Starting phenix.real_space_refine on Fri Jul 19 04:29:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc5_39923/07_2024/8zc5_39923.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc5_39923/07_2024/8zc5_39923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc5_39923/07_2024/8zc5_39923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc5_39923/07_2024/8zc5_39923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc5_39923/07_2024/8zc5_39923.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc5_39923/07_2024/8zc5_39923.cif" } resolution = 3.91 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= 0.026 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 32 5.16 5 C 4150 2.51 5 N 1102 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6515 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1562 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 12, 'TRANS': 183} Chain: "B" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1359 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 9, 'TRANS': 158} Chain breaks: 2 Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 810 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "D" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 810 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "E" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 973 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "F" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 973 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 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: 4.44, per 1000 atoms: 0.68 Number of scatterers: 6515 At special positions: 0 Unit cell: (111.232, 94.336, 116.864, 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 32 16.00 O 1231 8.00 N 1102 7.00 C 4150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 103 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 103 " - pdb=" SG CYS F 108 " 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 601 " - " ASN A 343 " " NAG B 601 " - " ASN B 343 " Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.1 seconds 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1518 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 18 sheets defined 8.9% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.707A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.554A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.579A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.733A pdb=" N ASN B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 339 through 343' Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.152A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.590A pdb=" N ASP E 31 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.881A pdb=" N GLN E 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.682A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 112 removed outlier: 3.572A pdb=" N TRP E 111 " --> pdb=" O CYS E 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.957A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 112 removed outlier: 3.541A pdb=" N TRP F 111 " --> pdb=" O CYS F 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.698A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.667A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 433 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE B 377 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA B 435 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.557A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.568A pdb=" N ALA C 10 " --> pdb=" O LYS C 106 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR C 108 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY C 12 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.568A pdb=" N ALA C 10 " --> pdb=" O LYS C 106 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR C 108 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY C 12 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AB1, first strand: chain 'D' and resid 9 through 10 Processing sheet with id=AB2, first strand: chain 'D' and resid 17 through 22 Processing sheet with id=AB3, first strand: chain 'D' and resid 45 through 49 removed outlier: 6.499A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP D 86 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP D 93 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY D 98 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.592A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL E 20 " --> pdb=" O MET E 81 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.600A pdb=" N THR E 116 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.619A pdb=" N TYR E 94 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA E 121 " --> pdb=" O TYR E 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.697A pdb=" N VAL F 5 " --> pdb=" O LYS F 23 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 58 through 59 removed outlier: 3.505A pdb=" N ASN F 59 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP F 50 " --> pdb=" O ASN F 59 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG F 98 " --> pdb=" O ASP F 115 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 58 through 59 removed outlier: 3.505A pdb=" N ASN F 59 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP F 50 " --> pdb=" O ASN F 59 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA F 121 " --> pdb=" O TYR F 94 " (cutoff:3.500A) 178 hydrogen bonds defined for protein. 444 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: 1.60 Time building geometry restraints manager: 2.36 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: 2045 1.34 - 1.46: 1458 1.46 - 1.58: 3152 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 6695 Sorted by residual: bond pdb=" CA CYS A 480 " pdb=" C CYS A 480 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.29e-02 6.01e+03 4.23e+00 bond pdb=" C PHE B 342 " pdb=" N ASN B 343 " ideal model delta sigma weight residual 1.331 1.304 0.026 1.48e-02 4.57e+03 3.21e+00 bond pdb=" C CYS A 480 " pdb=" N ASN A 481 " ideal model delta sigma weight residual 1.332 1.308 0.025 1.40e-02 5.10e+03 3.13e+00 bond pdb=" CA ASN B 343 " pdb=" C ASN B 343 " ideal model delta sigma weight residual 1.523 1.498 0.024 1.41e-02 5.03e+03 2.96e+00 bond pdb=" N CYS A 480 " pdb=" CA CYS A 480 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.23e-02 6.61e+03 2.58e+00 ... (remaining 6690 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.57: 216 106.57 - 113.42: 3393 113.42 - 120.27: 2372 120.27 - 127.12: 3032 127.12 - 133.97: 91 Bond angle restraints: 9104 Sorted by residual: angle pdb=" C CYS A 480 " pdb=" N ASN A 481 " pdb=" CA ASN A 481 " ideal model delta sigma weight residual 122.07 127.76 -5.69 1.43e+00 4.89e-01 1.58e+01 angle pdb=" C ILE E 76 " pdb=" N THR E 77 " pdb=" CA THR E 77 " ideal model delta sigma weight residual 121.54 129.08 -7.54 1.91e+00 2.74e-01 1.56e+01 angle pdb=" N THR D 31 " pdb=" CA THR D 31 " pdb=" C THR D 31 " ideal model delta sigma weight residual 113.18 108.06 5.12 1.33e+00 5.65e-01 1.48e+01 angle pdb=" CB MET F 112 " pdb=" CG MET F 112 " pdb=" SD MET F 112 " ideal model delta sigma weight residual 112.70 123.65 -10.95 3.00e+00 1.11e-01 1.33e+01 angle pdb=" C LYS D 51 " pdb=" N ASN D 52 " pdb=" CA ASN D 52 " ideal model delta sigma weight residual 121.54 128.34 -6.80 1.91e+00 2.74e-01 1.27e+01 ... (remaining 9099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 3497 15.97 - 31.93: 359 31.93 - 47.90: 68 47.90 - 63.87: 10 63.87 - 79.83: 11 Dihedral angle restraints: 3945 sinusoidal: 1554 harmonic: 2391 Sorted by residual: 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 93.00 13.17 79.83 1 1.00e+01 1.00e-02 7.91e+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 -86.00 -138.08 52.08 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -137.53 51.53 1 1.00e+01 1.00e-02 3.63e+01 ... (remaining 3942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 592 0.042 - 0.083: 262 0.083 - 0.124: 88 0.124 - 0.166: 18 0.166 - 0.207: 4 Chirality restraints: 964 Sorted by residual: chirality pdb=" CA ASN A 481 " pdb=" N ASN A 481 " pdb=" C ASN A 481 " pdb=" CB ASN A 481 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA THR E 77 " pdb=" N THR E 77 " pdb=" C THR E 77 " pdb=" CB THR E 77 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CB VAL A 367 " pdb=" CA VAL A 367 " pdb=" CG1 VAL A 367 " pdb=" CG2 VAL A 367 " both_signs ideal model delta sigma weight residual False -2.63 -2.80 0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 961 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 601 " -0.132 2.00e-02 2.50e+03 1.10e-01 1.51e+02 pdb=" C7 NAG B 601 " 0.036 2.00e-02 2.50e+03 pdb=" C8 NAG B 601 " -0.098 2.00e-02 2.50e+03 pdb=" N2 NAG B 601 " 0.178 2.00e-02 2.50e+03 pdb=" O7 NAG B 601 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.044 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" C7 NAG A 601 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.057 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 480 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.24e+00 pdb=" C CYS A 480 " -0.040 2.00e-02 2.50e+03 pdb=" O CYS A 480 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 481 " 0.014 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1484 2.79 - 3.31: 5404 3.31 - 3.84: 10277 3.84 - 4.37: 11329 4.37 - 4.90: 20499 Nonbonded interactions: 48993 Sorted by model distance: nonbonded pdb=" OE1 GLN D 6 " pdb=" OG1 THR D 105 " model vdw 2.258 2.440 nonbonded pdb=" OG SER A 443 " pdb=" O PHE A 497 " model vdw 2.267 2.440 nonbonded pdb=" O CYS A 480 " pdb=" OD1 ASN A 481 " model vdw 2.273 3.040 nonbonded pdb=" OG SER A 359 " pdb=" OD1 ASN A 394 " model vdw 2.280 2.440 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.295 2.440 ... (remaining 48988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 338 through 359 or resid 367 through 390 or resid 394 thro \ ugh 515 or resid 601)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.050 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.004 0.041 6695 Z= 0.250 Angle : 0.755 10.951 9104 Z= 0.405 Chirality : 0.051 0.207 964 Planarity : 0.006 0.110 1176 Dihedral : 13.545 79.536 2391 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -1.55 (0.28), residues: 814 helix: -4.45 (0.61), residues: 14 sheet: -0.13 (0.32), residues: 257 loop : -1.46 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 50 HIS 0.003 0.001 HIS E 35 PHE 0.037 0.002 PHE A 456 TYR 0.030 0.002 TYR A 495 ARG 0.015 0.001 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: B 467 ASP cc_start: 0.8247 (p0) cc_final: 0.7961 (p0) REVERT: D 6 GLN cc_start: 0.8499 (pt0) cc_final: 0.7664 (pt0) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1949 time to fit residues: 42.3141 Evaluate side-chains 136 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 0.0060 chunk 71 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 439 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6695 Z= 0.228 Angle : 0.573 9.834 9104 Z= 0.296 Chirality : 0.046 0.168 964 Planarity : 0.004 0.033 1176 Dihedral : 4.650 27.107 955 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.57 % Allowed : 11.54 % Favored : 87.89 % 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: -1.19 (0.29), residues: 814 helix: -3.66 (0.80), residues: 20 sheet: 0.02 (0.30), residues: 269 loop : -1.15 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 36 HIS 0.003 0.001 HIS E 35 PHE 0.028 0.002 PHE F 29 TYR 0.016 0.001 TYR A 495 ARG 0.007 0.000 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: B 467 ASP cc_start: 0.8204 (p0) cc_final: 0.7925 (p0) REVERT: C 47 LEU cc_start: 0.8046 (tp) cc_final: 0.7753 (tp) REVERT: D 6 GLN cc_start: 0.8343 (pt0) cc_final: 0.7732 (pt0) REVERT: F 39 GLN cc_start: 0.7805 (tp40) cc_final: 0.7402 (tp40) outliers start: 4 outliers final: 3 residues processed: 143 average time/residue: 0.2002 time to fit residues: 37.1647 Evaluate side-chains 137 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain F residue 70 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.6513 > 50: distance: 16 - 21: 4.378 distance: 22 - 23: 8.081 distance: 22 - 25: 3.969 distance: 23 - 24: 7.147 distance: 23 - 32: 5.406 distance: 26 - 27: 5.758 distance: 26 - 28: 5.795 distance: 27 - 29: 3.565 distance: 28 - 30: 7.513 distance: 29 - 31: 6.758 distance: 30 - 31: 5.614 distance: 32 - 33: 3.664 distance: 32 - 182: 6.413 distance: 33 - 36: 7.518 distance: 34 - 35: 8.055 distance: 34 - 43: 4.902 distance: 36 - 37: 8.713 distance: 37 - 39: 10.053 distance: 38 - 40: 5.936 distance: 39 - 41: 4.530 distance: 40 - 42: 7.815 distance: 41 - 42: 9.664 distance: 43 - 44: 13.753 distance: 44 - 45: 9.521 distance: 44 - 47: 12.633 distance: 45 - 46: 6.762 distance: 45 - 48: 5.174 distance: 48 - 49: 9.869 distance: 49 - 50: 7.015 distance: 49 - 52: 5.571 distance: 50 - 51: 19.096 distance: 52 - 53: 13.079 distance: 53 - 54: 9.404 distance: 53 - 55: 10.668 distance: 54 - 56: 10.505 distance: 55 - 57: 12.555 distance: 56 - 58: 8.995 distance: 57 - 58: 7.706 distance: 59 - 60: 4.798 distance: 60 - 61: 5.022 distance: 60 - 63: 4.435 distance: 61 - 62: 7.484 distance: 61 - 68: 10.497 distance: 63 - 64: 10.755 distance: 64 - 65: 12.800 distance: 65 - 66: 18.945 distance: 66 - 67: 21.936 distance: 68 - 69: 5.353 distance: 69 - 72: 4.921 distance: 70 - 71: 5.889 distance: 70 - 74: 7.822 distance: 72 - 73: 5.433 distance: 73 - 164: 7.077 distance: 75 - 78: 3.345 distance: 76 - 77: 6.275 distance: 76 - 86: 7.360 distance: 78 - 79: 4.804 distance: 79 - 80: 3.604 distance: 79 - 81: 4.443 distance: 80 - 82: 4.649 distance: 81 - 83: 3.460 distance: 82 - 84: 4.375 distance: 83 - 84: 4.842 distance: 84 - 85: 8.170 distance: 86 - 87: 9.494 distance: 87 - 88: 20.837 distance: 88 - 89: 4.395 distance: 88 - 90: 7.587 distance: 90 - 91: 8.221 distance: 91 - 92: 19.788 distance: 91 - 94: 21.995 distance: 92 - 93: 19.869 distance: 92 - 97: 7.979 distance: 94 - 95: 27.271 distance: 94 - 96: 15.575 distance: 97 - 98: 16.029 distance: 98 - 99: 19.601 distance: 98 - 101: 8.975 distance: 99 - 100: 14.633 distance: 99 - 103: 7.575 distance: 101 - 102: 37.377