Starting phenix.real_space_refine on Sat Aug 3 13:48:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt6_33440/08_2024/7xt6_33440.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt6_33440/08_2024/7xt6_33440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt6_33440/08_2024/7xt6_33440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt6_33440/08_2024/7xt6_33440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt6_33440/08_2024/7xt6_33440.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt6_33440/08_2024/7xt6_33440.cif" } resolution = 3.63 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= 0.068 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 5067 2.51 5 N 1342 2.21 5 O 1591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 538": "OE1" <-> "OE2" Residue "B GLU 572": "OE1" <-> "OE2" Residue "D GLU 521": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8040 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1072 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 125} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2781 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 336} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1120 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 135} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2785 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 338} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: "C" 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: "D" 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 Time building chain proxies: 5.65, per 1000 atoms: 0.70 Number of scatterers: 8040 At special positions: 0 Unit cell: (71.5, 105.6, 191.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1591 8.00 N 1342 7.00 C 5067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS D 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 380 " - pdb=" SG CYS B 439 " distance=2.04 Simple disulfide: pdb=" SG CYS B 487 " - pdb=" SG CYS B 549 " distance=2.04 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 122 " distance=2.04 Simple disulfide: pdb=" SG CYS D 270 " - pdb=" SG CYS D 333 " distance=2.03 Simple disulfide: pdb=" SG CYS D 380 " - pdb=" SG CYS D 439 " distance=2.03 Simple disulfide: pdb=" SG CYS D 487 " - pdb=" SG CYS D 549 " distance=2.04 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " BETA1-2 " MAN F 4 " - " NAG F 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A 201 " - " ASN A 73 " " NAG A 202 " - " ASN A 57 " " NAG A 203 " - " ASN A 63 " " NAG A 204 " - " ASN A 97 " " NAG A 205 " - " ASN A 88 " " NAG A 206 " - " ASN A 112 " " NAG B 701 " - " ASN B 345 " " NAG B 702 " - " ASN B 408 " " NAG C 201 " - " ASN C 101 " " NAG C 202 " - " ASN C 73 " " NAG D 701 " - " ASN D 345 " " NAG D 702 " - " ASN D 408 " " NAG F 1 " - " ASN B 415 " " NAG G 1 " - " ASN D 415 " Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.5 seconds 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 24 sheets defined 19.1% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 137 through 156 removed outlier: 3.795A pdb=" N ASN A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 169 removed outlier: 3.526A pdb=" N ARG A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TRP A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 427 through 434 removed outlier: 3.515A pdb=" N TRP B 431 " --> pdb=" O CYS B 427 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 434 " --> pdb=" O ASP B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.542A pdb=" N ASN B 542 " --> pdb=" O GLU B 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 538 through 542' Processing helix chain 'B' and resid 581 through 607 removed outlier: 3.631A pdb=" N ALA B 587 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 594 " --> pdb=" O PHE B 590 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE B 599 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 181 removed outlier: 3.535A pdb=" N LEU C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE C 164 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN C 165 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Proline residue: C 176 - end of helix Processing helix chain 'D' and resid 322 through 326 Processing helix chain 'D' and resid 366 through 374 removed outlier: 3.569A pdb=" N ILE D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR D 373 " --> pdb=" O SER D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 433 removed outlier: 3.700A pdb=" N ASN D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 480 removed outlier: 3.766A pdb=" N LEU D 479 " --> pdb=" O GLU D 475 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG D 480 " --> pdb=" O GLN D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.681A pdb=" N ASN D 542 " --> pdb=" O GLU D 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 542' Processing helix chain 'D' and resid 576 through 608 removed outlier: 3.662A pdb=" N VAL D 592 " --> pdb=" O SER D 588 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D 596 " --> pdb=" O VAL D 592 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER D 597 " --> pdb=" O LEU D 593 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 598 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.807A pdb=" N LEU A 42 " --> pdb=" O ARG A 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 51 removed outlier: 3.812A pdb=" N ILE A 93 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 83 removed outlier: 6.387A pdb=" N PHE A 80 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG A 68 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 82 " --> pdb=" O TRP A 66 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A 103 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 248 through 249 removed outlier: 3.503A pdb=" N LYS B 248 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR B 273 " --> pdb=" O LYS B 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 265 through 270 removed outlier: 3.852A pdb=" N SER B 316 " --> pdb=" O CYS B 270 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 289 through 290 Processing sheet with id=AA7, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AA8, first strand: chain 'B' and resid 361 through 363 removed outlier: 3.531A pdb=" N THR B 379 " --> pdb=" O ILE B 363 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N PHE B 418 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 394 through 396 Processing sheet with id=AB1, first strand: chain 'B' and resid 466 through 470 removed outlier: 3.618A pdb=" N THR B 490 " --> pdb=" O ASP B 466 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS B 487 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B 532 " --> pdb=" O CYS B 487 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 498 through 500 removed outlier: 3.631A pdb=" N THR B 561 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 502 through 503 removed outlier: 3.503A pdb=" N GLN B 503 " --> pdb=" O GLN B 506 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 519 through 520 removed outlier: 3.648A pdb=" N MET B 519 " --> pdb=" O PHE B 529 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 47 through 49 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.693A pdb=" N ILE C 53 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N MET C 143 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG C 55 " --> pdb=" O MET C 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.722A pdb=" N TYR C 133 " --> pdb=" O GLN C 124 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 248 through 252 removed outlier: 3.810A pdb=" N THR D 273 " --> pdb=" O LYS D 248 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 320 " --> pdb=" O SER D 266 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 280 through 286 removed outlier: 3.503A pdb=" N CYS D 333 " --> pdb=" O GLN D 344 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 301 through 302 Processing sheet with id=AC2, first strand: chain 'D' and resid 360 through 363 removed outlier: 3.748A pdb=" N PHE D 361 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR D 379 " --> pdb=" O ILE D 363 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR D 379 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA D 424 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU D 381 " --> pdb=" O GLY D 422 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY D 422 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N THR D 383 " --> pdb=" O ALA D 420 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA D 420 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU D 385 " --> pdb=" O PHE D 418 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 392 through 396 Processing sheet with id=AC4, first strand: chain 'D' and resid 466 through 470 removed outlier: 3.737A pdb=" N ASP D 466 " --> pdb=" O THR D 490 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D 490 " --> pdb=" O ASP D 466 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TYR D 528 " --> pdb=" O GLY D 491 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 466 through 470 removed outlier: 3.737A pdb=" N ASP D 466 " --> pdb=" O THR D 490 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D 490 " --> pdb=" O ASP D 466 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TYR D 528 " --> pdb=" O GLY D 491 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET D 519 " --> pdb=" O PHE D 529 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 506 through 507 removed outlier: 3.672A pdb=" N GLN D 503 " --> pdb=" O GLN D 506 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR D 561 " --> pdb=" O VAL D 551 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 672 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2578 1.34 - 1.46: 1934 1.46 - 1.58: 3656 1.58 - 1.71: 1 1.71 - 1.83: 56 Bond restraints: 8225 Sorted by residual: bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.592 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sigma weight residual 1.417 1.462 -0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" C2 MAN F 4 " pdb=" C3 MAN F 4 " ideal model delta sigma weight residual 1.525 1.569 -0.044 2.00e-02 2.50e+03 4.88e+00 bond pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sigma weight residual 1.417 1.459 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.561 -0.042 2.00e-02 2.50e+03 4.32e+00 ... (remaining 8220 not shown) Histogram of bond angle deviations from ideal: 94.17 - 102.15: 24 102.15 - 110.13: 1752 110.13 - 118.11: 4726 118.11 - 126.09: 4546 126.09 - 134.07: 163 Bond angle restraints: 11211 Sorted by residual: angle pdb=" CA PRO A 129 " pdb=" N PRO A 129 " pdb=" CD PRO A 129 " ideal model delta sigma weight residual 112.00 105.87 6.13 1.40e+00 5.10e-01 1.91e+01 angle pdb=" N PRO A 128 " pdb=" CA PRO A 128 " pdb=" C PRO A 128 " ideal model delta sigma weight residual 110.70 115.41 -4.71 1.22e+00 6.72e-01 1.49e+01 angle pdb=" N GLY C 137 " pdb=" CA GLY C 137 " pdb=" C GLY C 137 " ideal model delta sigma weight residual 112.22 118.85 -6.63 1.74e+00 3.30e-01 1.45e+01 angle pdb=" C VAL B 565 " pdb=" N ASP B 566 " pdb=" CA ASP B 566 " ideal model delta sigma weight residual 121.90 117.15 4.75 1.26e+00 6.30e-01 1.42e+01 angle pdb=" CB PRO A 132 " pdb=" CG PRO A 132 " pdb=" CD PRO A 132 " ideal model delta sigma weight residual 106.10 94.17 11.93 3.20e+00 9.77e-02 1.39e+01 ... (remaining 11206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.86: 4676 21.86 - 43.71: 441 43.71 - 65.57: 72 65.57 - 87.43: 20 87.43 - 109.28: 14 Dihedral angle restraints: 5223 sinusoidal: 2318 harmonic: 2905 Sorted by residual: dihedral pdb=" CB CYS B 270 " pdb=" SG CYS B 270 " pdb=" SG CYS B 333 " pdb=" CB CYS B 333 " ideal model delta sinusoidal sigma weight residual 93.00 178.25 -85.25 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 175.03 -82.03 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CA ARG A 131 " pdb=" C ARG A 131 " pdb=" N PRO A 132 " pdb=" CA PRO A 132 " ideal model delta harmonic sigma weight residual 180.00 -144.79 -35.21 0 5.00e+00 4.00e-02 4.96e+01 ... (remaining 5220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 1336 0.144 - 0.289: 9 0.289 - 0.433: 0 0.433 - 0.577: 0 0.577 - 0.721: 1 Chirality restraints: 1346 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN D 415 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" C1 NAG A 205 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG A 205 " pdb=" O5 NAG A 205 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1 NAG A 201 " pdb=" ND2 ASN A 73 " pdb=" C2 NAG A 201 " pdb=" O5 NAG A 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1343 not shown) Planarity restraints: 1432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 253 " 0.051 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO B 254 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 254 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 254 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 131 " 0.043 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO A 132 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 132 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 132 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 470 " -0.041 5.00e-02 4.00e+02 6.26e-02 6.28e+00 pdb=" N PRO D 471 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 471 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 471 " -0.034 5.00e-02 4.00e+02 ... (remaining 1429 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 492 2.73 - 3.27: 7594 3.27 - 3.81: 12030 3.81 - 4.36: 13091 4.36 - 4.90: 23584 Nonbonded interactions: 56791 Sorted by model distance: nonbonded pdb=" N GLN D 506 " pdb=" OE1 GLN D 506 " model vdw 2.182 3.120 nonbonded pdb=" NH2 ARG C 95 " pdb=" OD2 ASP C 116 " model vdw 2.216 3.120 nonbonded pdb=" OG1 THR D 356 " pdb=" OD2 ASP D 445 " model vdw 2.229 3.040 nonbonded pdb=" N GLU A 138 " pdb=" OE1 GLU A 138 " model vdw 2.249 3.120 nonbonded pdb=" OG1 THR D 373 " pdb=" OG SER D 375 " model vdw 2.275 3.040 ... (remaining 56786 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 245 through 302 or (resid 303 through 304 and (name N or n \ ame CA or name C or name O or name CB )) or resid 305 through 352 or (resid 353 \ through 355 and (name N or name CA or name C or name O or name CB )) or resid 35 \ 6 through 357 or (resid 358 through 359 and (name N or name CA or name C or name \ O or name CB )) or resid 360 or (resid 361 through 362 and (name N or name CA o \ r name C or name O or name CB )) or resid 363 through 395 or (resid 396 and (nam \ e N or name CA or name C or name O or name CB )) or resid 397 through 403 or (re \ sid 404 and (name N or name CA or name C or name O or name CB )) or resid 405 th \ rough 412 or (resid 413 and (name N or name CA or name C or name O or name CB )) \ or resid 414 through 435 or (resid 436 and (name N or name CA or name C or name \ O or name CB )) or resid 437 through 443 or (resid 444 and (name N or name CA o \ r name C or name O or name CB )) or resid 445 through 607 or resid 701 through 7 \ 02)) selection = (chain 'D' and (resid 245 through 247 or (resid 248 and (name N or name CA or na \ me C or name O or name CB )) or resid 249 through 255 or (resid 256 and (name N \ or name CA or name C or name O or name CB )) or resid 257 through 283 or (resid \ 284 and (name N or name CA or name C or name O or name CB )) or resid 285 throug \ h 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 331 or (resid 332 and (name N or name CA or name C or name O o \ r name CB )) or resid 333 through 347 or (resid 348 through 349 and (name N or n \ ame CA or name C or name O or name CB )) or resid 350 through 387 or (resid 388 \ and (name N or name CA or name C or name O or name CB )) or resid 389 through 41 \ 6 or (resid 417 and (name N or name CA or name C or name O or name CB )) or resi \ d 418 through 607 or resid 701 through 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.590 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 33.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 : 0.005 0.066 8225 Z= 0.310 Angle : 0.814 13.377 11211 Z= 0.408 Chirality : 0.052 0.721 1346 Planarity : 0.005 0.079 1418 Dihedral : 17.764 109.282 3307 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 0.81 % Allowed : 24.25 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.27), residues: 995 helix: 0.97 (0.43), residues: 156 sheet: -1.19 (0.29), residues: 332 loop : -2.26 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 395 HIS 0.004 0.001 HIS A 71 PHE 0.017 0.002 PHE B 418 TYR 0.013 0.001 TYR D 600 ARG 0.003 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.775 Fit side-chains REVERT: B 454 ILE cc_start: 0.8027 (tp) cc_final: 0.7801 (pt) REVERT: B 578 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7736 (pt0) REVERT: D 506 GLN cc_start: 0.7981 (pm20) cc_final: 0.6797 (mm-40) outliers start: 7 outliers final: 2 residues processed: 81 average time/residue: 0.2218 time to fit residues: 24.4545 Evaluate side-chains 74 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain D residue 431 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 0.0980 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 281 GLN ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8225 Z= 0.227 Angle : 0.716 12.444 11211 Z= 0.360 Chirality : 0.049 0.374 1346 Planarity : 0.005 0.063 1418 Dihedral : 11.732 98.820 1505 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.60 % Allowed : 24.13 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.27), residues: 995 helix: 0.77 (0.42), residues: 172 sheet: -0.88 (0.30), residues: 325 loop : -2.44 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 395 HIS 0.005 0.001 HIS A 71 PHE 0.013 0.002 PHE B 418 TYR 0.024 0.001 TYR D 547 ARG 0.003 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 72 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: B 454 ILE cc_start: 0.8192 (tp) cc_final: 0.7981 (pt) REVERT: B 578 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7731 (pt0) REVERT: C 67 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6759 (ppp) REVERT: D 469 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8568 (tt) REVERT: D 506 GLN cc_start: 0.7615 (pm20) cc_final: 0.6898 (mm-40) outliers start: 31 outliers final: 15 residues processed: 93 average time/residue: 0.1908 time to fit residues: 25.0728 Evaluate side-chains 81 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 605 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.0870 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 0.0370 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8225 Z= 0.203 Angle : 0.673 9.577 11211 Z= 0.337 Chirality : 0.047 0.345 1346 Planarity : 0.005 0.064 1418 Dihedral : 10.174 92.381 1503 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.76 % Allowed : 24.01 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.94 % Cis-general : 0.11 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.27), residues: 995 helix: 0.94 (0.42), residues: 169 sheet: -0.71 (0.30), residues: 322 loop : -2.44 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 395 HIS 0.004 0.001 HIS A 71 PHE 0.014 0.001 PHE B 418 TYR 0.031 0.001 TYR D 547 ARG 0.005 0.000 ARG B 474 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 69 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 94 GLN cc_start: 0.6755 (tp40) cc_final: 0.5528 (mt0) REVERT: B 454 ILE cc_start: 0.8212 (tp) cc_final: 0.8004 (pt) REVERT: B 578 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7688 (pt0) REVERT: C 67 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6721 (ppp) REVERT: C 68 ASN cc_start: 0.6121 (p0) cc_final: 0.5434 (p0) outliers start: 41 outliers final: 23 residues processed: 101 average time/residue: 0.1916 time to fit residues: 27.0701 Evaluate side-chains 88 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 63 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 380 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 605 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 60.0338 > 50: distance: 30 - 37: 23.795 distance: 31 - 52: 31.817 distance: 37 - 38: 10.244 distance: 38 - 39: 8.886 distance: 38 - 41: 7.193 distance: 39 - 48: 15.373 distance: 41 - 42: 16.113 distance: 42 - 43: 22.061 distance: 43 - 44: 6.611 distance: 44 - 45: 12.221 distance: 45 - 46: 6.501 distance: 45 - 47: 13.640 distance: 48 - 49: 5.367 distance: 50 - 51: 28.661 distance: 50 - 52: 6.817 distance: 52 - 53: 18.164 distance: 53 - 54: 37.626 distance: 53 - 56: 18.151 distance: 54 - 55: 7.554 distance: 54 - 61: 11.459 distance: 56 - 57: 27.136 distance: 57 - 58: 18.751 distance: 58 - 59: 20.997 distance: 58 - 60: 17.056 distance: 61 - 62: 11.875 distance: 61 - 67: 42.629 distance: 62 - 63: 21.374 distance: 62 - 65: 13.132 distance: 63 - 64: 27.899 distance: 63 - 68: 4.700 distance: 65 - 66: 36.010 distance: 66 - 67: 6.748 distance: 68 - 69: 9.178 distance: 69 - 70: 28.562 distance: 69 - 72: 16.905 distance: 70 - 71: 36.024 distance: 70 - 76: 21.458 distance: 72 - 73: 10.464 distance: 73 - 74: 32.832 distance: 73 - 75: 11.368 distance: 76 - 77: 19.059 distance: 77 - 78: 26.887 distance: 77 - 80: 8.619 distance: 78 - 79: 16.267 distance: 78 - 82: 16.777 distance: 80 - 81: 23.858 distance: 82 - 83: 22.415 distance: 82 - 88: 46.808 distance: 83 - 84: 6.947 distance: 83 - 86: 26.130 distance: 84 - 85: 39.535 distance: 84 - 89: 6.740 distance: 86 - 87: 19.340 distance: 87 - 88: 15.870 distance: 89 - 90: 20.878 distance: 90 - 91: 7.022 distance: 90 - 93: 10.070 distance: 91 - 92: 9.763 distance: 91 - 98: 3.850 distance: 93 - 94: 15.097 distance: 94 - 95: 25.004 distance: 95 - 96: 16.197 distance: 95 - 97: 29.132 distance: 98 - 99: 31.044 distance: 99 - 100: 5.064 distance: 99 - 102: 10.634 distance: 100 - 101: 5.250 distance: 102 - 103: 22.929 distance: 104 - 105: 20.609 distance: 105 - 106: 15.859 distance: 107 - 108: 8.331 distance: 108 - 109: 12.222 distance: 108 - 111: 34.536 distance: 109 - 110: 10.661 distance: 109 - 119: 15.133 distance: 111 - 112: 19.441 distance: 112 - 113: 18.005 distance: 113 - 115: 9.316 distance: 114 - 116: 13.336 distance: 115 - 117: 3.886 distance: 116 - 117: 9.388 distance: 117 - 118: 4.171