Starting phenix.real_space_refine on Wed Dec 13 04:02:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8skv_40568/12_2023/8skv_40568_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8skv_40568/12_2023/8skv_40568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8skv_40568/12_2023/8skv_40568.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8skv_40568/12_2023/8skv_40568.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8skv_40568/12_2023/8skv_40568_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8skv_40568/12_2023/8skv_40568_trim.pdb" } resolution = 3.1 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= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 7695 2.51 5 N 2087 2.21 5 O 2372 1.98 5 H 11341 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 378": "OD1" <-> "OD2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 85": "OD1" <-> "OD2" Residue "E PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 287": "OD1" <-> "OD2" Residue "E GLU 317": "OE1" <-> "OE2" Residue "E GLU 504": "OE1" <-> "OE2" Residue "J ASP 10": "OD1" <-> "OD2" Residue "J ASP 32": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 23561 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3034 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3148 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3144 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 80 Chain: "D" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 2978 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 8095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 8095 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1990 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "a" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 481 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "b" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 481 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 11.17, per 1000 atoms: 0.47 Number of scatterers: 23561 At special positions: 0 Unit cell: (123.5, 114.95, 179.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 O 2372 8.00 N 2087 7.00 C 7695 6.00 H 11341 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS J 69 " distance=2.03 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 299 " - pdb=" SG CYS D 242 " distance=2.04 Simple disulfide: pdb=" SG CYS C 311 " - pdb=" SG CYS E 468 " distance=2.03 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS J 15 " distance=2.03 Simple disulfide: pdb=" SG CYS D 266 " - pdb=" SG CYS D 323 " distance=2.03 Simple disulfide: pdb=" SG CYS D 369 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 38 " - pdb=" SG CYS E 46 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 202 " distance=2.03 Simple disulfide: pdb=" SG CYS E 239 " - pdb=" SG CYS E 307 " distance=2.03 Simple disulfide: pdb=" SG CYS E 253 " - pdb=" SG CYS E 261 " distance=2.06 Simple disulfide: pdb=" SG CYS E 464 " - pdb=" SG CYS E 526 " distance=2.03 Simple disulfide: pdb=" SG CYS E 478 " - pdb=" SG CYS E 485 " distance=2.03 Simple disulfide: pdb=" SG CYS J 13 " - pdb=" SG CYS J 101 " distance=2.03 Simple disulfide: pdb=" SG CYS J 72 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 109 " - pdb=" SG CYS J 134 " distance=2.03 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 263 " " NAG B 501 " - " ASN B 263 " " NAG B 502 " - " ASN B 459 " " NAG E 601 " - " ASN E 65 " " NAG E 602 " - " ASN E 481 " " NAG E 603 " - " ASN E 168 " " NAG E 604 " - " ASN E 403 " " NAG G 1 " - " ASN E 72 " " NAG H 1 " - " ASN E 451 " " NAG I 1 " - " ASN C 263 " " NAG O 1 " - " ASN J 49 " Time building additional restraints: 17.78 Conformation dependent library (CDL) restraints added in 2.6 seconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 35 sheets defined 13.3% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 311 through 318 Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.762A pdb=" N ASN A 362 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.640A pdb=" N GLY A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 311 through 318 Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.932A pdb=" N LEU B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 357 through 362' Processing helix chain 'B' and resid 391 through 395 removed outlier: 4.090A pdb=" N TYR B 395 " --> pdb=" O ARG B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.597A pdb=" N GLY B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 258 Processing helix chain 'C' and resid 311 through 318 removed outlier: 4.312A pdb=" N TRP C 315 " --> pdb=" O CYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'C' and resid 421 through 425 Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 391 through 395 removed outlier: 3.990A pdb=" N TYR D 395 " --> pdb=" O ARG D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 427 Processing helix chain 'E' and resid 27 through 33 Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.878A pdb=" N SER E 87 " --> pdb=" O GLN E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 193 through 197 removed outlier: 3.860A pdb=" N ALA E 197 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 246 Processing helix chain 'E' and resid 356 through 360 removed outlier: 3.889A pdb=" N SER E 360 " --> pdb=" O ARG E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 418 removed outlier: 3.892A pdb=" N ALA E 418 " --> pdb=" O SER E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 521 Processing helix chain 'J' and resid 64 through 69 Processing helix chain 'a' and resid 46 through 73 removed outlier: 3.512A pdb=" N LEU a 72 " --> pdb=" O LYS a 68 " (cutoff:3.500A) Processing helix chain 'b' and resid 46 through 73 removed outlier: 3.773A pdb=" N ALA b 50 " --> pdb=" O PRO b 46 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU b 73 " --> pdb=" O ILE b 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 249 removed outlier: 3.577A pdb=" N THR A 265 " --> pdb=" O HIS A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 245 through 249 removed outlier: 3.577A pdb=" N THR A 265 " --> pdb=" O HIS A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.618A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.618A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA7, first strand: chain 'A' and resid 459 through 462 removed outlier: 6.456A pdb=" N ASN A 459 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL B 462 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N SER A 461 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE J 61 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N SER B 461 " --> pdb=" O PHE J 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 245 through 249 removed outlier: 3.566A pdb=" N ARG B 245 " --> pdb=" O THR B 269 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR B 265 " --> pdb=" O HIS B 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 281 Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.602A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.602A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'C' and resid 245 through 249 removed outlier: 3.649A pdb=" N THR C 265 " --> pdb=" O HIS C 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 279 through 280 removed outlier: 3.661A pdb=" N LEU C 334 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 320 through 321 Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 352 removed outlier: 3.743A pdb=" N THR C 368 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AB9, first strand: chain 'D' and resid 459 through 463 removed outlier: 3.786A pdb=" N MET C 464 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N HIS C 457 " --> pdb=" O ARG J 36 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE J 38 " --> pdb=" O HIS C 457 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASN C 459 " --> pdb=" O ILE J 38 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE J 40 " --> pdb=" O ASN C 459 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER C 461 " --> pdb=" O ILE J 40 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL J 42 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C 463 " --> pdb=" O VAL J 42 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA J 16 " --> pdb=" O ASP J 10 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP J 10 " --> pdb=" O ALA J 16 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE J 18 " --> pdb=" O LEU J 8 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 245 through 248 removed outlier: 3.576A pdb=" N SER D 306 " --> pdb=" O CYS D 266 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 304 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS D 301 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 278 through 281 Processing sheet with id=AC3, first strand: chain 'D' and resid 348 through 352 removed outlier: 3.592A pdb=" N THR D 368 " --> pdb=" O LEU D 352 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N PHE D 411 " --> pdb=" O GLY D 373 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 348 through 352 removed outlier: 3.592A pdb=" N THR D 368 " --> pdb=" O LEU D 352 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N PHE D 411 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR D 410 " --> pdb=" O GLU D 403 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AC6, first strand: chain 'E' and resid 9 through 13 removed outlier: 3.945A pdb=" N PHE E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY E 93 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR E 36 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG E 39 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N THR E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 18 through 23 removed outlier: 3.604A pdb=" N THR E 74 " --> pdb=" O PHE E 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 122 through 125 removed outlier: 6.233A pdb=" N TYR E 122 " --> pdb=" O GLN E 218 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU E 220 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL E 124 " --> pdb=" O LEU E 220 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS E 213 " --> pdb=" O CYS E 202 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS E 202 " --> pdb=" O LYS E 213 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE E 159 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS E 149 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU E 157 " --> pdb=" O LYS E 149 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 130 through 135 removed outlier: 3.739A pdb=" N PHE E 185 " --> pdb=" O CYS E 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 225 through 229 removed outlier: 6.102A pdb=" N ARG E 254 " --> pdb=" O VAL E 263 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VAL E 263 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 234 through 239 Processing sheet with id=AD3, first strand: chain 'E' and resid 340 through 344 removed outlier: 3.697A pdb=" N THR E 433 " --> pdb=" O CYS E 423 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TRP E 366 " --> pdb=" O LEU E 380 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 348 through 354 Processing sheet with id=AD5, first strand: chain 'E' and resid 460 through 462 Processing sheet with id=AD6, first strand: chain 'E' and resid 486 through 487 removed outlier: 3.859A pdb=" N GLN E 486 " --> pdb=" O LYS E 479 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS E 479 " --> pdb=" O GLN E 486 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU E 536 " --> pdb=" O VAL E 528 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLN E 530 " --> pdb=" O TYR E 534 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR E 534 " --> pdb=" O GLN E 530 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 75 through 78 Processing sheet with id=AD8, first strand: chain 'J' and resid 111 through 116 478 hydrogen bonds defined for protein. 1191 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: 8.89 Time building geometry restraints manager: 18.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11336 1.04 - 1.24: 1194 1.24 - 1.43: 4090 1.43 - 1.63: 7137 1.63 - 1.83: 77 Bond restraints: 23834 Sorted by residual: bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 NAG B 502 " pdb=" O5 NAG B 502 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C1 NAG E 602 " pdb=" O5 NAG E 602 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.68e+00 ... (remaining 23829 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.35: 997 107.35 - 114.03: 28453 114.03 - 120.70: 6847 120.70 - 127.37: 6480 127.37 - 134.05: 187 Bond angle restraints: 42964 Sorted by residual: angle pdb=" C THR C 282 " pdb=" N PRO C 283 " pdb=" CA PRO C 283 " ideal model delta sigma weight residual 119.84 116.72 3.12 1.25e+00 6.40e-01 6.23e+00 angle pdb=" N SER J 51 " pdb=" CA SER J 51 " pdb=" C SER J 51 " ideal model delta sigma weight residual 108.79 105.54 3.25 1.53e+00 4.27e-01 4.52e+00 angle pdb=" C GLY E 114 " pdb=" N LEU E 115 " pdb=" CA LEU E 115 " ideal model delta sigma weight residual 121.54 125.54 -4.00 1.91e+00 2.74e-01 4.39e+00 angle pdb=" CA GLY E 484 " pdb=" C GLY E 484 " pdb=" N CYS E 485 " ideal model delta sigma weight residual 115.43 117.44 -2.01 9.80e-01 1.04e+00 4.20e+00 angle pdb=" C ILE J 50 " pdb=" N SER J 51 " pdb=" CA SER J 51 " ideal model delta sigma weight residual 121.62 125.36 -3.74 1.83e+00 2.99e-01 4.19e+00 ... (remaining 42959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 10197 17.74 - 35.49: 891 35.49 - 53.23: 227 53.23 - 70.97: 33 70.97 - 88.72: 12 Dihedral angle restraints: 11360 sinusoidal: 6010 harmonic: 5350 Sorted by residual: dihedral pdb=" CB CYS A 299 " pdb=" SG CYS A 299 " pdb=" SG CYS B 242 " pdb=" CB CYS B 242 " ideal model delta sinusoidal sigma weight residual 93.00 165.09 -72.09 1 1.00e+01 1.00e-02 6.65e+01 dihedral pdb=" CB CYS E 253 " pdb=" SG CYS E 253 " pdb=" SG CYS E 261 " pdb=" CB CYS E 261 " ideal model delta sinusoidal sigma weight residual 93.00 26.85 66.15 1 1.00e+01 1.00e-02 5.72e+01 dihedral pdb=" CB CYS C 311 " pdb=" SG CYS C 311 " pdb=" SG CYS E 468 " pdb=" CB CYS E 468 " ideal model delta sinusoidal sigma weight residual -86.00 -145.27 59.27 1 1.00e+01 1.00e-02 4.70e+01 ... (remaining 11357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1774 0.054 - 0.109: 217 0.109 - 0.163: 63 0.163 - 0.218: 0 0.218 - 0.272: 1 Chirality restraints: 2055 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN E 451 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 5.99e-01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN E 72 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 2052 not shown) Planarity restraints: 3723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 282 " 0.063 5.00e-02 4.00e+02 9.66e-02 1.49e+01 pdb=" N PRO C 283 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO C 283 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 283 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 243 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO C 244 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 244 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 244 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 52 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO J 53 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO J 53 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 53 " -0.023 5.00e-02 4.00e+02 ... (remaining 3720 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1358 2.20 - 2.80: 45974 2.80 - 3.40: 56222 3.40 - 4.00: 78167 4.00 - 4.60: 117624 Nonbonded interactions: 299345 Sorted by model distance: nonbonded pdb=" O PRO E 3 " pdb=" HH TYR E 228 " model vdw 1.601 1.850 nonbonded pdb=" O ASN E 505 " pdb=" H ARG E 507 " model vdw 1.610 1.850 nonbonded pdb="HH11 ARG B 346 " pdb=" OH TYR J 135 " model vdw 1.625 1.850 nonbonded pdb=" HD1 HIS E 310 " pdb=" OD1 ASP E 312 " model vdw 1.628 1.850 nonbonded pdb=" O GLU E 359 " pdb=" HG SER E 362 " model vdw 1.633 1.850 ... (remaining 299340 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 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 256 through 421 or (r \ esid 422 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 423 through 425 or (resid 426 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 427 through 445 or (resid 4 \ 46 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 447 through 449 or (resid 450 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 451 through 453 or (resid 454 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 455 through 458 or (resid 459 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or n \ ame HB3 or name HD21)) or resid 460 through 464)) selection = (chain 'B' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 256 through 259 or (r \ esid 260 through 261 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 262 through 345 or (resid 346 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 347 through 356 \ or (resid 357 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 358 through 404 or (resid 405 through 406 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 407 throu \ gh 424 or (resid 425 through 426 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 427 through 449 or (resid 450 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 451 \ through 464)) selection = (chain 'C' and (resid 242 through 310 or (resid 311 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 312 through 345 or (r \ esid 346 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 347 through 356 or (resid 357 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 358 through 424 or (resid 4 \ 25 through 426 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 427 through 449 or (resid 450 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 451 through 453 or (r \ esid 454 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 455 through 458 or (resid 459 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or n \ ame HB2 or name HB3 or name HD21)) or resid 460 through 464)) selection = (chain 'D' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 256 through 262 or (r \ esid 263 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or \ resid 264 through 356 or (resid 357 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 358 through 445 or (resid 446 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 447 through 458 or (resid 459 and (name N or name CA or name C or name O or nam \ e CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name \ HB3 or name HD21)) or resid 460 through 464)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.940 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: 0.360 Extract box with map and model: 11.050 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 74.850 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 0.003 0.047 12493 Z= 0.199 Angle : 0.572 5.942 17108 Z= 0.285 Chirality : 0.042 0.272 2055 Planarity : 0.004 0.097 2197 Dihedral : 14.900 88.718 4591 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.04 % Rotamer: Outliers : 0.08 % Allowed : 23.28 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.22), residues: 1612 helix: 1.57 (0.47), residues: 152 sheet: 0.84 (0.21), residues: 630 loop : -1.51 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 366 HIS 0.004 0.001 HIS A 436 PHE 0.015 0.001 PHE E 75 TYR 0.009 0.001 TYR E 228 ARG 0.003 0.000 ARG E 416 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.874 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.6149 time to fit residues: 66.6270 Evaluate side-chains 76 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.910 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.0458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12493 Z= 0.367 Angle : 0.613 5.512 17108 Z= 0.311 Chirality : 0.044 0.167 2055 Planarity : 0.005 0.072 2197 Dihedral : 6.679 57.645 2045 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.44 % Favored : 91.50 % Rotamer: Outliers : 2.16 % Allowed : 23.12 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1612 helix: 1.41 (0.45), residues: 158 sheet: 0.78 (0.21), residues: 624 loop : -1.74 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 366 HIS 0.005 0.001 HIS A 436 PHE 0.023 0.002 PHE E 75 TYR 0.016 0.002 TYR E 228 ARG 0.003 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 72 time to evaluate : 2.168 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 19 residues processed: 94 average time/residue: 0.5761 time to fit residues: 79.4028 Evaluate side-chains 90 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 1.731 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2446 time to fit residues: 10.9002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.0501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12493 Z= 0.243 Angle : 0.558 5.457 17108 Z= 0.279 Chirality : 0.042 0.182 2055 Planarity : 0.004 0.065 2197 Dihedral : 6.341 59.618 2045 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.26 % Favored : 92.68 % Rotamer: Outliers : 1.36 % Allowed : 23.20 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.22), residues: 1612 helix: 1.54 (0.45), residues: 159 sheet: 0.80 (0.21), residues: 623 loop : -1.69 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 366 HIS 0.004 0.001 HIS A 436 PHE 0.019 0.001 PHE E 75 TYR 0.012 0.001 TYR E 228 ARG 0.002 0.000 ARG E 416 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 1.783 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 92 average time/residue: 0.5146 time to fit residues: 70.2808 Evaluate side-chains 86 residues out of total 1406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 1.815 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2495 time to fit residues: 7.3099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.2567 > 50: distance: 59 - 157: 5.756 distance: 104 - 105: 3.089 distance: 104 - 112: 5.870 distance: 105 - 108: 3.995 distance: 105 - 113: 3.184 distance: 106 - 107: 3.519 distance: 106 - 117: 3.256 distance: 108 - 114: 5.548 distance: 108 - 115: 3.408 distance: 109 - 110: 3.915 distance: 117 - 125: 3.544 distance: 118 - 119: 5.618 distance: 118 - 121: 7.115 distance: 118 - 126: 5.083 distance: 119 - 120: 14.537 distance: 119 - 131: 12.224 distance: 121 - 122: 3.374 distance: 121 - 127: 4.813 distance: 122 - 123: 3.522 distance: 122 - 124: 3.553 distance: 131 - 132: 7.197 distance: 131 - 138: 23.810 distance: 132 - 133: 5.708 distance: 132 - 135: 8.355 distance: 132 - 139: 9.248 distance: 133 - 134: 8.163 distance: 133 - 145: 4.051 distance: 135 - 136: 4.081 distance: 136 - 141: 7.106 distance: 137 - 142: 10.317 distance: 137 - 143: 12.349 distance: 137 - 144: 7.244 distance: 145 - 146: 4.933 distance: 145 - 149: 9.234 distance: 146 - 147: 7.415 distance: 146 - 150: 5.922 distance: 146 - 151: 3.882 distance: 147 - 148: 10.495 distance: 147 - 152: 8.708 distance: 152 - 153: 6.699 distance: 152 - 158: 10.555 distance: 153 - 154: 6.218 distance: 153 - 159: 4.282 distance: 154 - 155: 6.994 distance: 154 - 162: 8.073 distance: 156 - 157: 6.463 distance: 156 - 161: 4.363 distance: 162 - 163: 4.812 distance: 162 - 171: 12.535 distance: 163 - 164: 5.123 distance: 163 - 166: 5.711 distance: 163 - 172: 4.427 distance: 164 - 165: 11.569 distance: 164 - 179: 5.735 distance: 166 - 173: 5.857 distance: 166 - 174: 5.927 distance: 167 - 168: 3.929 distance: 167 - 176: 3.835 distance: 179 - 180: 6.282 distance: 179 - 184: 7.255 distance: 180 - 181: 6.714 distance: 180 - 183: 6.275 distance: 180 - 185: 8.282 distance: 181 - 182: 5.081 distance: 181 - 189: 9.486 distance: 183 - 186: 3.913 distance: 183 - 187: 7.120 distance: 183 - 188: 4.161 distance: 189 - 190: 6.020 distance: 189 - 197: 13.367 distance: 190 - 193: 3.550 distance: 191 - 192: 4.027 distance: 191 - 208: 4.700 distance: 193 - 194: 4.522 distance: 193 - 199: 4.171 distance: 193 - 200: 11.319 distance: 194 - 195: 8.412 distance: 194 - 201: 6.481 distance: 195 - 204: 5.075 distance: 196 - 206: 4.054 distance: 196 - 207: 3.122 distance: 208 - 209: 10.333 distance: 208 - 214: 6.579 distance: 209 - 210: 9.079 distance: 209 - 212: 7.122 distance: 209 - 215: 6.162 distance: 210 - 211: 17.453 distance: 210 - 222: 11.505 distance: 212 - 213: 4.712 distance: 213 - 214: 4.259 distance: 213 - 218: 3.356 distance: 214 - 220: 4.212 distance: 214 - 221: 3.708 distance: 222 - 223: 4.027 distance: 222 - 228: 15.274 distance: 223 - 229: 4.521 distance: 224 - 225: 11.425 distance: 226 - 230: 3.719