Starting phenix.real_space_refine on Wed Sep 25 18:54:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/09_2024/4uis_2974_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/09_2024/4uis_2974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/09_2024/4uis_2974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/09_2024/4uis_2974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/09_2024/4uis_2974_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uis_2974/09_2024/4uis_2974_neut.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2965 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5352 2.51 5 N 1523 2.21 5 O 1611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8518 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3757 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 457} Chain breaks: 7 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 615 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain breaks: 4 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'UNK:plan-1': 61} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 210 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 577 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'TRANS': 87} Chain breaks: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'UNK:plan-1': 50} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 457 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'TRANS': 79} Chain breaks: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'UNK:plan-1': 58} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 268 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Classifications: {'peptide': 2} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 969 Classifications: {'peptide': 196} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 185} Link IDs: {'CIS': 1, 'TRANS': 194} Chain breaks: 4 Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 610 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'UNK:plan-1': 196} Unresolved non-hydrogen planarities: 196 Chain: "D" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 306 Classifications: {'peptide': 62} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 58} Link IDs: {'TRANS': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 62} Unresolved non-hydrogen planarities: 62 Chain: "G" Number of atoms: 1349 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 162, 1292 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 3, 'TRANS': 158} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 162, 1292 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 3, 'TRANS': 158} Chain breaks: 6 bond proxies already assigned to first conformer: 1250 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AGLU G 5 " occ=0.32 ... (16 atoms not shown) pdb=" OE2BGLU G 5 " occ=0.68 residue: pdb=" N AARG G 76 " occ=0.57 ... (20 atoms not shown) pdb=" NH2BARG G 76 " occ=0.43 residue: pdb=" N ALYS G 135 " occ=0.29 ... (16 atoms not shown) pdb=" NZ BLYS G 135 " occ=0.71 residue: pdb=" N AARG G 137 " occ=0.41 ... (20 atoms not shown) pdb=" NH2BARG G 137 " occ=0.59 residue: pdb=" N AASN G 140 " occ=0.46 ... (14 atoms not shown) pdb=" ND2BASN G 140 " occ=0.54 residue: pdb=" N AGLN G 141 " occ=0.46 ... (16 atoms not shown) pdb=" NE2BGLN G 141 " occ=0.54 Time building chain proxies: 5.65, per 1000 atoms: 0.66 Number of scatterers: 8518 At special positions: 0 Unit cell: (122.76, 113.52, 142.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1611 8.00 N 1523 7.00 C 5352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied TRANS " UNK B 101 " - " ILE B 100 " " UNK B 234 " - " MET B 233 " " UNK B 424 " - " LEU B 423 " " UNK B 464 " - " HIS B 463 " Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 866.9 milliseconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 97.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 78 through 87 removed outlier: 4.440A pdb=" N LEU A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 4.042A pdb=" N GLY A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 201 removed outlier: 4.087A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS A 199 " --> pdb=" O CYS A 195 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.707A pdb=" N PHE A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.652A pdb=" N VAL A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR A 319 " --> pdb=" O PRO A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.753A pdb=" N SER A 341 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 408 removed outlier: 4.089A pdb=" N SER A 396 " --> pdb=" O GLN A 392 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 432 removed outlier: 3.774A pdb=" N PHE A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 483 through 503 removed outlier: 3.797A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.988A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.583A pdb=" N ASP A 541 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 542 " --> pdb=" O ARG A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 561 through 575 removed outlier: 3.584A pdb=" N TYR A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 665 through 687 removed outlier: 3.576A pdb=" N UNK A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 101 removed outlier: 3.723A pdb=" N UNK B 73 " --> pdb=" O UNK B 69 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 137 through 155 Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.679A pdb=" N UNK B 171 " --> pdb=" O UNK B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 216 removed outlier: 3.570A pdb=" N UNK B 198 " --> pdb=" O UNK B 194 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N UNK B 216 " --> pdb=" O UNK B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 241 removed outlier: 3.671A pdb=" N GLN B 222 " --> pdb=" O UNK B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 271 removed outlier: 3.851A pdb=" N UNK B 250 " --> pdb=" O UNK B 246 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP B 257 " --> pdb=" O UNK B 253 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N UNK B 265 " --> pdb=" O UNK B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 400 removed outlier: 3.941A pdb=" N UNK B 399 " --> pdb=" O UNK B 395 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N UNK B 400 " --> pdb=" O UNK B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 Processing helix chain 'B' and resid 434 through 452 removed outlier: 3.672A pdb=" N UNK B 438 " --> pdb=" O UNK B 434 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL B 444 " --> pdb=" O UNK B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 removed outlier: 3.645A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 22 removed outlier: 4.389A pdb=" N UNK C 18 " --> pdb=" O UNK C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 34 Processing helix chain 'C' and resid 36 through 56 removed outlier: 4.133A pdb=" N UNK C 40 " --> pdb=" O UNK C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 102 removed outlier: 3.851A pdb=" N UNK C 86 " --> pdb=" O UNK C 82 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N UNK C 87 " --> pdb=" O UNK C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 122 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'C' and resid 152 through 178 removed outlier: 4.032A pdb=" N UNK C 156 " --> pdb=" O UNK C 152 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N UNK C 177 " --> pdb=" O UNK C 173 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N UNK C 178 " --> pdb=" O UNK C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.744A pdb=" N UNK C 183 " --> pdb=" O UNK C 179 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N UNK C 184 " --> pdb=" O UNK C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 179 through 184' Processing helix chain 'C' and resid 184 through 198 removed outlier: 3.643A pdb=" N UNK C 188 " --> pdb=" O UNK C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 220 removed outlier: 4.123A pdb=" N UNK C 208 " --> pdb=" O UNK C 204 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N UNK C 213 " --> pdb=" O UNK C 209 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N UNK C 214 " --> pdb=" O UNK C 210 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N UNK C 215 " --> pdb=" O UNK C 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 removed outlier: 4.057A pdb=" N UNK D 13 " --> pdb=" O UNK D 9 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N UNK D 16 " --> pdb=" O UNK D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 21 through 31 removed outlier: 3.753A pdb=" N UNK D 25 " --> pdb=" O UNK D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 72 removed outlier: 4.028A pdb=" N UNK D 47 " --> pdb=" O UNK D 43 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N UNK D 49 " --> pdb=" O UNK D 45 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N UNK D 50 " --> pdb=" O UNK D 46 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N UNK D 51 " --> pdb=" O UNK D 47 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N UNK D 55 " --> pdb=" O UNK D 51 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N UNK D 56 " --> pdb=" O UNK D 52 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N UNK D 57 " --> pdb=" O UNK D 53 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N UNK D 65 " --> pdb=" O UNK D 61 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N UNK D 66 " --> pdb=" O UNK D 62 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N UNK D 67 " --> pdb=" O UNK D 63 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N UNK D 68 " --> pdb=" O UNK D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'G' and resid 6 through 12 Processing helix chain 'G' and resid 38 through 51 removed outlier: 3.888A pdb=" N ALA G 42 " --> pdb=" O SER G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 75 Processing helix chain 'G' and resid 77 through 81 Processing helix chain 'G' and resid 83 through 91 removed outlier: 3.924A pdb=" N VAL G 87 " --> pdb=" O LYS G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 106 removed outlier: 3.969A pdb=" N ALA G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 114 through 123 Processing helix chain 'G' and resid 125 through 134 Processing helix chain 'G' and resid 142 through 156 Processing helix chain 'G' and resid 158 through 162 Processing sheet with id=AA, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AB, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AC, first strand: chain 'A' and resid 94 through 95 removed outlier: 6.378A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 248 through 250 Processing sheet with id=AE, first strand: chain 'A' and resid 253 through 255 removed outlier: 3.813A pdb=" N ASP A 253 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 275 through 277 removed outlier: 3.735A pdb=" N VAL A 276 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AH, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AI, first strand: chain 'A' and resid 605 through 606 Processing sheet with id=GA, first strand: chain 'G' and resid 17 through 19 removed outlier: 7.694A pdb=" N TYR G 25 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS G 31 " --> pdb=" O ILE G 27 " (cutoff:3.500A) 517 hydrogen bonds defined for protein. 1521 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: 2.30 Time building geometry restraints manager: 2.76 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: 2889 1.34 - 1.46: 1592 1.46 - 1.58: 4089 1.58 - 1.70: 0 1.70 - 1.82: 51 Bond restraints: 8621 Sorted by residual: bond pdb=" CA PHE A 302 " pdb=" C PHE A 302 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.27e-02 6.20e+03 1.10e+01 bond pdb=" CA VAL A 256 " pdb=" CB VAL A 256 " ideal model delta sigma weight residual 1.540 1.503 0.037 1.36e-02 5.41e+03 7.32e+00 bond pdb=" N VAL A 303 " pdb=" CA VAL A 303 " ideal model delta sigma weight residual 1.459 1.427 0.032 1.25e-02 6.40e+03 6.39e+00 bond pdb=" CA ALA A 119 " pdb=" CB ALA A 119 " ideal model delta sigma weight residual 1.530 1.493 0.037 1.51e-02 4.39e+03 5.94e+00 bond pdb=" C ALA A 556 " pdb=" O ALA A 556 " ideal model delta sigma weight residual 1.239 1.215 0.023 9.60e-03 1.09e+04 5.94e+00 ... (remaining 8616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 11108 2.52 - 5.05: 536 5.05 - 7.57: 88 7.57 - 10.09: 16 10.09 - 12.62: 4 Bond angle restraints: 11752 Sorted by residual: angle pdb=" C GLY A 89 " pdb=" N PRO A 90 " pdb=" CA PRO A 90 " ideal model delta sigma weight residual 119.84 109.60 10.24 1.25e+00 6.40e-01 6.70e+01 angle pdb=" N VAL A 85 " pdb=" CA VAL A 85 " pdb=" C VAL A 85 " ideal model delta sigma weight residual 111.67 104.39 7.28 9.50e-01 1.11e+00 5.87e+01 angle pdb=" N LEU A 542 " pdb=" CA LEU A 542 " pdb=" C LEU A 542 " ideal model delta sigma weight residual 108.23 117.36 -9.13 1.38e+00 5.25e-01 4.38e+01 angle pdb=" C ALA A 48 " pdb=" N PRO A 49 " pdb=" CA PRO A 49 " ideal model delta sigma weight residual 119.78 126.51 -6.73 1.03e+00 9.43e-01 4.26e+01 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 118.35 -7.65 1.22e+00 6.72e-01 3.93e+01 ... (remaining 11747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4976 17.72 - 35.44: 120 35.44 - 53.16: 26 53.16 - 70.88: 3 70.88 - 88.60: 5 Dihedral angle restraints: 5130 sinusoidal: 1489 harmonic: 3641 Sorted by residual: dihedral pdb=" CA TYR B 451 " pdb=" C TYR B 451 " pdb=" N LEU B 452 " pdb=" CA LEU B 452 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA GLN A 552 " pdb=" C GLN A 552 " pdb=" N HIS A 553 " pdb=" CA HIS A 553 " ideal model delta harmonic sigma weight residual -180.00 -154.77 -25.23 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA TYR A 453 " pdb=" C TYR A 453 " pdb=" N GLN A 454 " pdb=" CA GLN A 454 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 5127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1024 0.059 - 0.118: 365 0.118 - 0.177: 41 0.177 - 0.236: 7 0.236 - 0.295: 1 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CB ILE A 338 " pdb=" CA ILE A 338 " pdb=" CG1 ILE A 338 " pdb=" CG2 ILE A 338 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA CYS A 159 " pdb=" N CYS A 159 " pdb=" C CYS A 159 " pdb=" CB CYS A 159 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA UNK A 626 " pdb=" N UNK A 626 " pdb=" C UNK A 626 " pdb=" CB UNK A 626 " both_signs ideal model delta sigma weight residual False 2.52 2.32 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1435 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 164 " 0.018 2.00e-02 2.50e+03 1.64e-02 6.69e+00 pdb=" CG TRP A 164 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 164 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 164 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 164 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 164 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 472 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO A 473 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 138 " -0.018 2.00e-02 2.50e+03 1.33e-02 4.39e+00 pdb=" CG TRP G 138 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP G 138 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP G 138 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 138 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 138 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 138 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 138 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 138 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 138 " -0.001 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 17 2.22 - 2.89: 3662 2.89 - 3.56: 13515 3.56 - 4.23: 18866 4.23 - 4.90: 29792 Nonbonded interactions: 65852 Sorted by model distance: nonbonded pdb=" O UNK D 42 " pdb=" N UNK D 44 " model vdw 1.546 3.120 nonbonded pdb=" OE2 GLU G 11 " pdb=" NH1 ARG G 145 " model vdw 1.835 3.120 nonbonded pdb=" O GLN A 516 " pdb=" CD ARG A 520 " model vdw 1.874 3.440 nonbonded pdb=" CB SER A 219 " pdb=" CG2 ILE A 656 " model vdw 1.909 3.860 nonbonded pdb=" OD2 ASP G 10 " pdb=" ND2 ASN G 101 " model vdw 2.006 3.120 ... (remaining 65847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.29 max=1.00 mean=0.99 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.900 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5799 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 0.068 8621 Z= 0.541 Angle : 1.295 12.617 11752 Z= 0.835 Chirality : 0.057 0.295 1438 Planarity : 0.005 0.055 1533 Dihedral : 9.921 88.595 2717 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 4.97 % Allowed : 7.65 % Favored : 87.38 % Rotamer: Outliers : 1.19 % Allowed : 1.04 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.97 (0.30), residues: 750 helix: -1.94 (0.21), residues: 332 sheet: -3.07 (0.65), residues: 53 loop : -0.13 (0.37), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP A 164 HIS 0.010 0.003 HIS A 444 PHE 0.019 0.003 PHE A 335 TYR 0.017 0.003 TYR A 453 ARG 0.010 0.001 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 226 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9238 (m-30) cc_final: 0.9018 (m-30) REVERT: A 84 TRP cc_start: 0.8763 (m100) cc_final: 0.8317 (m-90) REVERT: A 91 ASN cc_start: 0.9134 (m-40) cc_final: 0.8854 (m-40) REVERT: A 325 VAL cc_start: 0.9472 (t) cc_final: 0.9211 (p) REVERT: A 327 PHE cc_start: 0.9148 (m-80) cc_final: 0.8943 (m-80) REVERT: A 401 VAL cc_start: 0.6247 (t) cc_final: 0.6019 (t) REVERT: A 552 GLN cc_start: 0.8863 (pm20) cc_final: 0.8471 (pm20) REVERT: B 173 LEU cc_start: 0.6682 (tt) cc_final: 0.5890 (tt) REVERT: B 176 PHE cc_start: 0.8457 (t80) cc_final: 0.8244 (t80) REVERT: B 202 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6913 (tt) REVERT: B 205 PHE cc_start: 0.6050 (t80) cc_final: 0.5767 (t80) REVERT: B 229 ILE cc_start: 0.9075 (mm) cc_final: 0.8674 (mm) REVERT: B 407 THR cc_start: 0.7762 (t) cc_final: 0.7072 (p) REVERT: B 447 PHE cc_start: 0.7973 (m-10) cc_final: 0.7565 (m-80) outliers start: 8 outliers final: 3 residues processed: 229 average time/residue: 0.2071 time to fit residues: 63.7683 Evaluate side-chains 147 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 80 optimal weight: 40.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 HIS A 216 GLN A 290 ASN A 313 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5805 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8621 Z= 0.316 Angle : 0.879 10.735 11752 Z= 0.447 Chirality : 0.043 0.257 1438 Planarity : 0.005 0.054 1533 Dihedral : 6.415 31.822 1287 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 1.74 % Allowed : 9.26 % Favored : 88.99 % Rotamer: Outliers : 0.74 % Allowed : 4.75 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.74 (0.29), residues: 750 helix: -0.64 (0.25), residues: 331 sheet: -3.42 (0.57), residues: 58 loop : -1.12 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 164 HIS 0.009 0.002 HIS A 199 PHE 0.027 0.003 PHE G 153 TYR 0.019 0.002 TYR A 345 ARG 0.009 0.001 ARG A 398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 192 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8612 (pt0) REVERT: A 81 ASP cc_start: 0.9253 (m-30) cc_final: 0.8894 (m-30) REVERT: A 84 TRP cc_start: 0.8596 (m100) cc_final: 0.8243 (m-90) REVERT: A 91 ASN cc_start: 0.9237 (m-40) cc_final: 0.8824 (p0) REVERT: A 111 LEU cc_start: 0.9384 (tt) cc_final: 0.9076 (tt) REVERT: A 213 CYS cc_start: 0.2407 (t) cc_final: 0.0895 (t) REVERT: A 215 MET cc_start: 0.9009 (ttt) cc_final: 0.8662 (ttm) REVERT: A 230 CYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6766 (t) REVERT: A 231 MET cc_start: 0.8213 (mmm) cc_final: 0.7857 (mmm) REVERT: A 254 TYR cc_start: 0.7815 (m-10) cc_final: 0.7577 (m-10) REVERT: A 302 PHE cc_start: 0.8668 (m-10) cc_final: 0.8395 (m-80) REVERT: A 305 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8940 (tp40) REVERT: A 327 PHE cc_start: 0.9151 (m-80) cc_final: 0.8852 (m-80) REVERT: A 345 TYR cc_start: 0.8585 (t80) cc_final: 0.8280 (t80) REVERT: A 453 TYR cc_start: 0.6419 (t80) cc_final: 0.5839 (t80) REVERT: A 501 LEU cc_start: 0.9313 (tp) cc_final: 0.8914 (pp) REVERT: A 552 GLN cc_start: 0.9018 (pm20) cc_final: 0.8665 (pm20) REVERT: A 565 TYR cc_start: 0.2490 (t80) cc_final: 0.2222 (t80) REVERT: B 202 ILE cc_start: 0.7779 (mp) cc_final: 0.7381 (tt) REVERT: B 229 ILE cc_start: 0.9188 (mm) cc_final: 0.8466 (mm) REVERT: B 406 THR cc_start: 0.6887 (p) cc_final: 0.6591 (p) outliers start: 5 outliers final: 0 residues processed: 195 average time/residue: 0.1718 time to fit residues: 47.5802 Evaluate side-chains 138 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 8621 Z= 0.504 Angle : 1.030 13.684 11752 Z= 0.516 Chirality : 0.047 0.301 1438 Planarity : 0.006 0.050 1533 Dihedral : 6.723 29.788 1287 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 1.61 % Allowed : 11.14 % Favored : 87.25 % Rotamer: Outliers : 0.74 % Allowed : 6.09 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -2.19 (0.29), residues: 750 helix: -0.77 (0.26), residues: 332 sheet: -3.62 (0.54), residues: 54 loop : -1.70 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 653 HIS 0.008 0.002 HIS A 553 PHE 0.031 0.003 PHE A 181 TYR 0.030 0.003 TYR A 565 ARG 0.007 0.001 ARG G 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9276 (m-30) cc_final: 0.9022 (m-30) REVERT: A 91 ASN cc_start: 0.9270 (m-40) cc_final: 0.8809 (p0) REVERT: A 180 ILE cc_start: 0.9262 (mp) cc_final: 0.9054 (mp) REVERT: A 230 CYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6592 (t) REVERT: A 305 GLN cc_start: 0.9441 (mm-40) cc_final: 0.9060 (mm-40) REVERT: A 519 THR cc_start: 0.6957 (p) cc_final: 0.6757 (p) REVERT: A 574 LEU cc_start: 0.9388 (tp) cc_final: 0.9182 (tp) REVERT: B 202 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7784 (tt) REVERT: B 205 PHE cc_start: 0.6475 (t80) cc_final: 0.6240 (t80) REVERT: B 229 ILE cc_start: 0.9251 (mm) cc_final: 0.8807 (mm) REVERT: B 406 THR cc_start: 0.7897 (p) cc_final: 0.7605 (p) outliers start: 5 outliers final: 2 residues processed: 155 average time/residue: 0.1795 time to fit residues: 38.9102 Evaluate side-chains 127 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 86 optimal weight: 50.0000 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5876 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8621 Z= 0.333 Angle : 0.845 13.224 11752 Z= 0.422 Chirality : 0.042 0.278 1438 Planarity : 0.005 0.053 1533 Dihedral : 6.171 30.327 1287 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 1.61 % Allowed : 10.34 % Favored : 88.05 % Rotamer: Outliers : 0.30 % Allowed : 5.20 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.90 (0.30), residues: 750 helix: -0.30 (0.27), residues: 330 sheet: -3.38 (0.48), residues: 66 loop : -1.72 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 164 HIS 0.005 0.002 HIS A 199 PHE 0.028 0.003 PHE G 153 TYR 0.020 0.002 TYR A 565 ARG 0.005 0.001 ARG G 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 VAL cc_start: 0.9529 (p) cc_final: 0.8866 (p) REVERT: A 91 ASN cc_start: 0.9238 (m-40) cc_final: 0.8992 (m110) REVERT: A 213 CYS cc_start: 0.4288 (m) cc_final: 0.3296 (m) REVERT: A 305 GLN cc_start: 0.9408 (mm-40) cc_final: 0.9166 (mm-40) REVERT: A 552 GLN cc_start: 0.9058 (pm20) cc_final: 0.8630 (pm20) REVERT: B 82 VAL cc_start: 0.7551 (t) cc_final: 0.7174 (p) REVERT: B 229 ILE cc_start: 0.9131 (mm) cc_final: 0.8192 (mm) REVERT: B 458 ASP cc_start: 0.7400 (t0) cc_final: 0.7102 (t0) REVERT: G 126 TRP cc_start: 0.3674 (m100) cc_final: 0.3402 (m-90) outliers start: 2 outliers final: 0 residues processed: 163 average time/residue: 0.1716 time to fit residues: 39.9890 Evaluate side-chains 118 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 8621 Z= 0.439 Angle : 0.930 11.851 11752 Z= 0.469 Chirality : 0.045 0.289 1438 Planarity : 0.005 0.055 1533 Dihedral : 6.407 29.359 1287 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 1.48 % Allowed : 11.28 % Favored : 87.25 % Rotamer: Outliers : 0.30 % Allowed : 4.16 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.29), residues: 750 helix: -0.39 (0.27), residues: 331 sheet: -3.42 (0.49), residues: 72 loop : -1.86 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP A 164 HIS 0.007 0.002 HIS A 553 PHE 0.029 0.003 PHE A 218 TYR 0.017 0.002 TYR A 467 ARG 0.005 0.001 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7396 (pp) REVERT: A 81 ASP cc_start: 0.9165 (m-30) cc_final: 0.8789 (m-30) REVERT: A 84 TRP cc_start: 0.8823 (m100) cc_final: 0.8571 (m-90) REVERT: A 91 ASN cc_start: 0.9231 (m-40) cc_final: 0.9004 (m-40) REVERT: A 213 CYS cc_start: 0.4641 (m) cc_final: 0.3624 (m) REVERT: A 343 MET cc_start: 0.9422 (tpt) cc_final: 0.8982 (tpp) REVERT: A 378 MET cc_start: 0.8420 (tmm) cc_final: 0.7731 (tmm) REVERT: A 430 PHE cc_start: 0.8222 (m-80) cc_final: 0.7778 (m-10) REVERT: B 82 VAL cc_start: 0.7845 (t) cc_final: 0.7504 (p) REVERT: B 229 ILE cc_start: 0.9261 (mm) cc_final: 0.8757 (mm) REVERT: G 126 TRP cc_start: 0.3601 (m100) cc_final: 0.3384 (m-90) outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.1714 time to fit residues: 36.8250 Evaluate side-chains 118 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8621 Z= 0.372 Angle : 0.871 11.569 11752 Z= 0.441 Chirality : 0.043 0.285 1438 Planarity : 0.005 0.052 1533 Dihedral : 6.229 28.326 1287 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 1.48 % Allowed : 11.01 % Favored : 87.52 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -2.00 (0.30), residues: 750 helix: -0.28 (0.28), residues: 328 sheet: -3.49 (0.54), residues: 62 loop : -1.90 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 164 HIS 0.005 0.002 HIS A 553 PHE 0.031 0.003 PHE B 86 TYR 0.026 0.002 TYR A 565 ARG 0.004 0.001 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 VAL cc_start: 0.9386 (p) cc_final: 0.8916 (p) REVERT: A 81 ASP cc_start: 0.9161 (m-30) cc_final: 0.8806 (m-30) REVERT: A 91 ASN cc_start: 0.9202 (m-40) cc_final: 0.8985 (m-40) REVERT: A 213 CYS cc_start: 0.4664 (m) cc_final: 0.3729 (m) REVERT: A 231 MET cc_start: 0.7571 (mmp) cc_final: 0.7138 (mmm) REVERT: A 305 GLN cc_start: 0.9351 (mm-40) cc_final: 0.8775 (mm-40) REVERT: A 330 PHE cc_start: 0.7598 (m-80) cc_final: 0.7265 (m-80) REVERT: A 343 MET cc_start: 0.9420 (tpt) cc_final: 0.9030 (tpp) REVERT: A 430 PHE cc_start: 0.8210 (m-80) cc_final: 0.7766 (m-10) REVERT: B 82 VAL cc_start: 0.7974 (t) cc_final: 0.7448 (p) REVERT: B 229 ILE cc_start: 0.9312 (mm) cc_final: 0.8465 (mm) REVERT: B 405 ASN cc_start: 0.7193 (p0) cc_final: 0.6941 (p0) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1751 time to fit residues: 37.9488 Evaluate side-chains 122 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5951 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8621 Z= 0.409 Angle : 0.899 11.528 11752 Z= 0.458 Chirality : 0.044 0.285 1438 Planarity : 0.005 0.051 1533 Dihedral : 6.304 27.458 1287 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 1.34 % Allowed : 12.21 % Favored : 86.44 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -2.23 (0.29), residues: 750 helix: -0.52 (0.28), residues: 331 sheet: -3.20 (0.61), residues: 54 loop : -2.11 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP A 164 HIS 0.007 0.002 HIS A 553 PHE 0.026 0.003 PHE A 218 TYR 0.015 0.002 TYR B 225 ARG 0.006 0.001 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9185 (m-30) cc_final: 0.8847 (m-30) REVERT: A 91 ASN cc_start: 0.9198 (m-40) cc_final: 0.8972 (m-40) REVERT: A 213 CYS cc_start: 0.4182 (m) cc_final: 0.3106 (m) REVERT: A 302 PHE cc_start: 0.8803 (m-10) cc_final: 0.8548 (m-80) REVERT: A 343 MET cc_start: 0.9297 (tpt) cc_final: 0.8567 (tpp) REVERT: A 404 LEU cc_start: 0.2482 (mm) cc_final: 0.1927 (mm) REVERT: A 430 PHE cc_start: 0.8093 (m-80) cc_final: 0.7761 (m-10) REVERT: B 82 VAL cc_start: 0.8015 (t) cc_final: 0.7362 (p) REVERT: B 229 ILE cc_start: 0.9274 (mm) cc_final: 0.8674 (mm) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1801 time to fit residues: 38.2386 Evaluate side-chains 117 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 78 optimal weight: 0.0020 chunk 82 optimal weight: 30.0000 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 overall best weight: 3.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 379 HIS ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 GLN G 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8621 Z= 0.286 Angle : 0.812 11.546 11752 Z= 0.414 Chirality : 0.041 0.286 1438 Planarity : 0.004 0.053 1533 Dihedral : 5.986 27.471 1287 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 1.34 % Allowed : 11.01 % Favored : 87.65 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -2.04 (0.30), residues: 750 helix: -0.31 (0.28), residues: 332 sheet: -3.28 (0.59), residues: 56 loop : -2.03 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 164 HIS 0.004 0.001 HIS A 199 PHE 0.024 0.002 PHE B 86 TYR 0.022 0.002 TYR B 181 ARG 0.005 0.001 ARG G 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9194 (m-30) cc_final: 0.8893 (m-30) REVERT: A 91 ASN cc_start: 0.9224 (m-40) cc_final: 0.8926 (m-40) REVERT: A 330 PHE cc_start: 0.7424 (m-80) cc_final: 0.7169 (m-80) REVERT: A 343 MET cc_start: 0.9295 (tpt) cc_final: 0.8576 (tpp) REVERT: A 430 PHE cc_start: 0.8081 (m-80) cc_final: 0.7730 (m-10) REVERT: A 552 GLN cc_start: 0.9196 (pm20) cc_final: 0.8926 (pm20) REVERT: B 82 VAL cc_start: 0.7843 (t) cc_final: 0.7206 (p) REVERT: B 229 ILE cc_start: 0.9250 (mm) cc_final: 0.8613 (mm) REVERT: B 418 LEU cc_start: 0.8625 (mm) cc_final: 0.8357 (mt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1830 time to fit residues: 40.3369 Evaluate side-chains 119 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 84 optimal weight: 40.0000 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5951 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 8621 Z= 0.376 Angle : 0.884 11.764 11752 Z= 0.450 Chirality : 0.044 0.287 1438 Planarity : 0.005 0.053 1533 Dihedral : 6.227 27.430 1287 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 1.34 % Allowed : 11.95 % Favored : 86.71 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -2.23 (0.29), residues: 750 helix: -0.50 (0.28), residues: 328 sheet: -2.74 (0.63), residues: 54 loop : -2.21 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 164 HIS 0.009 0.002 HIS A 379 PHE 0.027 0.003 PHE A 218 TYR 0.021 0.002 TYR B 181 ARG 0.005 0.001 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9169 (m-30) cc_final: 0.8931 (m-30) REVERT: A 91 ASN cc_start: 0.9220 (m-40) cc_final: 0.8993 (m-40) REVERT: A 330 PHE cc_start: 0.7512 (m-80) cc_final: 0.7222 (m-80) REVERT: A 343 MET cc_start: 0.9288 (tpt) cc_final: 0.8658 (tpp) REVERT: A 404 LEU cc_start: 0.2495 (mm) cc_final: 0.2168 (mm) REVERT: A 430 PHE cc_start: 0.8066 (m-80) cc_final: 0.7736 (m-10) REVERT: B 82 VAL cc_start: 0.7917 (t) cc_final: 0.7253 (p) REVERT: B 229 ILE cc_start: 0.9230 (mm) cc_final: 0.8582 (mm) REVERT: B 408 ILE cc_start: 0.8178 (mm) cc_final: 0.7975 (mm) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1743 time to fit residues: 36.3447 Evaluate side-chains 112 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 70 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 8621 Z= 0.373 Angle : 0.903 17.270 11752 Z= 0.457 Chirality : 0.044 0.285 1438 Planarity : 0.005 0.053 1533 Dihedral : 6.208 27.181 1287 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 1.34 % Allowed : 11.95 % Favored : 86.71 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -2.25 (0.30), residues: 750 helix: -0.50 (0.28), residues: 330 sheet: -2.54 (0.57), residues: 64 loop : -2.26 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 164 HIS 0.010 0.002 HIS A 379 PHE 0.024 0.003 PHE A 218 TYR 0.021 0.002 TYR B 181 ARG 0.005 0.001 ARG A 543 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9124 (m-30) cc_final: 0.8889 (m-30) REVERT: A 91 ASN cc_start: 0.9252 (m-40) cc_final: 0.9017 (m-40) REVERT: A 121 LEU cc_start: 0.7572 (mt) cc_final: 0.7362 (mt) REVERT: A 230 CYS cc_start: 0.6415 (t) cc_final: 0.6108 (t) REVERT: A 302 PHE cc_start: 0.9159 (m-10) cc_final: 0.8836 (m-80) REVERT: A 330 PHE cc_start: 0.7446 (m-80) cc_final: 0.7215 (m-80) REVERT: A 343 MET cc_start: 0.9284 (tpt) cc_final: 0.8623 (tpp) REVERT: A 430 PHE cc_start: 0.8032 (m-80) cc_final: 0.7710 (m-10) REVERT: B 82 VAL cc_start: 0.7911 (t) cc_final: 0.7250 (p) REVERT: B 229 ILE cc_start: 0.9269 (mm) cc_final: 0.8447 (mm) REVERT: B 418 LEU cc_start: 0.8676 (mm) cc_final: 0.8447 (mt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1764 time to fit residues: 35.2395 Evaluate side-chains 113 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 30.0000 chunk 29 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.106396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.078223 restraints weight = 147107.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.078676 restraints weight = 64846.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.079398 restraints weight = 38844.601| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.6226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8621 Z= 0.233 Angle : 0.778 11.481 11752 Z= 0.394 Chirality : 0.040 0.274 1438 Planarity : 0.005 0.092 1533 Dihedral : 5.771 27.921 1287 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 1.34 % Allowed : 9.66 % Favored : 88.99 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % 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: -1.94 (0.30), residues: 750 helix: -0.20 (0.28), residues: 336 sheet: -2.40 (0.56), residues: 64 loop : -2.17 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 164 HIS 0.007 0.001 HIS A 199 PHE 0.012 0.002 PHE G 153 TYR 0.020 0.002 TYR B 181 ARG 0.005 0.001 ARG G 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1542.77 seconds wall clock time: 28 minutes 13.99 seconds (1693.99 seconds total)