Starting phenix.real_space_refine on Mon Mar 11 00:42:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdi_31544/03_2024/7fdi_31544.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdi_31544/03_2024/7fdi_31544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdi_31544/03_2024/7fdi_31544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdi_31544/03_2024/7fdi_31544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdi_31544/03_2024/7fdi_31544.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdi_31544/03_2024/7fdi_31544.pdb" } resolution = 3.12 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= 0.003 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 36 5.16 5 C 4097 2.51 5 N 1058 2.21 5 O 1212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 428": "OD1" <-> "OD2" Residue "E GLU 484": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6403 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4802 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 594, 4795 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Conformer: "B" Number of residues, atoms: 594, 4795 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 bond proxies already assigned to first conformer: 4922 Chain: "E" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1531 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 183} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" 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 Chain: "E" 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 Time building chain proxies: 6.28, per 1000 atoms: 0.98 Number of scatterers: 6403 At special positions: 0 Unit cell: (113.36, 88.4, 79.04, 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 36 16.00 O 1212 8.00 N 1058 7.00 C 4097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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 NAG-ASN " NAG A 701 " - " ASN A 546 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 322 " " NAG A 704 " - " ASN A 53 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.8 seconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 7 sheets defined 58.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.647A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 82 removed outlier: 3.908A pdb=" N MET A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.609A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.529A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.699A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.836A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.556A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 253 through 256 removed outlier: 4.198A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.552A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.567A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.540A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.881A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 466 removed outlier: 3.732A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.625A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.265A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.668A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.808A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.859A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 385 through 390 Processing helix chain 'E' and resid 406 through 410 Processing helix chain 'E' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.457A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.552A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.691A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474 324 hydrogen bonds defined for protein. 908 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: 1.89 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2055 1.35 - 1.47: 1740 1.47 - 1.59: 2735 1.59 - 1.71: 0 1.71 - 1.84: 56 Bond restraints: 6586 Sorted by residual: bond pdb=" CB TRP A 478 " pdb=" CG TRP A 478 " ideal model delta sigma weight residual 1.498 1.452 0.046 3.10e-02 1.04e+03 2.20e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG A 704 " pdb=" O5 NAG A 704 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" CG MET A 455 " pdb=" SD MET A 455 " ideal model delta sigma weight residual 1.803 1.773 0.030 2.50e-02 1.60e+03 1.48e+00 bond pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.38e+00 ... (remaining 6581 not shown) Histogram of bond angle deviations from ideal: 96.70 - 104.16: 101 104.16 - 111.62: 2925 111.62 - 119.08: 2329 119.08 - 126.54: 3471 126.54 - 134.00: 136 Bond angle restraints: 8962 Sorted by residual: angle pdb=" C LEU A 529 " pdb=" N CYS A 530 " pdb=" CA CYS A 530 " ideal model delta sigma weight residual 122.65 118.39 4.26 1.66e+00 3.63e-01 6.58e+00 angle pdb=" CB MET A 152 " pdb=" CG MET A 152 " pdb=" SD MET A 152 " ideal model delta sigma weight residual 112.70 120.23 -7.53 3.00e+00 1.11e-01 6.30e+00 angle pdb=" N LYS A 234 " pdb=" CA LYS A 234 " pdb=" C LYS A 234 " ideal model delta sigma weight residual 109.81 115.33 -5.52 2.21e+00 2.05e-01 6.25e+00 angle pdb=" CA LEU A 266 " pdb=" CB LEU A 266 " pdb=" CG LEU A 266 " ideal model delta sigma weight residual 116.30 124.78 -8.48 3.50e+00 8.16e-02 5.87e+00 angle pdb=" CA GLU A 435 " pdb=" CB GLU A 435 " pdb=" CG GLU A 435 " ideal model delta sigma weight residual 114.10 118.90 -4.80 2.00e+00 2.50e-01 5.77e+00 ... (remaining 8957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.93: 3647 21.93 - 43.86: 243 43.86 - 65.78: 21 65.78 - 87.71: 16 87.71 - 109.64: 9 Dihedral angle restraints: 3936 sinusoidal: 1622 harmonic: 2314 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual -86.00 -17.03 -68.97 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CA CYS A 530 " pdb=" C CYS A 530 " pdb=" N GLN A 531 " pdb=" CA GLN A 531 " ideal model delta harmonic sigma weight residual 180.00 149.60 30.40 0 5.00e+00 4.00e-02 3.70e+01 dihedral pdb=" CA CYS A 344 " pdb=" C CYS A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta harmonic sigma weight residual 180.00 154.31 25.69 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 3933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 753 0.054 - 0.108: 181 0.108 - 0.162: 18 0.162 - 0.216: 2 0.216 - 0.269: 1 Chirality restraints: 955 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA CYS A 530 " pdb=" N CYS A 530 " pdb=" C CYS A 530 " pdb=" CB CYS A 530 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CB ILE A 468 " pdb=" CA ILE A 468 " pdb=" CG1 ILE A 468 " pdb=" CG2 ILE A 468 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 952 not shown) Planarity restraints: 1162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 478 " 0.040 2.00e-02 2.50e+03 3.06e-02 2.34e+01 pdb=" CG TRP A 478 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP A 478 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 478 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 478 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 478 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 478 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 478 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 478 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 478 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 252 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO A 253 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 347 " -0.016 2.00e-02 2.50e+03 1.48e-02 3.84e+00 pdb=" CG PHE E 347 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE E 347 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE E 347 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE E 347 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 347 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE E 347 " -0.002 2.00e-02 2.50e+03 ... (remaining 1159 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 127 2.67 - 3.23: 6444 3.23 - 3.78: 10606 3.78 - 4.34: 14672 4.34 - 4.90: 23636 Nonbonded interactions: 55485 Sorted by model distance: nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.109 2.440 nonbonded pdb=" NH1 ARG A 460 " pdb=" O TYR A 510 " model vdw 2.133 2.520 nonbonded pdb=" O ASN E 439 " pdb=" OG SER E 443 " model vdw 2.181 2.440 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR E 500 " model vdw 2.182 2.440 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.208 2.520 ... (remaining 55480 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.120 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: 6.090 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 24.680 Find NCS groups from input model: 0.180 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: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 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 0.046 6586 Z= 0.318 Angle : 0.643 8.479 8962 Z= 0.344 Chirality : 0.046 0.269 955 Planarity : 0.005 0.070 1157 Dihedral : 15.545 109.641 2431 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.15 % Allowed : 0.00 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.19 (0.30), residues: 785 helix: 0.41 (0.25), residues: 397 sheet: 0.28 (0.79), residues: 48 loop : -0.74 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.003 TRP A 478 HIS 0.003 0.001 HIS E 493 PHE 0.034 0.002 PHE E 347 TYR 0.021 0.002 TYR E 495 ARG 0.002 0.000 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.6717 (t80) cc_final: 0.6351 (t80) REVERT: A 156 LEU cc_start: 0.8303 (mp) cc_final: 0.7829 (tt) REVERT: A 480 MET cc_start: 0.5235 (ptm) cc_final: 0.5000 (ptt) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1709 time to fit residues: 20.3926 Evaluate side-chains 68 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 chunk 70 optimal weight: 0.0270 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN A 239 HIS ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6586 Z= 0.155 Angle : 0.570 11.039 8962 Z= 0.288 Chirality : 0.042 0.167 955 Planarity : 0.005 0.053 1157 Dihedral : 6.525 59.266 960 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.44 % Allowed : 5.47 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.63 (0.31), residues: 785 helix: 1.02 (0.26), residues: 396 sheet: 0.47 (0.80), residues: 49 loop : -0.20 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 478 HIS 0.003 0.001 HIS A 378 PHE 0.017 0.001 PHE A 369 TYR 0.020 0.001 TYR A 385 ARG 0.004 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.6599 (t80) cc_final: 0.6162 (t80) outliers start: 3 outliers final: 2 residues processed: 82 average time/residue: 0.1583 time to fit residues: 18.4025 Evaluate side-chains 69 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain E residue 367 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 48 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 0.0070 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6586 Z= 0.163 Angle : 0.556 11.984 8962 Z= 0.277 Chirality : 0.041 0.169 955 Planarity : 0.004 0.047 1157 Dihedral : 5.373 59.120 960 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.74 % Allowed : 7.98 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.31), residues: 785 helix: 1.15 (0.26), residues: 397 sheet: 0.63 (0.78), residues: 50 loop : -0.11 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 478 HIS 0.003 0.001 HIS A 378 PHE 0.017 0.001 PHE A 369 TYR 0.018 0.001 TYR A 385 ARG 0.001 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.6768 (t80) cc_final: 0.6295 (t80) REVERT: A 376 MET cc_start: 0.8122 (tpp) cc_final: 0.7874 (mmm) REVERT: A 408 MET cc_start: 0.7909 (mmt) cc_final: 0.7594 (mmt) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.1534 time to fit residues: 17.0115 Evaluate side-chains 70 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS E 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6586 Z= 0.178 Angle : 0.556 12.101 8962 Z= 0.276 Chirality : 0.041 0.169 955 Planarity : 0.004 0.047 1157 Dihedral : 5.151 56.472 960 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.74 % Allowed : 9.31 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.89 (0.31), residues: 785 helix: 1.21 (0.26), residues: 397 sheet: 0.55 (0.78), residues: 50 loop : -0.02 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 378 PHE 0.017 0.001 PHE A 369 TYR 0.019 0.001 TYR A 385 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.6850 (t80) cc_final: 0.6315 (t80) REVERT: A 376 MET cc_start: 0.8117 (tpp) cc_final: 0.7902 (mmm) REVERT: A 408 MET cc_start: 0.7933 (mmt) cc_final: 0.7600 (mmt) outliers start: 5 outliers final: 2 residues processed: 77 average time/residue: 0.1554 time to fit residues: 17.2917 Evaluate side-chains 72 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 64 optimal weight: 0.0970 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6586 Z= 0.181 Angle : 0.555 12.307 8962 Z= 0.275 Chirality : 0.041 0.165 955 Planarity : 0.004 0.044 1157 Dihedral : 5.018 54.038 960 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.03 % Allowed : 9.90 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.96 (0.31), residues: 785 helix: 1.21 (0.26), residues: 399 sheet: 0.53 (0.78), residues: 50 loop : 0.08 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 478 HIS 0.002 0.001 HIS E 493 PHE 0.012 0.001 PHE A 369 TYR 0.019 0.001 TYR A 385 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.6888 (t80) cc_final: 0.6333 (t80) REVERT: A 408 MET cc_start: 0.7953 (mmt) cc_final: 0.7625 (mmt) outliers start: 7 outliers final: 4 residues processed: 78 average time/residue: 0.1546 time to fit residues: 17.2296 Evaluate side-chains 75 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 66.1879 > 50: distance: 77 - 81: 30.077 distance: 81 - 82: 16.713 distance: 81 - 87: 10.752 distance: 82 - 83: 43.039 distance: 82 - 85: 23.849 distance: 83 - 84: 34.249 distance: 83 - 88: 35.090 distance: 85 - 86: 27.971 distance: 86 - 87: 31.564 distance: 88 - 89: 35.734 distance: 89 - 92: 20.882 distance: 90 - 91: 34.751 distance: 90 - 96: 8.343 distance: 92 - 93: 23.317 distance: 92 - 94: 36.738 distance: 93 - 95: 12.655 distance: 96 - 97: 36.879 distance: 97 - 98: 41.565 distance: 98 - 99: 37.670 distance: 101 - 102: 15.275 distance: 101 - 104: 45.503 distance: 102 - 103: 40.137 distance: 102 - 106: 15.383 distance: 104 - 105: 19.382 distance: 106 - 107: 25.756 distance: 107 - 108: 22.008 distance: 107 - 110: 43.775 distance: 108 - 109: 31.636 distance: 108 - 114: 19.165 distance: 110 - 111: 30.788 distance: 111 - 112: 29.585 distance: 111 - 113: 38.441 distance: 114 - 115: 16.265 distance: 114 - 120: 23.854 distance: 115 - 116: 24.692 distance: 115 - 118: 28.465 distance: 116 - 117: 12.237 distance: 116 - 121: 19.812 distance: 118 - 119: 31.581 distance: 119 - 120: 13.805 distance: 121 - 122: 55.231 distance: 122 - 123: 13.417 distance: 122 - 125: 19.548 distance: 123 - 126: 40.944 distance: 126 - 127: 46.335 distance: 127 - 128: 13.337 distance: 127 - 130: 39.086 distance: 128 - 129: 7.484 distance: 128 - 136: 36.122 distance: 130 - 131: 12.414 distance: 131 - 133: 40.378 distance: 133 - 135: 11.763 distance: 134 - 135: 28.673 distance: 136 - 137: 46.237 distance: 137 - 140: 30.087 distance: 138 - 139: 39.284 distance: 138 - 144: 15.427 distance: 140 - 141: 30.397 distance: 141 - 142: 35.161 distance: 141 - 143: 34.119 distance: 144 - 145: 24.998 distance: 145 - 148: 24.397 distance: 146 - 147: 26.970 distance: 146 - 152: 26.789 distance: 148 - 149: 42.324 distance: 149 - 150: 27.453 distance: 149 - 151: 30.575