Starting phenix.real_space_refine on Thu Mar 21 05:08:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avc_15678/03_2024/8avc_15678.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avc_15678/03_2024/8avc_15678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avc_15678/03_2024/8avc_15678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avc_15678/03_2024/8avc_15678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avc_15678/03_2024/8avc_15678.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avc_15678/03_2024/8avc_15678.pdb" } resolution = 4.6 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11844 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ni 3 6.56 5 S 81 5.16 5 C 11199 2.51 5 N 2940 2.21 5 O 3282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 44": "OD1" <-> "OD2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 778": "OD1" <-> "OD2" Residue "B PHE 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 294": "OD1" <-> "OD2" Residue "D ASP 406": "OD1" <-> "OD2" Residue "D PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 136": "OE1" <-> "OE2" Residue "F PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 384": "OD1" <-> "OD2" Residue "F PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17505 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "B" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4757 Classifications: {'peptide': 593} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555} Chain: "C" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "D" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4757 Classifications: {'peptide': 593} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555} Chain: "E" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "F" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4757 Classifications: {'peptide': 593} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.85, per 1000 atoms: 0.51 Number of scatterers: 17505 At special positions: 0 Unit cell: (137.614, 142.588, 169.116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ni 3 28.00 S 81 16.00 O 3282 8.00 N 2940 7.00 C 11199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 167 " distance=2.04 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 410 " distance=2.03 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 526 " distance=2.02 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 496 " distance=2.03 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 167 " distance=2.03 Simple disulfide: pdb=" SG CYS D 350 " - pdb=" SG CYS D 410 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 416 " distance=2.03 Simple disulfide: pdb=" SG CYS D 434 " - pdb=" SG CYS D 445 " distance=2.05 Simple disulfide: pdb=" SG CYS D 471 " - pdb=" SG CYS D 526 " distance=2.03 Simple disulfide: pdb=" SG CYS D 486 " - pdb=" SG CYS D 496 " distance=2.03 Simple disulfide: pdb=" SG CYS D 602 " - pdb=" SG CYS D 672 " distance=2.03 Simple disulfide: pdb=" SG CYS E 117 " - pdb=" SG CYS E 167 " distance=2.03 Simple disulfide: pdb=" SG CYS F 350 " - pdb=" SG CYS F 410 " distance=2.04 Simple disulfide: pdb=" SG CYS F 411 " - pdb=" SG CYS F 416 " distance=2.03 Simple disulfide: pdb=" SG CYS F 434 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 471 " - pdb=" SG CYS F 526 " distance=2.03 Simple disulfide: pdb=" SG CYS F 486 " - pdb=" SG CYS F 496 " distance=2.03 Simple disulfide: pdb=" SG CYS F 602 " - pdb=" SG CYS F 672 " 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 Time building additional restraints: 6.56 Conformation dependent library (CDL) restraints added in 2.9 seconds 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4212 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 42 sheets defined 16.6% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 23 through 45 removed outlier: 3.823A pdb=" N ILE A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.655A pdb=" N GLN A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 71 through 89 removed outlier: 3.847A pdb=" N SER A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 116 Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.758A pdb=" N VAL A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 160 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.975A pdb=" N VAL B 533 " --> pdb=" O ASP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'C' and resid 23 through 45 removed outlier: 3.594A pdb=" N ILE C 45 " --> pdb=" O ARG C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 50 removed outlier: 3.629A pdb=" N GLN C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 50' Processing helix chain 'C' and resid 71 through 89 removed outlier: 3.884A pdb=" N SER C 88 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 116 Processing helix chain 'C' and resid 130 through 138 removed outlier: 3.631A pdb=" N VAL C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 160 Processing helix chain 'D' and resid 528 through 533 removed outlier: 3.819A pdb=" N VAL D 533 " --> pdb=" O ASP D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 671 Processing helix chain 'D' and resid 732 through 736 Processing helix chain 'E' and resid 23 through 45 removed outlier: 3.527A pdb=" N ILE E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 50 removed outlier: 3.940A pdb=" N SER E 50 " --> pdb=" O SER E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 89 removed outlier: 3.793A pdb=" N SER E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 89 " --> pdb=" O VAL E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 116 Processing helix chain 'E' and resid 130 through 138 removed outlier: 3.801A pdb=" N VAL E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 160 Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 375 through 377 No H-bonds generated for 'chain 'F' and resid 375 through 377' Processing helix chain 'F' and resid 528 through 533 removed outlier: 3.868A pdb=" N VAL F 532 " --> pdb=" O LEU F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 736 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 246 removed outlier: 3.679A pdb=" N LEU B 240 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 242 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER B 255 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N MET B 244 " --> pdb=" O LYS B 253 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS B 253 " --> pdb=" O MET B 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 279 through 286 Processing sheet with id=AA4, first strand: chain 'B' and resid 332 through 334 Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 341 removed outlier: 3.571A pdb=" N GLU B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 341 removed outlier: 6.833A pdb=" N CYS B 410 " --> pdb=" O HIS B 417 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N HIS B 417 " --> pdb=" O CYS B 410 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N CYS B 416 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 433 through 436 Processing sheet with id=AA8, first strand: chain 'B' and resid 482 through 484 removed outlier: 4.250A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 482 through 484 removed outlier: 4.250A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 539 through 545 removed outlier: 3.672A pdb=" N VAL B 541 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N SER B 555 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA B 543 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS B 553 " --> pdb=" O ALA B 543 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 582 through 586 Processing sheet with id=AB3, first strand: chain 'B' and resid 643 through 648 Processing sheet with id=AB4, first strand: chain 'B' and resid 690 through 694 removed outlier: 5.842A pdb=" N TYR B 677 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 739 through 748 removed outlier: 5.459A pdb=" N LEU B 742 " --> pdb=" O THR B 757 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N THR B 757 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ALA B 744 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N SER B 755 " --> pdb=" O ALA B 744 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B 753 " --> pdb=" O PRO B 746 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 782 through 787 removed outlier: 3.599A pdb=" N TYR B 767 " --> pdb=" O VAL B 812 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 240 through 246 removed outlier: 5.457A pdb=" N GLY D 241 " --> pdb=" O ASP D 257 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP D 257 " --> pdb=" O GLY D 241 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 279 through 286 Processing sheet with id=AB9, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AC1, first strand: chain 'D' and resid 337 through 340 removed outlier: 3.805A pdb=" N GLU D 372 " --> pdb=" O ARG D 368 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 416 through 417 removed outlier: 7.468A pdb=" N CYS D 416 " --> pdb=" O THR E 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 433 through 436 Processing sheet with id=AC4, first strand: chain 'D' and resid 482 through 484 removed outlier: 4.177A pdb=" N LEU D 462 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 482 through 484 removed outlier: 4.177A pdb=" N LEU D 462 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 539 through 545 removed outlier: 4.102A pdb=" N VAL D 541 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER D 555 " --> pdb=" O VAL D 541 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA D 543 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS D 553 " --> pdb=" O ALA D 543 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 582 through 586 Processing sheet with id=AC8, first strand: chain 'D' and resid 643 through 648 Processing sheet with id=AC9, first strand: chain 'D' and resid 687 through 694 removed outlier: 5.788A pdb=" N TYR D 677 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 739 through 745 Processing sheet with id=AD2, first strand: chain 'D' and resid 782 through 787 removed outlier: 3.642A pdb=" N TYR D 767 " --> pdb=" O VAL D 812 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS D 773 " --> pdb=" O GLN D 806 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 240 through 246 removed outlier: 6.045A pdb=" N GLY F 241 " --> pdb=" O ASP F 257 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP F 257 " --> pdb=" O GLY F 241 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 279 through 286 Processing sheet with id=AD5, first strand: chain 'F' and resid 331 through 334 Processing sheet with id=AD6, first strand: chain 'F' and resid 337 through 341 Processing sheet with id=AD7, first strand: chain 'F' and resid 433 through 436 Processing sheet with id=AD8, first strand: chain 'F' and resid 482 through 484 removed outlier: 4.479A pdb=" N LEU F 462 " --> pdb=" O LYS F 484 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 482 through 484 removed outlier: 4.479A pdb=" N LEU F 462 " --> pdb=" O LYS F 484 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 539 through 545 removed outlier: 5.594A pdb=" N ASN F 540 " --> pdb=" O GLU F 557 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU F 557 " --> pdb=" O ASN F 540 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 582 through 586 Processing sheet with id=AE3, first strand: chain 'F' and resid 643 through 648 Processing sheet with id=AE4, first strand: chain 'F' and resid 687 through 694 removed outlier: 5.818A pdb=" N TYR F 677 " --> pdb=" O VAL F 693 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 739 through 745 Processing sheet with id=AE6, first strand: chain 'F' and resid 782 through 787 removed outlier: 3.544A pdb=" N TYR F 767 " --> pdb=" O VAL F 812 " (cutoff:3.500A) 790 hydrogen bonds defined for protein. 2076 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: 6.86 Time building geometry restraints manager: 7.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2938 1.32 - 1.46: 6297 1.46 - 1.59: 8585 1.59 - 1.73: 0 1.73 - 1.87: 114 Bond restraints: 17934 Sorted by residual: bond pdb=" CB GLN C 96 " pdb=" CG GLN C 96 " ideal model delta sigma weight residual 1.520 1.424 0.096 3.00e-02 1.11e+03 1.02e+01 bond pdb=" CD GLN C 96 " pdb=" NE2 GLN C 96 " ideal model delta sigma weight residual 1.328 1.274 0.054 2.10e-02 2.27e+03 6.67e+00 bond pdb=" CB ASN C 99 " pdb=" CG ASN C 99 " ideal model delta sigma weight residual 1.516 1.455 0.061 2.50e-02 1.60e+03 5.93e+00 bond pdb=" CG ASN A 103 " pdb=" OD1 ASN A 103 " ideal model delta sigma weight residual 1.231 1.186 0.045 1.90e-02 2.77e+03 5.51e+00 bond pdb=" CG GLN C 96 " pdb=" CD GLN C 96 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.44e+00 ... (remaining 17929 not shown) Histogram of bond angle deviations from ideal: 94.95 - 102.77: 79 102.77 - 110.59: 5545 110.59 - 118.41: 8694 118.41 - 126.23: 9719 126.23 - 134.06: 404 Bond angle restraints: 24441 Sorted by residual: angle pdb=" CB GLN C 96 " pdb=" CG GLN C 96 " pdb=" CD GLN C 96 " ideal model delta sigma weight residual 112.60 94.95 17.65 1.70e+00 3.46e-01 1.08e+02 angle pdb=" N CYS D 434 " pdb=" CA CYS D 434 " pdb=" C CYS D 434 " ideal model delta sigma weight residual 108.38 116.42 -8.04 1.35e+00 5.49e-01 3.55e+01 angle pdb=" N GLN C 96 " pdb=" CA GLN C 96 " pdb=" C GLN C 96 " ideal model delta sigma weight residual 111.36 104.87 6.49 1.09e+00 8.42e-01 3.55e+01 angle pdb=" C ASN A 103 " pdb=" CA ASN A 103 " pdb=" CB ASN A 103 " ideal model delta sigma weight residual 110.63 120.80 -10.17 1.85e+00 2.92e-01 3.02e+01 angle pdb=" CA ASN A 103 " pdb=" CB ASN A 103 " pdb=" CG ASN A 103 " ideal model delta sigma weight residual 112.60 118.09 -5.49 1.00e+00 1.00e+00 3.02e+01 ... (remaining 24436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 10063 17.59 - 35.19: 653 35.19 - 52.78: 101 52.78 - 70.38: 27 70.38 - 87.97: 10 Dihedral angle restraints: 10854 sinusoidal: 4368 harmonic: 6486 Sorted by residual: dihedral pdb=" CA ILE D 501 " pdb=" C ILE D 501 " pdb=" N PHE D 502 " pdb=" CA PHE D 502 " ideal model delta harmonic sigma weight residual 180.00 137.16 42.84 0 5.00e+00 4.00e-02 7.34e+01 dihedral pdb=" CB CYS B 350 " pdb=" SG CYS B 350 " pdb=" SG CYS B 410 " pdb=" CB CYS B 410 " ideal model delta sinusoidal sigma weight residual -86.00 -22.47 -63.53 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 496 " pdb=" CB CYS B 496 " ideal model delta sinusoidal sigma weight residual 93.00 30.11 62.89 1 1.00e+01 1.00e-02 5.23e+01 ... (remaining 10851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2636 0.106 - 0.211: 154 0.211 - 0.317: 8 0.317 - 0.422: 0 0.422 - 0.528: 1 Chirality restraints: 2799 Sorted by residual: chirality pdb=" CA ASN A 103 " pdb=" N ASN A 103 " pdb=" C ASN A 103 " pdb=" CB ASN A 103 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.97e+00 chirality pdb=" CB ILE E 69 " pdb=" CA ILE E 69 " pdb=" CG1 ILE E 69 " pdb=" CG2 ILE E 69 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CG LEU A 60 " pdb=" CB LEU A 60 " pdb=" CD1 LEU A 60 " pdb=" CD2 LEU A 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 2796 not shown) Planarity restraints: 3078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 96 " 0.022 2.00e-02 2.50e+03 4.64e-02 2.16e+01 pdb=" CD GLN C 96 " -0.080 2.00e-02 2.50e+03 pdb=" OE1 GLN C 96 " 0.029 2.00e-02 2.50e+03 pdb=" NE2 GLN C 96 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 103 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" CG ASN A 103 " -0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN A 103 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 103 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 759 " -0.061 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO B 760 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 760 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 760 " -0.050 5.00e-02 4.00e+02 ... (remaining 3075 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 191 2.52 - 3.12: 13291 3.12 - 3.71: 28949 3.71 - 4.31: 39823 4.31 - 4.90: 63889 Nonbonded interactions: 146143 Sorted by model distance: nonbonded pdb=" OE1 GLN C 96 " pdb=" O ILE D 501 " model vdw 1.931 3.040 nonbonded pdb=" ND2 ASN A 103 " pdb=" N LEU B 504 " model vdw 1.987 3.200 nonbonded pdb=" NH1 ARG B 467 " pdb="NI NI B 901 " model vdw 2.014 2.260 nonbonded pdb=" NE2 GLN C 83 " pdb=" O ALA C 98 " model vdw 2.110 2.520 nonbonded pdb=" OH TYR B 409 " pdb=" CB SER C 141 " model vdw 2.122 3.440 ... (remaining 146138 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' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.010 Extract box with map and model: 3.330 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 47.500 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.080 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 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 0.096 17934 Z= 0.235 Angle : 0.799 17.651 24441 Z= 0.444 Chirality : 0.052 0.528 2799 Planarity : 0.005 0.089 3078 Dihedral : 12.050 87.969 6579 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.31 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2181 helix: -0.69 (0.26), residues: 327 sheet: 0.27 (0.17), residues: 847 loop : -0.08 (0.21), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 447 HIS 0.006 0.001 HIS B 465 PHE 0.052 0.001 PHE D 502 TYR 0.019 0.001 TYR D 268 ARG 0.010 0.001 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9694 (mt) cc_final: 0.9448 (mt) REVERT: A 102 GLU cc_start: 0.8539 (mp0) cc_final: 0.8269 (pm20) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1148 time to fit residues: 5.2130 Evaluate side-chains 32 residues out of total 129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.134 Evaluate side-chains 35 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.5244 (ppp) cc_final: 0.4220 (pmm) REVERT: B 443 MET cc_start: 0.9131 (tpp) cc_final: 0.8734 (tpp) REVERT: B 548 ASN cc_start: 0.8571 (m-40) cc_final: 0.8305 (m-40) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1695 time to fit residues: 8.1691 Evaluate side-chains 31 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 6.9990 chunk 165 optimal weight: 0.0870 chunk 92 optimal weight: 0.0770 chunk 56 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 171 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 overall best weight: 0.8718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 GLN ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 1.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17934 Z= 0.202 Angle : 0.660 7.227 24441 Z= 0.356 Chirality : 0.047 0.167 2799 Planarity : 0.004 0.049 3078 Dihedral : 5.483 58.897 2367 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2181 helix: -0.07 (0.26), residues: 339 sheet: 0.17 (0.16), residues: 891 loop : 0.21 (0.22), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 689 HIS 0.004 0.001 HIS D 465 PHE 0.009 0.001 PHE D 348 TYR 0.028 0.002 TYR B 333 ARG 0.007 0.000 ARG D 467 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1371 time to fit residues: 5.6094 Evaluate side-chains 30 residues out of total 129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.141 Evaluate side-chains 39 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.5046 (ppp) cc_final: 0.4276 (pmm) REVERT: B 443 MET cc_start: 0.8909 (tpp) cc_final: 0.8686 (tpp) REVERT: B 503 LEU cc_start: 0.9352 (tt) cc_final: 0.9094 (mm) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1566 time to fit residues: 8.6459 Evaluate side-chains 33 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 165 optimal weight: 0.3980 chunk 135 optimal weight: 0.2980 chunk 54 optimal weight: 4.9990 chunk 199 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 177 optimal weight: 0.0040 chunk 197 optimal weight: 2.9990 chunk 67 optimal weight: 0.0980 chunk 159 optimal weight: 0.0770 overall best weight: 0.1750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 1.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17934 Z= 0.336 Angle : 0.908 14.097 24441 Z= 0.479 Chirality : 0.054 0.372 2799 Planarity : 0.008 0.049 3078 Dihedral : 5.584 46.009 2367 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.30 % Favored : 96.56 % Rotamer: Outliers : 0.89 % Allowed : 4.30 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2181 helix: -0.65 (0.27), residues: 339 sheet: 0.15 (0.16), residues: 888 loop : -0.07 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP B 581 HIS 0.021 0.003 HIS F 478 PHE 0.032 0.004 PHE D 561 TYR 0.050 0.006 TYR A 140 ARG 0.020 0.002 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8382 (mm-30) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.1129 time to fit residues: 4.7438 Evaluate side-chains 28 residues out of total 129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.134 Evaluate side-chains 44 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.4860 (ppp) cc_final: 0.3743 (pmm) REVERT: B 443 MET cc_start: 0.9175 (tpp) cc_final: 0.8964 (tpp) REVERT: B 548 ASN cc_start: 0.8369 (m-40) cc_final: 0.8152 (m-40) outliers start: 5 outliers final: 2 residues processed: 44 average time/residue: 0.1711 time to fit residues: 10.5833 Evaluate side-chains 32 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.6651 > 50: distance: 2 - 3: 40.975 distance: 3 - 4: 6.044 distance: 3 - 6: 33.460 distance: 4 - 5: 9.661 distance: 4 - 8: 19.661 distance: 6 - 7: 12.034 distance: 8 - 9: 3.136 distance: 9 - 10: 3.328 distance: 9 - 12: 10.515 distance: 10 - 11: 7.713 distance: 10 - 15: 8.285 distance: 12 - 13: 10.590 distance: 12 - 14: 5.872 distance: 15 - 16: 21.962 distance: 16 - 17: 5.120 distance: 16 - 19: 30.878 distance: 17 - 18: 5.687 distance: 17 - 22: 9.570 distance: 19 - 20: 24.930 distance: 19 - 21: 14.206 distance: 22 - 23: 12.069 distance: 23 - 24: 12.336 distance: 23 - 26: 7.914 distance: 24 - 25: 6.408 distance: 24 - 31: 8.454 distance: 26 - 27: 7.199 distance: 27 - 28: 8.850 distance: 28 - 29: 19.735 distance: 29 - 30: 11.815 distance: 31 - 32: 10.001 distance: 31 - 37: 12.713 distance: 32 - 33: 12.162 distance: 32 - 35: 12.082 distance: 33 - 34: 19.128 distance: 33 - 38: 15.579 distance: 35 - 36: 17.625 distance: 36 - 37: 14.321 distance: 38 - 39: 11.588 distance: 39 - 40: 9.021 distance: 39 - 42: 5.467 distance: 40 - 41: 4.839 distance: 40 - 46: 6.986 distance: 42 - 43: 10.774 distance: 43 - 44: 21.108 distance: 43 - 45: 29.729 distance: 46 - 47: 11.254 distance: 46 - 52: 9.982 distance: 47 - 48: 8.433 distance: 47 - 50: 7.170 distance: 48 - 49: 14.748 distance: 48 - 53: 8.444 distance: 50 - 51: 16.829 distance: 51 - 52: 6.999 distance: 53 - 54: 3.005 distance: 53 - 59: 6.288 distance: 54 - 55: 3.503 distance: 54 - 57: 5.341 distance: 55 - 60: 10.740 distance: 57 - 58: 8.796 distance: 58 - 59: 11.264 distance: 60 - 61: 5.406 distance: 61 - 64: 6.584 distance: 62 - 63: 4.786 distance: 64 - 65: 6.259 distance: 66 - 67: 4.051 distance: 67 - 68: 7.352 distance: 67 - 70: 10.242 distance: 68 - 69: 10.176 distance: 70 - 71: 23.102 distance: 71 - 72: 9.094