Starting phenix.real_space_refine on Tue Aug 6 14:40:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuz_35734/08_2024/8iuz_35734.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuz_35734/08_2024/8iuz_35734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuz_35734/08_2024/8iuz_35734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuz_35734/08_2024/8iuz_35734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuz_35734/08_2024/8iuz_35734.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuz_35734/08_2024/8iuz_35734.cif" } resolution = 3.0 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= 0.014 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 87 5.16 5 C 10413 2.51 5 N 2892 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 23": "NH1" <-> "NH2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 486": "NH1" <-> "NH2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 447": "NH1" <-> "NH2" Residue "D ARG 486": "NH1" <-> "NH2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 23": "NH1" <-> "NH2" Residue "G TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 447": "NH1" <-> "NH2" Residue "G ARG 486": "NH1" <-> "NH2" Residue "H PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16692 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3782 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 927 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "A" 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 Chain: "D" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3782 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 469} Chain breaks: 1 Chain: "E" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 927 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "F" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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 Chain: "G" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3782 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 469} Chain breaks: 1 Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 927 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "I" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "G" 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: 10.67, per 1000 atoms: 0.64 Number of scatterers: 16692 At special positions: 0 Unit cell: (154.944, 150.64, 150.64, 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 87 16.00 O 3300 8.00 N 2892 7.00 C 10413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 463 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 269 " distance=2.02 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 130 " distance=2.02 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS A 297 " distance=2.02 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 5 " - pdb=" SG CYS D 463 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 269 " distance=2.02 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 67 " distance=2.03 Simple disulfide: pdb=" SG CYS D 88 " - pdb=" SG CYS D 130 " distance=2.02 Simple disulfide: pdb=" SG CYS D 273 " - pdb=" SG CYS D 297 " distance=2.02 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 474 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 5 " - pdb=" SG CYS G 463 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 269 " distance=2.02 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 67 " distance=2.03 Simple disulfide: pdb=" SG CYS G 88 " - pdb=" SG CYS G 130 " distance=2.02 Simple disulfide: pdb=" SG CYS G 273 " - pdb=" SG CYS G 297 " distance=2.02 Simple disulfide: pdb=" SG CYS G 470 " - pdb=" SG CYS G 474 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " 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 501 " - " ASN A 408 " " NAG A 502 " - " ASN A 29 " " NAG A 503 " - " ASN A 480 " " NAG D 501 " - " ASN D 408 " " NAG D 502 " - " ASN D 29 " " NAG D 503 " - " ASN D 480 " " NAG G 501 " - " ASN G 408 " " NAG G 502 " - " ASN G 29 " " NAG G 503 " - " ASN G 480 " Time building additional restraints: 6.13 Conformation dependent library (CDL) restraints added in 2.9 seconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3870 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 57 sheets defined 16.6% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.854A pdb=" N THR A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.992A pdb=" N LEU A 71 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.521A pdb=" N LEU A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.583A pdb=" N LYS A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 382 removed outlier: 3.901A pdb=" N ASP A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 452 removed outlier: 3.628A pdb=" N VAL A 406 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.530A pdb=" N ILE A 478 " --> pdb=" O CYS A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.699A pdb=" N ASP B 90 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 91 " --> pdb=" O THR B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 91' Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.175A pdb=" N ILE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.854A pdb=" N THR D 60 " --> pdb=" O LEU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 removed outlier: 3.992A pdb=" N LEU D 71 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 103 removed outlier: 3.520A pdb=" N LEU D 99 " --> pdb=" O ASN D 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.584A pdb=" N LYS D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 382 removed outlier: 3.901A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN D 373 " --> pdb=" O SER D 369 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 374 " --> pdb=" O ALA D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 452 removed outlier: 3.628A pdb=" N VAL D 406 " --> pdb=" O GLN D 402 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D 417 " --> pdb=" O SER D 413 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU D 423 " --> pdb=" O SER D 419 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS D 432 " --> pdb=" O MET D 428 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 434 " --> pdb=" O ASN D 430 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP D 435 " --> pdb=" O GLN D 431 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D 437 " --> pdb=" O THR D 433 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS D 449 " --> pdb=" O TYR D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 478 removed outlier: 3.530A pdb=" N ILE D 478 " --> pdb=" O CYS D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 488 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.699A pdb=" N ASP E 90 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR E 91 " --> pdb=" O THR E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.175A pdb=" N ILE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 removed outlier: 3.854A pdb=" N THR G 60 " --> pdb=" O LEU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 removed outlier: 3.992A pdb=" N LEU G 71 " --> pdb=" O ASP G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 103 removed outlier: 3.520A pdb=" N LEU G 99 " --> pdb=" O ASN G 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 185 removed outlier: 3.583A pdb=" N LYS G 185 " --> pdb=" O ALA G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 382 removed outlier: 3.901A pdb=" N ASP G 372 " --> pdb=" O GLN G 368 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN G 373 " --> pdb=" O SER G 369 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE G 374 " --> pdb=" O ALA G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 452 removed outlier: 3.629A pdb=" N VAL G 406 " --> pdb=" O GLN G 402 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL G 417 " --> pdb=" O SER G 413 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU G 423 " --> pdb=" O SER G 419 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS G 432 " --> pdb=" O MET G 428 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE G 434 " --> pdb=" O ASN G 430 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP G 435 " --> pdb=" O GLN G 431 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA G 437 " --> pdb=" O THR G 433 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET G 441 " --> pdb=" O ALA G 437 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU G 444 " --> pdb=" O GLU G 440 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS G 449 " --> pdb=" O TYR G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 473 through 478 removed outlier: 3.530A pdb=" N ILE G 478 " --> pdb=" O CYS G 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 488 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.700A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR H 91 " --> pdb=" O THR H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.175A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.910A pdb=" N GLY A 359 " --> pdb=" O HIS A 352 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN A 354 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 3 through 7 removed outlier: 4.702A pdb=" N TYR A 348 " --> pdb=" O ASP A 363 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=4, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=5, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=6, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.860A pdb=" N ILE A 42 " --> pdb=" O ASP A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=6 Processing sheet with id=7, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.540A pdb=" N ILE A 259 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 80 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 91 through 92 removed outlier: 6.695A pdb=" N LYS A 92 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N TRP A 226 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 170 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 110 through 113 removed outlier: 3.604A pdb=" N GLU A 112 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 121 through 122 removed outlier: 3.578A pdb=" N LEU A 145 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 156 through 161 Processing sheet with id=12, first strand: chain 'A' and resid 278 through 280 removed outlier: 4.122A pdb=" N CYS A 273 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 294 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'A' and resid 456 through 458 removed outlier: 3.592A pdb=" N GLU A 457 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU A 465 " --> pdb=" O GLU A 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=13 Processing sheet with id=14, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.507A pdb=" N GLN B 3 " --> pdb=" O THR B 25 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER B 59 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 45 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU B 47 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP B 37 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR B 51 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP B 35 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER B 59 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 45 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU B 47 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP B 37 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR B 51 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP B 35 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.748A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 102 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.748A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 102 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 90 " --> pdb=" O THR C 97 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'C' and resid 22 through 23 removed outlier: 3.656A pdb=" N PHE C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.910A pdb=" N GLY D 359 " --> pdb=" O HIS D 352 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN D 354 " --> pdb=" O GLY D 357 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'D' and resid 3 through 7 removed outlier: 4.702A pdb=" N TYR D 348 " --> pdb=" O ASP D 363 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'D' and resid 15 through 17 Processing sheet with id=23, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=24, first strand: chain 'D' and resid 34 through 35 Processing sheet with id=25, first strand: chain 'D' and resid 42 through 43 removed outlier: 5.861A pdb=" N ILE D 42 " --> pdb=" O ASP D 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=25 Processing sheet with id=26, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.540A pdb=" N ILE D 259 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU D 80 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'D' and resid 91 through 92 removed outlier: 6.694A pdb=" N LYS D 92 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N TRP D 226 " --> pdb=" O LYS D 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE D 170 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'D' and resid 110 through 113 removed outlier: 3.605A pdb=" N GLU D 112 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'D' and resid 121 through 122 removed outlier: 3.579A pdb=" N LEU D 145 " --> pdb=" O ARG D 122 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'D' and resid 156 through 161 Processing sheet with id=31, first strand: chain 'D' and resid 278 through 280 removed outlier: 4.123A pdb=" N CYS D 273 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL D 294 " --> pdb=" O TYR D 274 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'D' and resid 456 through 458 removed outlier: 3.592A pdb=" N GLU D 457 " --> pdb=" O GLU D 465 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU D 465 " --> pdb=" O GLU D 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=32 Processing sheet with id=33, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.507A pdb=" N GLN E 3 " --> pdb=" O THR E 25 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER E 59 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS E 45 " --> pdb=" O PHE E 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU E 47 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR E 51 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP E 35 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER E 59 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS E 45 " --> pdb=" O PHE E 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU E 47 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR E 51 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP E 35 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.749A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR F 102 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.749A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR F 102 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN F 90 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'F' and resid 22 through 23 removed outlier: 3.656A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.910A pdb=" N GLY G 359 " --> pdb=" O HIS G 352 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN G 354 " --> pdb=" O GLY G 357 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'G' and resid 3 through 7 removed outlier: 4.702A pdb=" N TYR G 348 " --> pdb=" O ASP G 363 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'G' and resid 15 through 17 Processing sheet with id=42, first strand: chain 'G' and resid 30 through 31 Processing sheet with id=43, first strand: chain 'G' and resid 34 through 35 Processing sheet with id=44, first strand: chain 'G' and resid 42 through 43 removed outlier: 5.860A pdb=" N ILE G 42 " --> pdb=" O ASP G 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=44 Processing sheet with id=45, first strand: chain 'G' and resid 49 through 51 removed outlier: 3.540A pdb=" N ILE G 259 " --> pdb=" O ILE G 78 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU G 80 " --> pdb=" O ILE G 259 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'G' and resid 91 through 92 removed outlier: 6.695A pdb=" N LYS G 92 " --> pdb=" O PHE G 224 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N TRP G 226 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE G 170 " --> pdb=" O LEU G 227 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'G' and resid 110 through 113 removed outlier: 3.604A pdb=" N GLU G 112 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'G' and resid 121 through 122 removed outlier: 3.577A pdb=" N LEU G 145 " --> pdb=" O ARG G 122 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'G' and resid 156 through 161 Processing sheet with id=50, first strand: chain 'G' and resid 278 through 280 removed outlier: 4.122A pdb=" N CYS G 273 " --> pdb=" O ILE G 280 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL G 294 " --> pdb=" O TYR G 274 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'G' and resid 456 through 458 removed outlier: 3.592A pdb=" N GLU G 457 " --> pdb=" O GLU G 465 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU G 465 " --> pdb=" O GLU G 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=51 Processing sheet with id=52, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.507A pdb=" N GLN H 3 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER H 59 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS H 45 " --> pdb=" O PHE H 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU H 47 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER H 59 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS H 45 " --> pdb=" O PHE H 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU H 47 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.748A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR I 102 " --> pdb=" O TYR I 86 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.748A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR I 102 " --> pdb=" O TYR I 86 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN I 90 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'I' and resid 22 through 23 removed outlier: 3.656A pdb=" N PHE I 71 " --> pdb=" O CYS I 23 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1305 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: 5.70 Time building geometry restraints manager: 6.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3819 1.33 - 1.45: 4174 1.45 - 1.58: 8918 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 17037 Sorted by residual: bond pdb=" CB VAL A 235 " pdb=" CG2 VAL A 235 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.05e+00 bond pdb=" CB VAL G 235 " pdb=" CG2 VAL G 235 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.04e+00 bond pdb=" CB VAL D 235 " pdb=" CG2 VAL D 235 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.04e+00 bond pdb=" C1 NAG D 503 " pdb=" O5 NAG D 503 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.77e+00 ... (remaining 17032 not shown) Histogram of bond angle deviations from ideal: 96.92 - 104.37: 231 104.37 - 111.82: 7342 111.82 - 119.27: 6525 119.27 - 126.73: 8718 126.73 - 134.18: 263 Bond angle restraints: 23079 Sorted by residual: angle pdb=" C ILE I 29 " pdb=" N ASN I 30 " pdb=" CA ASN I 30 " ideal model delta sigma weight residual 121.54 133.47 -11.93 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C ILE F 29 " pdb=" N ASN F 30 " pdb=" CA ASN F 30 " ideal model delta sigma weight residual 121.54 133.46 -11.92 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C ILE C 29 " pdb=" N ASN C 30 " pdb=" CA ASN C 30 " ideal model delta sigma weight residual 121.54 133.44 -11.90 1.91e+00 2.74e-01 3.88e+01 angle pdb=" N ILE F 29 " pdb=" CA ILE F 29 " pdb=" C ILE F 29 " ideal model delta sigma weight residual 113.71 108.88 4.83 9.50e-01 1.11e+00 2.59e+01 angle pdb=" N ILE I 29 " pdb=" CA ILE I 29 " pdb=" C ILE I 29 " ideal model delta sigma weight residual 113.71 108.89 4.82 9.50e-01 1.11e+00 2.58e+01 ... (remaining 23074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 9270 16.02 - 32.05: 804 32.05 - 48.07: 156 48.07 - 64.09: 33 64.09 - 80.12: 15 Dihedral angle restraints: 10278 sinusoidal: 4212 harmonic: 6066 Sorted by residual: dihedral pdb=" CA ASN G 397 " pdb=" C ASN G 397 " pdb=" N GLU G 398 " pdb=" CA GLU G 398 " ideal model delta harmonic sigma weight residual 180.00 137.42 42.58 0 5.00e+00 4.00e-02 7.25e+01 dihedral pdb=" CA ASN A 397 " pdb=" C ASN A 397 " pdb=" N GLU A 398 " pdb=" CA GLU A 398 " ideal model delta harmonic sigma weight residual 180.00 137.47 42.53 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" CA ASN D 397 " pdb=" C ASN D 397 " pdb=" N GLU D 398 " pdb=" CA GLU D 398 " ideal model delta harmonic sigma weight residual 180.00 137.53 42.47 0 5.00e+00 4.00e-02 7.21e+01 ... (remaining 10275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2329 0.119 - 0.238: 194 0.238 - 0.358: 21 0.358 - 0.477: 0 0.477 - 0.596: 3 Chirality restraints: 2547 Sorted by residual: chirality pdb=" CB ILE A 4 " pdb=" CA ILE A 4 " pdb=" CG1 ILE A 4 " pdb=" CG2 ILE A 4 " both_signs ideal model delta sigma weight residual False 2.64 2.05 0.60 2.00e-01 2.50e+01 8.88e+00 chirality pdb=" CB ILE D 4 " pdb=" CA ILE D 4 " pdb=" CG1 ILE D 4 " pdb=" CG2 ILE D 4 " both_signs ideal model delta sigma weight residual False 2.64 2.05 0.60 2.00e-01 2.50e+01 8.87e+00 chirality pdb=" CB ILE G 4 " pdb=" CA ILE G 4 " pdb=" CG1 ILE G 4 " pdb=" CG2 ILE G 4 " both_signs ideal model delta sigma weight residual False 2.64 2.05 0.60 2.00e-01 2.50e+01 8.86e+00 ... (remaining 2544 not shown) Planarity restraints: 3003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 143 " -0.025 2.00e-02 2.50e+03 1.97e-02 9.68e+00 pdb=" CG TRP G 143 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP G 143 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP G 143 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 143 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 143 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 143 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 143 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 143 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP G 143 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 143 " 0.025 2.00e-02 2.50e+03 1.97e-02 9.67e+00 pdb=" CG TRP A 143 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 143 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 143 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 143 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 143 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 143 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 143 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 143 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 143 " 0.026 2.00e-02 2.50e+03 1.97e-02 9.67e+00 pdb=" CG TRP D 143 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP D 143 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 143 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 143 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 143 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 143 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 143 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 143 " 0.004 2.00e-02 2.50e+03 ... (remaining 3000 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 6 1.99 - 2.71: 1262 2.71 - 3.44: 21731 3.44 - 4.17: 38588 4.17 - 4.90: 69014 Nonbonded interactions: 130601 Sorted by model distance: nonbonded pdb=" OE1 GLU D 457 " pdb=" NH2 ARG G 453 " model vdw 1.257 3.120 nonbonded pdb=" NH2 ARG A 453 " pdb=" OE1 GLU G 457 " model vdw 1.257 3.120 nonbonded pdb=" OE1 GLU A 457 " pdb=" NH2 ARG D 453 " model vdw 1.257 3.120 nonbonded pdb=" NE2 GLN A 202 " pdb=" CZ ARG G 212 " model vdw 1.888 3.350 nonbonded pdb=" CZ ARG A 212 " pdb=" NE2 GLN D 202 " model vdw 1.888 3.350 ... (remaining 130596 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } 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: 5.620 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: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 49.120 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4861 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 : 0.010 0.099 17037 Z= 0.661 Angle : 1.337 14.419 23079 Z= 0.744 Chirality : 0.074 0.596 2547 Planarity : 0.008 0.074 2994 Dihedral : 12.686 80.118 6336 Min Nonbonded Distance : 1.257 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 0.99 % Allowed : 4.28 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.15), residues: 2103 helix: -3.45 (0.19), residues: 291 sheet: -2.80 (0.18), residues: 663 loop : -2.93 (0.15), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.005 TRP G 143 HIS 0.013 0.004 HIS D 175 PHE 0.036 0.006 PHE G 335 TYR 0.052 0.004 TYR E 102 ARG 0.020 0.002 ARG D 450 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 355 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASN cc_start: 0.8468 (t0) cc_final: 0.8186 (t0) REVERT: B 67 ARG cc_start: 0.6017 (ptp-110) cc_final: 0.5638 (ptt180) REVERT: C 5 ASN cc_start: 0.6169 (m-40) cc_final: 0.5912 (m-40) REVERT: C 50 LYS cc_start: 0.6404 (mttt) cc_final: 0.6195 (mttt) REVERT: D 310 THR cc_start: 0.1801 (OUTLIER) cc_final: 0.1381 (m) REVERT: D 401 LYS cc_start: 0.4301 (mppt) cc_final: 0.4066 (mtmm) REVERT: D 412 ASP cc_start: 0.4848 (t70) cc_final: 0.4625 (t0) REVERT: G 87 VAL cc_start: 0.6014 (m) cc_final: 0.5654 (p) REVERT: G 408 ASN cc_start: 0.4323 (m-40) cc_final: 0.3933 (t160) REVERT: I 67 SER cc_start: 0.2164 (p) cc_final: 0.1766 (m) outliers start: 18 outliers final: 1 residues processed: 368 average time/residue: 1.0373 time to fit residues: 433.5998 Evaluate side-chains 204 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 310 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.8980 chunk 156 optimal weight: 0.4980 chunk 87 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 162 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 124 ASN A 155 GLN A 225 HIS A 421 ASN A 430 ASN A 455 ASN A 468 HIS A 481 ASN A 495 ASN B 61 ASN B 104 HIS C 42 ASN C 53 ASN D 155 GLN D 175 HIS D 225 HIS D 353 GLN D 388 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 455 ASN D 481 ASN D 495 ASN E 104 HIS F 42 ASN F 53 ASN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN G 288 ASN G 373 GLN G 430 ASN G 455 ASN G 481 ASN ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS I 42 ASN I 53 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17037 Z= 0.278 Angle : 0.802 9.573 23079 Z= 0.421 Chirality : 0.050 0.226 2547 Planarity : 0.007 0.055 2994 Dihedral : 7.643 71.763 2489 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.89 % Allowed : 11.57 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.16), residues: 2103 helix: -1.34 (0.27), residues: 318 sheet: -2.01 (0.21), residues: 546 loop : -2.66 (0.15), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 143 HIS 0.007 0.002 HIS G 275 PHE 0.030 0.003 PHE G 243 TYR 0.024 0.002 TYR D 488 ARG 0.013 0.001 ARG D 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 270 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.7329 (p0) cc_final: 0.6714 (t0) REVERT: A 170 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.6678 (mp) REVERT: D 141 MET cc_start: 0.5762 (mmt) cc_final: 0.4789 (mmm) REVERT: D 174 ILE cc_start: 0.6788 (OUTLIER) cc_final: 0.5988 (mm) REVERT: D 412 ASP cc_start: 0.6509 (t70) cc_final: 0.6250 (t0) REVERT: D 493 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.5348 (mtt) REVERT: E 1 MET cc_start: 0.0982 (tmt) cc_final: 0.0585 (tpp) REVERT: E 49 MET cc_start: 0.6424 (mmm) cc_final: 0.5803 (mmm) REVERT: E 68 MET cc_start: 0.6397 (tpp) cc_final: 0.6152 (mtm) REVERT: F 4 MET cc_start: 0.7009 (tpp) cc_final: 0.6655 (tpp) REVERT: G 62 THR cc_start: 0.6826 (OUTLIER) cc_final: 0.6573 (p) REVERT: G 201 TYR cc_start: 0.5303 (OUTLIER) cc_final: 0.4437 (t80) REVERT: G 252 LEU cc_start: 0.8009 (pp) cc_final: 0.7688 (mp) REVERT: G 386 ASN cc_start: 0.5716 (p0) cc_final: 0.5410 (p0) REVERT: G 475 MET cc_start: 0.4564 (tpp) cc_final: 0.4222 (mmt) REVERT: I 4 MET cc_start: 0.3434 (tpp) cc_final: 0.3056 (tpt) outliers start: 71 outliers final: 19 residues processed: 314 average time/residue: 0.8989 time to fit residues: 325.3127 Evaluate side-chains 201 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 420 TYR Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 274 TYR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 156 optimal weight: 0.4980 chunk 128 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 188 optimal weight: 0.7980 chunk 203 optimal weight: 7.9990 chunk 167 optimal weight: 0.7980 chunk 186 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 495 ASN B 40 GLN D 69 GLN D 175 HIS D 202 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN G 8 HIS G 54 GLN G 264 GLN G 430 ASN G 495 ASN H 40 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.7131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17037 Z= 0.229 Angle : 0.724 9.556 23079 Z= 0.375 Chirality : 0.047 0.217 2547 Planarity : 0.006 0.062 2994 Dihedral : 7.008 57.956 2488 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.84 % Allowed : 15.79 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.17), residues: 2103 helix: -0.64 (0.29), residues: 318 sheet: -1.70 (0.20), residues: 615 loop : -2.28 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 143 HIS 0.005 0.001 HIS G 8 PHE 0.021 0.002 PHE G 239 TYR 0.116 0.002 TYR D 420 ARG 0.010 0.001 ARG G 486 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 221 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5456 (OUTLIER) cc_final: 0.4607 (mp0) REVERT: A 119 ASN cc_start: 0.7246 (p0) cc_final: 0.6597 (t0) REVERT: A 170 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.6773 (mp) REVERT: A 485 HIS cc_start: 0.7073 (p90) cc_final: 0.6526 (p-80) REVERT: D 82 ARG cc_start: 0.7780 (mmm160) cc_final: 0.7469 (tpp-160) REVERT: D 174 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.7080 (mp) REVERT: D 328 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6441 (tt) REVERT: D 353 GLN cc_start: 0.6035 (OUTLIER) cc_final: 0.5627 (mp10) REVERT: D 401 LYS cc_start: 0.6162 (mppt) cc_final: 0.5723 (mmmt) REVERT: D 442 ASP cc_start: 0.6911 (t0) cc_final: 0.6111 (t0) REVERT: D 446 GLU cc_start: 0.7076 (pm20) cc_final: 0.6840 (pm20) REVERT: D 475 MET cc_start: 0.5846 (mmm) cc_final: 0.5604 (mmm) REVERT: E 49 MET cc_start: 0.5781 (mmm) cc_final: 0.5083 (mmm) REVERT: F 49 TYR cc_start: 0.5419 (p90) cc_final: 0.5142 (p90) REVERT: G 54 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.6929 (tm-30) REVERT: G 182 GLU cc_start: 0.4788 (tm-30) cc_final: 0.4344 (tp30) REVERT: G 239 PHE cc_start: 0.5003 (p90) cc_final: 0.4681 (p90) REVERT: G 252 LEU cc_start: 0.8441 (pp) cc_final: 0.8174 (mt) REVERT: G 387 GLN cc_start: 0.6453 (tp-100) cc_final: 0.6062 (mm-40) REVERT: G 436 LEU cc_start: 0.7265 (mp) cc_final: 0.6866 (mt) REVERT: G 442 ASP cc_start: 0.7419 (p0) cc_final: 0.7162 (p0) REVERT: G 454 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6520 (tm-30) REVERT: I 4 MET cc_start: 0.4529 (tpp) cc_final: 0.4271 (tpt) outliers start: 70 outliers final: 20 residues processed: 273 average time/residue: 1.0300 time to fit residues: 320.8353 Evaluate side-chains 183 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 54 GLN Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 338 ASN Chi-restraints excluded: chain G residue 429 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.6351 > 50: distance: 66 - 72: 6.985 distance: 72 - 73: 6.736 distance: 73 - 74: 6.628 distance: 73 - 76: 6.099 distance: 74 - 75: 21.696 distance: 74 - 80: 16.857 distance: 76 - 77: 15.179 distance: 77 - 78: 9.526 distance: 77 - 79: 7.851 distance: 80 - 81: 9.469 distance: 81 - 82: 13.424 distance: 81 - 84: 12.886 distance: 82 - 83: 14.792 distance: 82 - 88: 26.145 distance: 84 - 85: 18.916 distance: 84 - 86: 21.548 distance: 85 - 87: 12.918 distance: 88 - 89: 10.640 distance: 89 - 90: 13.107 distance: 89 - 92: 21.659 distance: 90 - 91: 19.968 distance: 90 - 102: 35.485 distance: 92 - 93: 14.714 distance: 93 - 94: 4.014 distance: 93 - 95: 6.921 distance: 94 - 96: 9.503 distance: 95 - 97: 7.187 distance: 95 - 98: 8.827 distance: 96 - 97: 8.285 distance: 97 - 99: 17.421 distance: 98 - 100: 11.608 distance: 99 - 101: 10.896 distance: 100 - 101: 11.677 distance: 102 - 103: 22.311 distance: 103 - 104: 13.817 distance: 103 - 106: 25.014 distance: 104 - 105: 9.835 distance: 104 - 110: 25.491 distance: 106 - 107: 12.843 distance: 107 - 108: 37.424 distance: 107 - 109: 29.864 distance: 110 - 111: 4.228 distance: 110 - 310: 22.855 distance: 111 - 112: 12.288 distance: 111 - 114: 7.328 distance: 112 - 113: 13.524 distance: 112 - 116: 21.200 distance: 113 - 307: 32.112 distance: 114 - 115: 14.845 distance: 116 - 117: 4.379 distance: 117 - 118: 12.753 distance: 117 - 120: 4.494 distance: 118 - 119: 17.346 distance: 118 - 130: 10.939 distance: 119 - 204: 18.192 distance: 120 - 121: 6.985 distance: 121 - 122: 5.657 distance: 122 - 124: 3.163 distance: 123 - 125: 4.285 distance: 123 - 126: 3.252 distance: 124 - 125: 3.474 distance: 125 - 127: 4.308 distance: 126 - 128: 4.683 distance: 127 - 129: 4.176 distance: 128 - 129: 4.384 distance: 130 - 131: 13.397 distance: 130 - 295: 3.589 distance: 131 - 132: 14.198 distance: 131 - 134: 7.449 distance: 132 - 133: 12.774 distance: 132 - 142: 15.349 distance: 133 - 292: 21.075 distance: 134 - 135: 16.988 distance: 135 - 136: 15.301 distance: 135 - 137: 6.232 distance: 137 - 139: 8.567 distance: 138 - 140: 3.158 distance: 139 - 140: 13.254 distance: 140 - 141: 3.565 distance: 142 - 143: 15.015 distance: 142 - 196: 10.990 distance: 143 - 144: 23.593 distance: 143 - 146: 16.917 distance: 144 - 145: 24.708 distance: 144 - 151: 4.871 distance: 145 - 193: 32.417 distance: 146 - 147: 49.947 distance: 147 - 148: 12.391 distance: 148 - 149: 4.915 distance: 148 - 150: 26.272 distance: 151 - 152: 19.656 distance: 152 - 153: 21.003 distance: 152 - 155: 6.642 distance: 153 - 154: 21.114 distance: 153 - 159: 33.631 distance: 155 - 156: 28.692 distance: 156 - 157: 11.455 distance: 156 - 158: 15.848 distance: 159 - 160: 16.341 distance: 160 - 161: 8.557 distance: 160 - 163: 24.042 distance: 161 - 162: 7.516 distance: 161 - 168: 15.830 distance: 163 - 164: 10.700 distance: 164 - 165: 9.960 distance: 165 - 166: 15.873 distance: 166 - 167: 13.127