Starting phenix.real_space_refine on Fri Jan 19 13:00:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyp_36729/01_2024/8jyp_36729.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyp_36729/01_2024/8jyp_36729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyp_36729/01_2024/8jyp_36729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyp_36729/01_2024/8jyp_36729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyp_36729/01_2024/8jyp_36729.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jyp_36729/01_2024/8jyp_36729.pdb" } resolution = 3.38 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4890 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4235 2.51 5 N 1081 2.21 5 O 1274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6627 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1581 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 14, 'TRANS': 184} Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} 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: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.82, per 1000 atoms: 0.58 Number of scatterers: 6627 At special positions: 0 Unit cell: (99.495, 80.4, 124.62, 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 37 16.00 O 1274 8.00 N 1081 7.00 C 4235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG B 1 " - " ASN D 546 " " NAG C 1 " - " ASN D 90 " " NAG D 701 " - " ASN D 322 " " NAG D 702 " - " ASN D 432 " " NAG D 703 " - " ASN D 53 " " NAG E 1 " - " ASN D 103 " Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.3 seconds 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 6 sheets defined 53.2% alpha, 5.7% 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 367 through 371 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.566A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.560A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.851A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 92 through 104 removed outlier: 3.666A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.652A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.837A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 233 removed outlier: 3.933A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.534A pdb=" N TYR D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.831A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.617A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.733A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 4.236A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.574A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.328A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 482 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.218A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.677A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 599 Proline residue: D 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.944A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.671A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.726A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.698A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.796A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 350 284 hydrogen bonds defined for protein. 810 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: 1.59 Time building geometry restraints manager: 2.83 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: 2091 1.34 - 1.46: 1769 1.46 - 1.58: 2895 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6813 Sorted by residual: bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" CA LEU D 351 " pdb=" C LEU D 351 " ideal model delta sigma weight residual 1.523 1.500 0.022 1.41e-02 5.03e+03 2.47e+00 bond pdb=" C1 MAN E 4 " pdb=" C2 MAN E 4 " ideal model delta sigma weight residual 1.526 1.556 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C1 NAG D 703 " pdb=" O5 NAG D 703 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 6808 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.52: 226 106.52 - 113.38: 3612 113.38 - 120.25: 2504 120.25 - 127.11: 2816 127.11 - 133.98: 104 Bond angle restraints: 9262 Sorted by residual: angle pdb=" C HIS D 34 " pdb=" N GLU D 35 " pdb=" CA GLU D 35 " ideal model delta sigma weight residual 120.31 114.89 5.42 1.52e+00 4.33e-01 1.27e+01 angle pdb=" C GLU D 182 " pdb=" N TYR D 183 " pdb=" CA TYR D 183 " ideal model delta sigma weight residual 120.44 124.57 -4.13 1.30e+00 5.92e-01 1.01e+01 angle pdb=" C PRO D 135 " pdb=" N ASP D 136 " pdb=" CA ASP D 136 " ideal model delta sigma weight residual 121.54 127.00 -5.46 1.91e+00 2.74e-01 8.17e+00 angle pdb=" C ALA A 344 " pdb=" N THR A 345 " pdb=" CA THR A 345 " ideal model delta sigma weight residual 121.54 126.77 -5.23 1.91e+00 2.74e-01 7.51e+00 angle pdb=" C ASN D 432 " pdb=" CA ASN D 432 " pdb=" CB ASN D 432 " ideal model delta sigma weight residual 110.84 106.66 4.18 1.66e+00 3.63e-01 6.35e+00 ... (remaining 9257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 3892 21.77 - 43.54: 234 43.54 - 65.31: 16 65.31 - 87.08: 18 87.08 - 108.85: 8 Dihedral angle restraints: 4168 sinusoidal: 1832 harmonic: 2336 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 36.06 56.94 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -141.77 55.77 1 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 46.67 46.33 1 1.00e+01 1.00e-02 2.97e+01 ... (remaining 4165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 998 0.125 - 0.250: 7 0.250 - 0.375: 5 0.375 - 0.500: 0 0.500 - 0.625: 1 Chirality restraints: 1011 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.76e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN D 546 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 1008 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 163 " 0.016 2.00e-02 2.50e+03 1.16e-02 3.34e+00 pdb=" CG TRP D 163 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP D 163 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP D 163 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 163 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 163 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 163 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 163 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 163 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 163 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 103 " 0.016 2.00e-02 2.50e+03 1.57e-02 3.08e+00 pdb=" CG ASN D 103 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN D 103 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN D 103 " -0.021 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A 373 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.021 5.00e-02 4.00e+02 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1896 2.81 - 3.33: 6469 3.33 - 3.86: 10683 3.86 - 4.38: 11942 4.38 - 4.90: 20760 Nonbonded interactions: 51750 Sorted by model distance: nonbonded pdb=" O ASP D 499 " pdb=" OG SER D 502 " model vdw 2.291 2.440 nonbonded pdb=" OG1 THR A 500 " pdb=" OH TYR D 41 " model vdw 2.294 2.440 nonbonded pdb=" OG SER D 611 " pdb=" O ALA D 614 " model vdw 2.296 2.440 nonbonded pdb=" O GLY D 268 " pdb=" ND2 ASN D 277 " model vdw 2.315 2.520 nonbonded pdb=" OD1 ASP D 494 " pdb=" OG1 THR D 496 " model vdw 2.322 2.440 ... (remaining 51745 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 12.000 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 20.520 Find NCS groups from input model: 0.150 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6813 Z= 0.213 Angle : 0.622 7.805 9262 Z= 0.312 Chirality : 0.051 0.625 1011 Planarity : 0.003 0.038 1179 Dihedral : 14.736 108.849 2647 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.31), residues: 791 helix: 1.06 (0.27), residues: 394 sheet: 1.22 (0.77), residues: 44 loop : -0.77 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 163 HIS 0.003 0.001 HIS D 34 PHE 0.016 0.001 PHE D 32 TYR 0.011 0.001 TYR A 453 ARG 0.001 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 493 GLN cc_start: 0.8999 (tp40) cc_final: 0.8665 (tp-100) REVERT: D 270 MET cc_start: 0.8223 (tpt) cc_final: 0.7974 (tpp) REVERT: D 474 MET cc_start: 0.8654 (mmp) cc_final: 0.8451 (mmp) REVERT: D 531 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8653 (tm-30) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1421 time to fit residues: 10.5805 Evaluate side-chains 38 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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: 4.9990 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6813 Z= 0.204 Angle : 0.546 7.342 9262 Z= 0.269 Chirality : 0.045 0.291 1011 Planarity : 0.003 0.036 1179 Dihedral : 10.294 76.014 1110 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.86 % Allowed : 5.01 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.31), residues: 791 helix: 1.71 (0.27), residues: 392 sheet: 0.93 (0.78), residues: 44 loop : -0.87 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 163 HIS 0.003 0.001 HIS D 378 PHE 0.007 0.001 PHE D 369 TYR 0.012 0.001 TYR A 453 ARG 0.001 0.000 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 493 GLN cc_start: 0.9010 (tp40) cc_final: 0.8717 (tp-100) REVERT: D 108 LEU cc_start: 0.9090 (mm) cc_final: 0.8829 (tp) REVERT: D 270 MET cc_start: 0.8256 (tpt) cc_final: 0.8055 (tpp) REVERT: D 531 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8690 (tm-30) outliers start: 6 outliers final: 2 residues processed: 39 average time/residue: 0.1422 time to fit residues: 8.7319 Evaluate side-chains 39 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6813 Z= 0.195 Angle : 0.527 7.875 9262 Z= 0.256 Chirality : 0.044 0.290 1011 Planarity : 0.003 0.036 1179 Dihedral : 8.106 64.316 1110 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.00 % Allowed : 7.45 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.31), residues: 791 helix: 1.77 (0.27), residues: 396 sheet: 0.64 (0.79), residues: 44 loop : -0.75 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 163 HIS 0.002 0.001 HIS D 373 PHE 0.009 0.001 PHE D 315 TYR 0.013 0.001 TYR A 453 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 493 GLN cc_start: 0.9004 (tp40) cc_final: 0.8709 (tp-100) REVERT: D 108 LEU cc_start: 0.9128 (mm) cc_final: 0.8856 (tp) REVERT: D 531 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8742 (tm-30) outliers start: 7 outliers final: 3 residues processed: 42 average time/residue: 0.1534 time to fit residues: 10.1154 Evaluate side-chains 37 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 427 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6813 Z= 0.166 Angle : 0.524 8.627 9262 Z= 0.250 Chirality : 0.044 0.291 1011 Planarity : 0.003 0.036 1179 Dihedral : 7.284 57.777 1110 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.15 % Allowed : 8.17 % Favored : 90.69 % 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: 1.00 (0.31), residues: 791 helix: 1.85 (0.27), residues: 396 sheet: 0.54 (0.79), residues: 44 loop : -0.71 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 163 HIS 0.002 0.001 HIS D 373 PHE 0.009 0.001 PHE D 315 TYR 0.010 0.001 TYR A 453 ARG 0.001 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 493 GLN cc_start: 0.9000 (tp40) cc_final: 0.8684 (tp-100) REVERT: D 75 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8721 (mt-10) REVERT: D 108 LEU cc_start: 0.9112 (mm) cc_final: 0.8841 (tp) REVERT: D 531 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8743 (tm-30) outliers start: 8 outliers final: 3 residues processed: 39 average time/residue: 0.1496 time to fit residues: 9.1437 Evaluate side-chains 39 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 579 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6813 Z= 0.326 Angle : 0.616 11.667 9262 Z= 0.298 Chirality : 0.046 0.305 1011 Planarity : 0.003 0.032 1179 Dihedral : 6.927 52.433 1110 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.72 % Allowed : 9.31 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.31), residues: 791 helix: 1.85 (0.27), residues: 392 sheet: 0.35 (0.76), residues: 48 loop : -0.79 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 271 HIS 0.005 0.001 HIS D 195 PHE 0.012 0.001 PHE D 315 TYR 0.017 0.001 TYR A 453 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 34 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.9014 (tp40) cc_final: 0.8689 (tp-100) REVERT: D 75 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8709 (mt-10) REVERT: D 108 LEU cc_start: 0.9136 (mm) cc_final: 0.8928 (tp) REVERT: D 133 CYS cc_start: 0.6415 (OUTLIER) cc_final: 0.5036 (p) REVERT: D 303 ASP cc_start: 0.6664 (OUTLIER) cc_final: 0.6321 (p0) REVERT: D 531 GLN cc_start: 0.9202 (tm-30) cc_final: 0.8826 (tm-30) outliers start: 12 outliers final: 4 residues processed: 43 average time/residue: 0.1733 time to fit residues: 11.8543 Evaluate side-chains 40 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 468 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 42 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6813 Z= 0.171 Angle : 0.556 10.043 9262 Z= 0.264 Chirality : 0.044 0.306 1011 Planarity : 0.003 0.034 1179 Dihedral : 6.391 53.630 1110 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.15 % Allowed : 9.46 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.31), residues: 791 helix: 1.88 (0.27), residues: 394 sheet: 0.54 (0.80), residues: 43 loop : -0.80 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 477 HIS 0.003 0.001 HIS D 195 PHE 0.011 0.001 PHE D 315 TYR 0.011 0.001 TYR A 453 ARG 0.001 0.000 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.9020 (tp40) cc_final: 0.8700 (tp-100) REVERT: D 133 CYS cc_start: 0.6290 (OUTLIER) cc_final: 0.5026 (p) REVERT: D 303 ASP cc_start: 0.6481 (OUTLIER) cc_final: 0.6201 (p0) REVERT: D 531 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8808 (tm-30) outliers start: 15 outliers final: 6 residues processed: 48 average time/residue: 0.1532 time to fit residues: 11.3965 Evaluate side-chains 42 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 468 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6813 Z= 0.291 Angle : 0.604 11.047 9262 Z= 0.288 Chirality : 0.045 0.313 1011 Planarity : 0.003 0.037 1179 Dihedral : 6.267 52.885 1110 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.86 % Allowed : 11.03 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.31), residues: 791 helix: 1.86 (0.27), residues: 391 sheet: 0.34 (0.79), residues: 43 loop : -0.85 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 610 HIS 0.004 0.001 HIS D 195 PHE 0.010 0.001 PHE D 315 TYR 0.013 0.001 TYR A 453 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 34 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.9020 (tp40) cc_final: 0.8708 (tp-100) REVERT: D 133 CYS cc_start: 0.6123 (OUTLIER) cc_final: 0.4837 (p) REVERT: D 152 MET cc_start: 0.9378 (mtm) cc_final: 0.8766 (ptp) REVERT: D 303 ASP cc_start: 0.6575 (OUTLIER) cc_final: 0.6268 (p0) REVERT: D 462 MET cc_start: 0.9337 (mmp) cc_final: 0.9112 (mtm) REVERT: D 531 GLN cc_start: 0.9234 (tm-30) cc_final: 0.8841 (tm-30) outliers start: 13 outliers final: 6 residues processed: 45 average time/residue: 0.1440 time to fit residues: 10.0953 Evaluate side-chains 41 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 468 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.0050 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 0.0970 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6813 Z= 0.144 Angle : 0.554 10.432 9262 Z= 0.259 Chirality : 0.044 0.313 1011 Planarity : 0.003 0.045 1179 Dihedral : 5.788 53.925 1110 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.29 % Allowed : 11.89 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.31), residues: 791 helix: 1.89 (0.27), residues: 393 sheet: 0.58 (0.83), residues: 42 loop : -0.77 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.002 0.000 HIS D 373 PHE 0.009 0.001 PHE D 315 TYR 0.008 0.001 TYR D 50 ARG 0.002 0.000 ARG D 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.9022 (tp40) cc_final: 0.8694 (tp-100) REVERT: D 152 MET cc_start: 0.9374 (mtm) cc_final: 0.8848 (ptp) REVERT: D 303 ASP cc_start: 0.6366 (OUTLIER) cc_final: 0.6074 (p0) REVERT: D 462 MET cc_start: 0.9302 (mmp) cc_final: 0.9091 (mtm) REVERT: D 531 GLN cc_start: 0.9218 (tm-30) cc_final: 0.8811 (tm-30) outliers start: 9 outliers final: 6 residues processed: 42 average time/residue: 0.1493 time to fit residues: 9.7752 Evaluate side-chains 41 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 468 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6813 Z= 0.215 Angle : 0.565 10.276 9262 Z= 0.267 Chirality : 0.044 0.307 1011 Planarity : 0.003 0.045 1179 Dihedral : 5.689 52.991 1110 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.72 % Allowed : 11.46 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.31), residues: 791 helix: 1.90 (0.27), residues: 394 sheet: 0.38 (0.80), residues: 43 loop : -0.77 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 271 HIS 0.003 0.001 HIS D 195 PHE 0.009 0.001 PHE D 315 TYR 0.011 0.001 TYR A 453 ARG 0.001 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 34 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.9023 (tp40) cc_final: 0.8676 (tp-100) REVERT: D 133 CYS cc_start: 0.5997 (OUTLIER) cc_final: 0.4704 (p) REVERT: D 152 MET cc_start: 0.9360 (mtm) cc_final: 0.8917 (ptp) REVERT: D 303 ASP cc_start: 0.6485 (OUTLIER) cc_final: 0.6220 (p0) REVERT: D 462 MET cc_start: 0.9347 (mmp) cc_final: 0.9085 (mtm) REVERT: D 531 GLN cc_start: 0.9240 (tm-30) cc_final: 0.8834 (tm-30) outliers start: 12 outliers final: 7 residues processed: 44 average time/residue: 0.1424 time to fit residues: 9.8402 Evaluate side-chains 43 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.0670 chunk 9 optimal weight: 4.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6813 Z= 0.184 Angle : 0.557 9.822 9262 Z= 0.262 Chirality : 0.043 0.316 1011 Planarity : 0.003 0.046 1179 Dihedral : 5.584 53.194 1110 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.58 % Allowed : 11.75 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.31), residues: 791 helix: 1.90 (0.27), residues: 394 sheet: 0.39 (0.81), residues: 43 loop : -0.78 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS D 373 PHE 0.008 0.001 PHE D 315 TYR 0.010 0.001 TYR A 453 ARG 0.001 0.000 ARG D 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.9023 (tp40) cc_final: 0.8664 (tp-100) REVERT: D 133 CYS cc_start: 0.5987 (OUTLIER) cc_final: 0.4669 (p) REVERT: D 152 MET cc_start: 0.9361 (mtm) cc_final: 0.8981 (ptp) REVERT: D 303 ASP cc_start: 0.6436 (OUTLIER) cc_final: 0.6183 (p0) REVERT: D 455 MET cc_start: 0.9031 (tpp) cc_final: 0.8810 (tpt) REVERT: D 462 MET cc_start: 0.9348 (mmp) cc_final: 0.9067 (mtm) REVERT: D 531 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8806 (tm-30) outliers start: 11 outliers final: 7 residues processed: 44 average time/residue: 0.1402 time to fit residues: 9.5630 Evaluate side-chains 44 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 68.4871 > 50: distance: 31 - 200: 31.499 distance: 34 - 197: 36.994 distance: 64 - 212: 27.220 distance: 67 - 209: 15.138 distance: 132 - 137: 11.412 distance: 137 - 138: 18.890 distance: 138 - 139: 32.319 distance: 138 - 141: 13.004 distance: 139 - 140: 24.068 distance: 139 - 144: 31.428 distance: 141 - 142: 25.800 distance: 141 - 143: 22.087 distance: 144 - 145: 24.100 distance: 145 - 146: 18.121 distance: 145 - 148: 13.825 distance: 146 - 147: 14.838 distance: 146 - 156: 44.485 distance: 148 - 149: 18.247 distance: 149 - 150: 18.433 distance: 149 - 151: 26.335 distance: 150 - 152: 19.460 distance: 151 - 153: 9.459 distance: 152 - 154: 28.183 distance: 153 - 154: 21.636 distance: 154 - 155: 39.199 distance: 156 - 157: 45.987 distance: 157 - 158: 22.927 distance: 158 - 159: 19.758 distance: 158 - 160: 17.339 distance: 160 - 161: 33.139 distance: 161 - 162: 55.539 distance: 161 - 164: 12.575 distance: 162 - 163: 5.035 distance: 162 - 167: 35.282 distance: 164 - 165: 43.782 distance: 164 - 166: 18.975 distance: 167 - 168: 40.445 distance: 168 - 169: 10.459 distance: 169 - 170: 55.773 distance: 169 - 171: 34.752 distance: 171 - 172: 3.728 distance: 172 - 175: 39.873 distance: 173 - 174: 40.839 distance: 173 - 181: 30.682 distance: 175 - 176: 8.845 distance: 176 - 177: 27.461 distance: 176 - 178: 15.463 distance: 177 - 179: 7.811 distance: 178 - 180: 15.217 distance: 179 - 180: 7.652 distance: 181 - 182: 31.893 distance: 182 - 183: 8.807 distance: 182 - 185: 41.786 distance: 183 - 184: 42.512 distance: 183 - 190: 35.137 distance: 185 - 186: 15.813 distance: 186 - 187: 28.543 distance: 187 - 188: 27.632 distance: 187 - 189: 44.985 distance: 190 - 191: 31.660 distance: 190 - 196: 33.726 distance: 191 - 192: 32.150 distance: 191 - 194: 17.005 distance: 192 - 193: 24.687 distance: 192 - 197: 28.410 distance: 194 - 195: 30.214 distance: 195 - 196: 19.644 distance: 197 - 198: 15.732 distance: 198 - 199: 12.728 distance: 198 - 201: 13.743 distance: 199 - 200: 22.092 distance: 199 - 209: 16.993 distance: 201 - 202: 30.727 distance: 202 - 203: 37.634 distance: 202 - 204: 37.823 distance: 203 - 205: 16.783 distance: 204 - 206: 20.688 distance: 205 - 207: 27.061 distance: 206 - 207: 23.758 distance: 209 - 210: 8.417 distance: 210 - 211: 25.637 distance: 210 - 213: 24.756 distance: 211 - 212: 13.282 distance: 211 - 220: 31.627 distance: 213 - 214: 15.713 distance: 214 - 215: 7.248 distance: 215 - 216: 11.914 distance: 216 - 217: 10.250 distance: 217 - 218: 7.384 distance: 217 - 219: 5.249