Starting phenix.real_space_refine (version: dev) on Thu Mar 16 13:51:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/03_2023/6c26_7336_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/03_2023/6c26_7336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/03_2023/6c26_7336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/03_2023/6c26_7336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/03_2023/6c26_7336_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c26_7336/03_2023/6c26_7336_neut_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.007 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 Process input model Symmetric amino acids flipped Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 497": "NH1" <-> "NH2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A ARG 605": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 651": "NH1" <-> "NH2" Residue "A TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "1 TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 270": "NH1" <-> "NH2" Residue "1 PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 424": "NH1" <-> "NH2" Residue "1 TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 241": "NH1" <-> "NH2" Residue "3 ARG 295": "NH1" <-> "NH2" Residue "3 PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ASP 275": "OD1" <-> "OD2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 17188 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5225 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 624} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "1" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3496 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 23, 'TRANS': 408} Chain breaks: 2 Chain: "5" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 659 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "4" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 259 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "2" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 883 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "3" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1028 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1940 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 234} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3218 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 16, 'TRANS': 380} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'EGY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "1" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'EGY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'EGY': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'EGY': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'EGY': 1} Classifications: {'undetermined': 1} Chain: "B" 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 chiralities: 1 Time building chain proxies: 9.40, per 1000 atoms: 0.55 Number of scatterers: 17188 At special positions: 0 Unit cell: (140.352, 130.56, 154.496, 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 55 16.00 P 8 15.00 O 3135 8.00 N 2684 7.00 C 11306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-2 " BMA D 3 " - " BMA D 4 " " BMA D 4 " - " BMA D 5 " " BMA D 5 " - " BMA D 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " BETA1-6 " BMA D 3 " - " BMA D 7 " NAG-ASN " NAG B 601 " - " ASN B 60 " " NAG D 1 " - " ASN A 539 " " NAG E 1 " - " ASN 1 336 " Time building additional restraints: 6.75 Conformation dependent library (CDL) restraints added in 2.5 seconds 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3946 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 19 sheets defined 36.3% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 6 through 24 Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 34 through 37 No H-bonds generated for 'chain 'A' and resid 34 through 37' Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.737A pdb=" N PHE A 50 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR A 52 " --> pdb=" O TRP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 92 through 103 removed outlier: 3.554A pdb=" N ASN A 103 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 118 removed outlier: 3.533A pdb=" N PHE A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 removed outlier: 4.358A pdb=" N GLY A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 removed outlier: 4.265A pdb=" N LEU A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 187 removed outlier: 4.023A pdb=" N THR A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 205 Processing helix chain 'A' and resid 212 through 227 removed outlier: 4.015A pdb=" N ILE A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 3.671A pdb=" N LEU A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 252 removed outlier: 3.984A pdb=" N THR A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 No H-bonds generated for 'chain 'A' and resid 259 through 262' Processing helix chain 'A' and resid 267 through 281 removed outlier: 3.888A pdb=" N PHE A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 293 through 296 No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 366 through 378 Proline residue: A 371 - end of helix removed outlier: 3.630A pdb=" N VAL A 374 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE A 375 " --> pdb=" O PRO A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 removed outlier: 3.704A pdb=" N VAL A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 4.082A pdb=" N VAL A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 removed outlier: 4.320A pdb=" N ILE A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 428 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 472 removed outlier: 3.713A pdb=" N TYR A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 472 " --> pdb=" O TRP A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 505 removed outlier: 4.243A pdb=" N LEU A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 removed outlier: 3.839A pdb=" N GLY A 520 " --> pdb=" O TRP A 517 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR A 521 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 522 " --> pdb=" O TYR A 519 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 523 " --> pdb=" O GLY A 520 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A 524 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET A 526 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 549 Processing helix chain 'A' and resid 554 through 562 removed outlier: 4.558A pdb=" N GLU A 559 " --> pdb=" O GLU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 removed outlier: 4.267A pdb=" N LEU A 588 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TRP A 589 " --> pdb=" O LYS A 586 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET A 590 " --> pdb=" O PHE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 692 through 700 removed outlier: 3.744A pdb=" N GLY A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain '1' and resid 192 through 194 No H-bonds generated for 'chain '1' and resid 192 through 194' Processing helix chain '1' and resid 270 through 278 Processing helix chain '1' and resid 345 through 347 No H-bonds generated for 'chain '1' and resid 345 through 347' Processing helix chain '1' and resid 443 through 468 removed outlier: 4.012A pdb=" N PHE 1 447 " --> pdb=" O LYS 1 443 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS 1 448 " --> pdb=" O SER 1 444 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS 1 449 " --> pdb=" O SER 1 445 " (cutoff:3.500A) Proline residue: 1 450 - end of helix removed outlier: 3.746A pdb=" N MET 1 462 " --> pdb=" O PHE 1 458 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY 1 463 " --> pdb=" O THR 1 459 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL 1 464 " --> pdb=" O ALA 1 460 " (cutoff:3.500A) Processing helix chain '5' and resid 3 through 10 Processing helix chain '5' and resid 25 through 47 removed outlier: 4.138A pdb=" N ILE 5 30 " --> pdb=" O PRO 5 26 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE 5 34 " --> pdb=" O ILE 5 30 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL 5 35 " --> pdb=" O CYS 5 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU 5 37 " --> pdb=" O LEU 5 33 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA 5 46 " --> pdb=" O SER 5 42 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL 5 47 " --> pdb=" O ALA 5 43 " (cutoff:3.500A) Processing helix chain '5' and resid 53 through 79 removed outlier: 4.256A pdb=" N LEU 5 73 " --> pdb=" O LEU 5 69 " (cutoff:3.500A) Processing helix chain '4' and resid 4 through 31 removed outlier: 3.889A pdb=" N LEU 4 21 " --> pdb=" O VAL 4 17 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE 4 22 " --> pdb=" O MET 4 18 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL 4 23 " --> pdb=" O MET 4 19 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE 4 24 " --> pdb=" O THR 4 20 " (cutoff:3.500A) Processing helix chain '2' and resid 23 through 40 removed outlier: 3.848A pdb=" N GLN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 67 removed outlier: 3.909A pdb=" N PHE 2 53 " --> pdb=" O THR 2 49 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY 2 58 " --> pdb=" O LEU 2 54 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE 2 65 " --> pdb=" O GLN 2 61 " (cutoff:3.500A) Processing helix chain '2' and resid 74 through 99 removed outlier: 4.177A pdb=" N GLY 2 80 " --> pdb=" O ALA 2 76 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE 2 81 " --> pdb=" O PHE 2 77 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 2 91 " --> pdb=" O GLN 2 87 " (cutoff:3.500A) Processing helix chain '2' and resid 109 through 124 removed outlier: 4.031A pdb=" N LEU 2 121 " --> pdb=" O ALA 2 117 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS 2 122 " --> pdb=" O SER 2 118 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE 2 123 " --> pdb=" O LEU 2 119 " (cutoff:3.500A) Processing helix chain '3' and resid 210 through 215 Processing helix chain '3' and resid 218 through 232 Processing helix chain '3' and resid 235 through 240 Processing helix chain '3' and resid 269 through 288 Processing helix chain '3' and resid 292 through 296 Processing helix chain '3' and resid 306 through 334 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 196 through 216 removed outlier: 3.936A pdb=" N LEU C 208 " --> pdb=" O PHE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 253 removed outlier: 3.688A pdb=" N ALA C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 282 Proline residue: C 270 - end of helix Processing helix chain 'B' and resid 38 through 47 removed outlier: 3.733A pdb=" N SER B 41 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL B 42 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR B 43 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS B 45 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP B 46 " --> pdb=" O TYR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 96 through 105 removed outlier: 4.111A pdb=" N ASN B 105 " --> pdb=" O LYS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.599A pdb=" N LYS B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 411 removed outlier: 3.855A pdb=" N GLY B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 568 through 572 removed outlier: 3.572A pdb=" N PHE A 670 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLN A 681 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU A 668 " --> pdb=" O GLN A 681 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 645 through 647 Processing sheet with id= C, first strand: chain '1' and resid 174 through 178 removed outlier: 4.044A pdb=" N ARG 1 38 " --> pdb=" O SER 1 174 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS 1 37 " --> pdb=" O GLU 1 52 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR 1 50 " --> pdb=" O THR 1 39 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '1' and resid 66 through 70 removed outlier: 3.556A pdb=" N GLN 1 95 " --> pdb=" O ILE 1 116 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 154 through 158 removed outlier: 3.721A pdb=" N GLN 1 154 " --> pdb=" O HIS 1 226 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '1' and resid 197 through 199 Processing sheet with id= G, first strand: chain '1' and resid 231 through 233 Processing sheet with id= H, first strand: chain '1' and resid 303 through 305 removed outlier: 3.541A pdb=" N GLY 1 340 " --> pdb=" O TYR 1 303 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR 1 338 " --> pdb=" O THR 1 305 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN 1 376 " --> pdb=" O LEU 1 236 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ARG 1 238 " --> pdb=" O ASN 1 376 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU 1 378 " --> pdb=" O ARG 1 238 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ILE 1 240 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N SER 1 380 " --> pdb=" O ILE 1 240 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU 1 242 " --> pdb=" O SER 1 380 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE 1 382 " --> pdb=" O LEU 1 242 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL 1 417 " --> pdb=" O LEU 1 383 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '1' and resid 290 through 294 removed outlier: 3.785A pdb=" N MET 1 293 " --> pdb=" O PHE 1 321 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE 1 321 " --> pdb=" O MET 1 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE 1 322 " --> pdb=" O HIS 1 315 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS 1 315 " --> pdb=" O PHE 1 322 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '1' and resid 349 through 351 removed outlier: 3.860A pdb=" N ASP 1 391 " --> pdb=" O LYS 1 438 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP 1 440 " --> pdb=" O ILE 1 389 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE 1 389 " --> pdb=" O ASP 1 440 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 25 through 27 Processing sheet with id= L, first strand: chain 'C' and resid 92 through 96 removed outlier: 4.245A pdb=" N ALA C 135 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU C 155 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 137 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU C 153 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N LEU C 139 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N PHE C 151 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 78 through 80 removed outlier: 6.282A pdb=" N ASN B 108 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL B 218 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLY B 220 " --> pdb=" O PRO B 190 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 131 through 133 Processing sheet with id= O, first strand: chain 'B' and resid 139 through 142 removed outlier: 3.531A pdb=" N ARG B 141 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 199 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 151 through 154 removed outlier: 3.580A pdb=" N LEU B 151 " --> pdb=" O PHE B 174 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 263 through 267 removed outlier: 4.329A pdb=" N VAL B 263 " --> pdb=" O TRP B 299 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP B 299 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY B 295 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 270 through 273 removed outlier: 3.764A pdb=" N SER B 272 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 372 through 375 removed outlier: 3.706A pdb=" N TYR B 323 " --> pdb=" O LEU B 316 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1593 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: 4.37 Time building geometry restraints manager: 7.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2642 1.30 - 1.43: 5072 1.43 - 1.56: 9788 1.56 - 1.69: 33 1.69 - 1.82: 92 Bond restraints: 17627 Sorted by residual: bond pdb=" C2 BMA D 4 " pdb=" O2 BMA D 4 " ideal model delta sigma weight residual 1.402 1.566 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" C1 BMA D 4 " pdb=" C2 BMA D 4 " ideal model delta sigma weight residual 1.519 1.634 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.632 -0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" C2 BMA D 5 " pdb=" O2 BMA D 5 " ideal model delta sigma weight residual 1.402 1.509 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C21 EGY C 301 " pdb=" O21 EGY C 301 " ideal model delta sigma weight residual 1.330 1.430 -0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 17622 not shown) Histogram of bond angle deviations from ideal: 96.41 - 106.41: 499 106.41 - 116.41: 11246 116.41 - 126.41: 11854 126.41 - 136.41: 284 136.41 - 146.41: 2 Bond angle restraints: 23885 Sorted by residual: angle pdb=" C TYR A 76 " pdb=" N PRO A 77 " pdb=" CA PRO A 77 " ideal model delta sigma weight residual 119.56 103.90 15.66 1.01e+00 9.80e-01 2.41e+02 angle pdb=" N GLU 1 209 " pdb=" CA GLU 1 209 " pdb=" C GLU 1 209 " ideal model delta sigma weight residual 111.28 120.85 -9.57 1.09e+00 8.42e-01 7.71e+01 angle pdb=" C LEU B 346 " pdb=" N PRO B 347 " pdb=" CA PRO B 347 " ideal model delta sigma weight residual 119.92 129.02 -9.10 1.07e+00 8.73e-01 7.24e+01 angle pdb=" N ILE A 278 " pdb=" CA ILE A 278 " pdb=" C ILE A 278 " ideal model delta sigma weight residual 110.62 118.99 -8.37 1.02e+00 9.61e-01 6.74e+01 angle pdb=" N TYR A 76 " pdb=" CA TYR A 76 " pdb=" C TYR A 76 " ideal model delta sigma weight residual 113.45 123.89 -10.44 1.39e+00 5.18e-01 5.64e+01 ... (remaining 23880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.72: 9922 31.72 - 63.45: 245 63.45 - 95.17: 47 95.17 - 126.90: 19 126.90 - 158.62: 5 Dihedral angle restraints: 10238 sinusoidal: 4138 harmonic: 6100 Sorted by residual: dihedral pdb=" CA TYR 1 84 " pdb=" C TYR 1 84 " pdb=" N PHE 1 85 " pdb=" CA PHE 1 85 " ideal model delta harmonic sigma weight residual 180.00 151.64 28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ASN A 60 " pdb=" C ASN A 60 " pdb=" N ASN A 61 " pdb=" CA ASN A 61 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA ASN B 225 " pdb=" C ASN B 225 " pdb=" N ASN B 226 " pdb=" CA ASN B 226 " ideal model delta harmonic sigma weight residual -180.00 -152.61 -27.39 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 10235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2214 0.086 - 0.173: 389 0.173 - 0.259: 63 0.259 - 0.345: 17 0.345 - 0.431: 5 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CA TYR A 76 " pdb=" N TYR A 76 " pdb=" C TYR A 76 " pdb=" CB TYR A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" C2 BMA D 3 " pdb=" C1 BMA D 3 " pdb=" C3 BMA D 3 " pdb=" O2 BMA D 3 " both_signs ideal model delta sigma weight residual False 2.47 2.90 -0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" C2 NAG E 1 " pdb=" C1 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" N2 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.07 -0.43 2.00e-01 2.50e+01 4.52e+00 ... (remaining 2685 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA 3 234 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C ALA 3 234 " -0.051 2.00e-02 2.50e+03 pdb=" O ALA 3 234 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR 3 235 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 597 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C ILE A 597 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE A 597 " -0.019 2.00e-02 2.50e+03 pdb=" N TRP A 598 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 1 398 " 0.016 2.00e-02 2.50e+03 2.14e-02 8.01e+00 pdb=" CG PHE 1 398 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE 1 398 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE 1 398 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE 1 398 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE 1 398 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE 1 398 " 0.001 2.00e-02 2.50e+03 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 49 2.45 - 3.06: 10236 3.06 - 3.67: 23628 3.67 - 4.29: 32969 4.29 - 4.90: 56385 Nonbonded interactions: 123267 Sorted by model distance: nonbonded pdb=" NZ LYS C 77 " pdb=" OG1 THR C 143 " model vdw 1.833 2.520 nonbonded pdb=" OH TYR B 69 " pdb=" ND2 ASN B 105 " model vdw 1.955 2.520 nonbonded pdb=" O LYS 1 171 " pdb=" O GLU 1 209 " model vdw 2.001 3.040 nonbonded pdb=" O PRO B 321 " pdb=" O4 BMA D 4 " model vdw 2.131 2.440 nonbonded pdb=" CG2 ILE B 291 " pdb=" O GLY B 342 " model vdw 2.139 3.460 ... (remaining 123262 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 55 5.16 5 C 11306 2.51 5 N 2684 2.21 5 O 3135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.890 Check model and map are aligned: 0.230 Process input model: 42.750 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.011 0.164 17627 Z= 0.739 Angle : 1.407 22.899 23885 Z= 0.704 Chirality : 0.073 0.431 2688 Planarity : 0.008 0.067 2928 Dihedral : 15.779 158.619 6292 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.79 % Favored : 90.16 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.14), residues: 2043 helix: -2.90 (0.13), residues: 779 sheet: -2.07 (0.27), residues: 353 loop : -3.55 (0.15), residues: 911 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 378 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 18 residues processed: 408 average time/residue: 0.3154 time to fit residues: 188.3957 Evaluate side-chains 219 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 2.089 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2082 time to fit residues: 9.1013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 193 HIS ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN A 540 ASN A 674 ASN 1 343 ASN 1 425 ASN ** 1 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN B 307 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 17627 Z= 0.262 Angle : 0.742 14.121 23885 Z= 0.366 Chirality : 0.047 0.384 2688 Planarity : 0.005 0.056 2928 Dihedral : 15.789 157.688 2450 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer Outliers : 4.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.16), residues: 2043 helix: -1.10 (0.17), residues: 776 sheet: -1.85 (0.28), residues: 340 loop : -3.30 (0.16), residues: 927 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 230 time to evaluate : 1.855 Fit side-chains revert: symmetry clash outliers start: 75 outliers final: 36 residues processed: 293 average time/residue: 0.2707 time to fit residues: 121.6462 Evaluate side-chains 231 residues out of total 1835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 195 time to evaluate : 1.851 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.1606 time to fit residues: 13.0542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/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-dev-4893/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-dev-4893/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-dev-4893/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-dev-4893/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/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-dev-4893/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-dev-4893/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-dev-4893/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-dev-4893/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-dev-4893/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: 53.5506 > 50: distance: 45 - 51: 8.290 distance: 51 - 52: 7.189 distance: 52 - 53: 10.684 distance: 52 - 55: 4.640 distance: 53 - 54: 8.808 distance: 53 - 59: 5.766 distance: 55 - 56: 15.081 distance: 56 - 57: 19.790 distance: 56 - 58: 4.909 distance: 59 - 60: 17.447 distance: 60 - 61: 19.837 distance: 60 - 63: 18.396 distance: 61 - 62: 5.444 distance: 61 - 67: 22.849 distance: 63 - 64: 11.883 distance: 64 - 65: 14.685 distance: 64 - 66: 27.310 distance: 67 - 68: 13.758 distance: 68 - 69: 26.083 distance: 68 - 71: 12.561 distance: 69 - 70: 7.633 distance: 69 - 72: 20.004 distance: 72 - 73: 14.386 distance: 73 - 74: 6.239 distance: 73 - 76: 19.920 distance: 74 - 75: 11.110 distance: 74 - 77: 9.123 distance: 77 - 78: 15.547 distance: 78 - 79: 13.634 distance: 78 - 81: 20.491 distance: 79 - 80: 28.093 distance: 79 - 85: 12.514 distance: 80 - 111: 37.404 distance: 81 - 82: 4.545 distance: 82 - 83: 5.247 distance: 82 - 84: 4.644 distance: 85 - 86: 18.765 distance: 86 - 87: 20.174 distance: 86 - 89: 7.872 distance: 87 - 88: 13.617 distance: 87 - 93: 9.111 distance: 89 - 90: 9.768 distance: 90 - 91: 18.070 distance: 90 - 92: 18.762 distance: 94 - 95: 8.863 distance: 94 - 97: 7.078 distance: 95 - 96: 30.600 distance: 95 - 102: 13.215 distance: 97 - 98: 35.376 distance: 98 - 99: 14.814 distance: 99 - 100: 15.095 distance: 99 - 101: 16.822 distance: 102 - 103: 9.964 distance: 103 - 104: 11.484 distance: 103 - 106: 26.149 distance: 104 - 105: 17.635 distance: 104 - 111: 19.801 distance: 106 - 107: 9.028 distance: 107 - 108: 9.838 distance: 108 - 109: 3.183 distance: 108 - 110: 9.515 distance: 111 - 112: 9.960 distance: 112 - 113: 13.639 distance: 112 - 115: 20.403 distance: 113 - 114: 22.596 distance: 113 - 116: 11.008 distance: 116 - 117: 13.932 distance: 117 - 118: 13.592 distance: 117 - 120: 14.171 distance: 118 - 119: 14.077 distance: 118 - 122: 23.832 distance: 120 - 121: 19.688