.214 1360 Planarity : 0.005 0.055 1502 Dihedral : 9.015 87.138 1228 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.09 % Allowed : 28.45 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.27), residues: 1071 helix: 1.23 (0.21), residues: 672 sheet: 0.17 (0.69), residues: 56 loop : -0.58 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 189 HIS 0.005 0.000 HIS B 82 PHE 0.022 0.001 PHE A 539 TYR 0.011 0.001 TYR B 135 ARG 0.005 0.000 ARG A 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3029.17 seconds wall clock time: 53 minutes 37.08 seconds (3217.08 seconds total)