Starting phenix.real_space_refine on Sat Mar 16 14:06:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t4d_8354/03_2024/5t4d_8354.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t4d_8354/03_2024/5t4d_8354.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/5t4d_8354/03_2024/5t4d_8354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t4d_8354/03_2024/5t4d_8354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t4d_8354/03_2024/5t4d_8354.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t4d_8354/03_2024/5t4d_8354.pdb" } 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= 0.001 sd= 0.013 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 72 5.16 5 C 9860 2.51 5 N 2360 2.21 5 O 2584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 251": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 654": "NH1" <-> "NH2" Residue "A PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 361": "NH1" <-> "NH2" Residue "B TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 654": "NH1" <-> "NH2" Residue "B PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 361": "NH1" <-> "NH2" Residue "C TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 397": "NH1" <-> "NH2" Residue "C ARG 399": "NH1" <-> "NH2" Residue "C PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 654": "NH1" <-> "NH2" Residue "C PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 361": "NH1" <-> "NH2" Residue "D TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D ARG 399": "NH1" <-> "NH2" Residue "D PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "D ARG 528": "NH1" <-> "NH2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 654": "NH1" <-> "NH2" Residue "D PHE 670": "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: 14876 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3677 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 449} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "B" Number of atoms: 3677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3677 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 449} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "C" Number of atoms: 3677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3677 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 449} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "D" Number of atoms: 3677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3677 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 449} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 98 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: "B" 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: "C" 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: 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: 7.73, per 1000 atoms: 0.52 Number of scatterers: 14876 At special positions: 0 Unit cell: (110.62, 110.62, 102.11, 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 72 16.00 O 2584 8.00 N 2360 7.00 C 9860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " 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 801 " - " ASN A 328 " " NAG A 802 " - " ASN A 362 " " NAG A 803 " - " ASN A 375 " " NAG B 801 " - " ASN B 328 " " NAG B 802 " - " ASN B 362 " " NAG B 803 " - " ASN B 375 " " NAG C 801 " - " ASN C 328 " " NAG C 802 " - " ASN C 362 " " NAG C 803 " - " ASN C 375 " " NAG D 801 " - " ASN D 328 " " NAG D 802 " - " ASN D 362 " " NAG D 803 " - " ASN D 375 " Time building additional restraints: 6.90 Conformation dependent library (CDL) restraints added in 2.9 seconds 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 60.7% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 216 through 242 removed outlier: 3.541A pdb=" N THR A 226 " --> pdb=" O ARG A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.770A pdb=" N TYR A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.709A pdb=" N SER A 330 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N CYS A 331 " --> pdb=" O ASN A 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 331' Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 467 through 492 removed outlier: 3.569A pdb=" N CYS A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 484 " --> pdb=" O PHE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 528 Processing helix chain 'A' and resid 532 through 541 removed outlier: 3.811A pdb=" N LEU A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 572 Processing helix chain 'A' and resid 573 through 579 removed outlier: 4.521A pdb=" N ASN A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A 579 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 619 removed outlier: 3.746A pdb=" N THR A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 642 Processing helix chain 'A' and resid 646 through 653 Processing helix chain 'A' and resid 655 through 670 Processing helix chain 'A' and resid 672 through 693 removed outlier: 3.661A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 242 removed outlier: 3.542A pdb=" N THR B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 258 removed outlier: 3.770A pdb=" N TYR B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 284 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.708A pdb=" N SER B 330 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N CYS B 331 " --> pdb=" O ASN B 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 327 through 331' Processing helix chain 'B' and resid 334 through 338 Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 492 removed outlier: 3.569A pdb=" N CYS B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 484 " --> pdb=" O PHE B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 528 Processing helix chain 'B' and resid 532 through 541 removed outlier: 3.811A pdb=" N LEU B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 572 Processing helix chain 'B' and resid 573 through 579 removed outlier: 4.522A pdb=" N ASN B 578 " --> pdb=" O LYS B 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE B 579 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 619 removed outlier: 3.747A pdb=" N THR B 589 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 627 Processing helix chain 'B' and resid 628 through 642 Processing helix chain 'B' and resid 646 through 653 Processing helix chain 'B' and resid 655 through 670 Processing helix chain 'B' and resid 672 through 693 removed outlier: 3.661A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 242 removed outlier: 3.541A pdb=" N THR C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.769A pdb=" N TYR C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 284 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 327 through 331 removed outlier: 3.709A pdb=" N SER C 330 " --> pdb=" O ARG C 327 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N CYS C 331 " --> pdb=" O ASN C 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 327 through 331' Processing helix chain 'C' and resid 334 through 338 Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 492 removed outlier: 3.570A pdb=" N CYS C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 484 " --> pdb=" O PHE C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 528 Processing helix chain 'C' and resid 532 through 541 removed outlier: 3.811A pdb=" N LEU C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 572 Processing helix chain 'C' and resid 573 through 579 removed outlier: 4.522A pdb=" N ASN C 578 " --> pdb=" O LYS C 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE C 579 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 619 removed outlier: 3.746A pdb=" N THR C 589 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 628 through 642 Processing helix chain 'C' and resid 646 through 653 Processing helix chain 'C' and resid 655 through 670 Processing helix chain 'C' and resid 672 through 693 removed outlier: 3.661A pdb=" N PHE C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 242 removed outlier: 3.542A pdb=" N THR D 226 " --> pdb=" O ARG D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.770A pdb=" N TYR D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 285 through 292 Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.709A pdb=" N SER D 330 " --> pdb=" O ARG D 327 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N CYS D 331 " --> pdb=" O ASN D 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 327 through 331' Processing helix chain 'D' and resid 334 through 338 Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 492 removed outlier: 3.568A pdb=" N CYS D 476 " --> pdb=" O PHE D 472 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D 484 " --> pdb=" O PHE D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 528 Processing helix chain 'D' and resid 532 through 541 removed outlier: 3.811A pdb=" N LEU D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP D 541 " --> pdb=" O GLN D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 572 Processing helix chain 'D' and resid 573 through 579 removed outlier: 4.521A pdb=" N ASN D 578 " --> pdb=" O LYS D 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE D 579 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 619 removed outlier: 3.746A pdb=" N THR D 589 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET D 603 " --> pdb=" O GLY D 599 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 627 Processing helix chain 'D' and resid 628 through 642 Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 655 through 670 Processing helix chain 'D' and resid 672 through 693 removed outlier: 3.660A pdb=" N PHE D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 309 removed outlier: 6.694A pdb=" N LEU A 316 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR A 429 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 318 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N SER A 427 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 421 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 309 Processing sheet with id=AA5, first strand: chain 'B' and resid 308 through 309 removed outlier: 6.693A pdb=" N LEU B 316 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR B 429 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 318 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N SER B 427 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 421 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AA7, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AA8, first strand: chain 'C' and resid 308 through 309 removed outlier: 6.694A pdb=" N LEU C 316 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR C 429 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 318 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N SER C 427 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 421 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AB2, first strand: chain 'D' and resid 308 through 309 removed outlier: 6.694A pdb=" N LEU D 316 " --> pdb=" O TYR D 429 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR D 429 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL D 318 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N SER D 427 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D 421 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 379 through 380 921 hydrogen bonds defined for protein. 2619 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: 4.73 Time building geometry restraints manager: 7.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4454 1.34 - 1.45: 3166 1.45 - 1.57: 7536 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 15264 Sorted by residual: bond pdb=" CA ALA B 356 " pdb=" C ALA B 356 " ideal model delta sigma weight residual 1.528 1.505 0.022 1.08e-02 8.57e+03 4.21e+00 bond pdb=" CA ALA C 356 " pdb=" C ALA C 356 " ideal model delta sigma weight residual 1.528 1.506 0.022 1.08e-02 8.57e+03 4.10e+00 bond pdb=" CA ALA D 356 " pdb=" C ALA D 356 " ideal model delta sigma weight residual 1.528 1.506 0.021 1.08e-02 8.57e+03 3.93e+00 bond pdb=" CA ALA A 356 " pdb=" C ALA A 356 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.08e-02 8.57e+03 3.61e+00 bond pdb=" CA ALA A 303 " pdb=" C ALA A 303 " ideal model delta sigma weight residual 1.523 1.545 -0.021 1.30e-02 5.92e+03 2.73e+00 ... (remaining 15259 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.40: 232 106.40 - 113.30: 8487 113.30 - 120.20: 5751 120.20 - 127.10: 6182 127.10 - 134.00: 132 Bond angle restraints: 20784 Sorted by residual: angle pdb=" N ALA C 303 " pdb=" CA ALA C 303 " pdb=" C ALA C 303 " ideal model delta sigma weight residual 111.28 116.09 -4.81 1.09e+00 8.42e-01 1.95e+01 angle pdb=" N ALA B 303 " pdb=" CA ALA B 303 " pdb=" C ALA B 303 " ideal model delta sigma weight residual 111.28 116.07 -4.79 1.09e+00 8.42e-01 1.93e+01 angle pdb=" N ALA A 303 " pdb=" CA ALA A 303 " pdb=" C ALA A 303 " ideal model delta sigma weight residual 111.28 116.06 -4.78 1.09e+00 8.42e-01 1.92e+01 angle pdb=" N ALA D 303 " pdb=" CA ALA D 303 " pdb=" C ALA D 303 " ideal model delta sigma weight residual 111.28 116.06 -4.78 1.09e+00 8.42e-01 1.92e+01 angle pdb=" C LYS D 294 " pdb=" N MET D 295 " pdb=" CA MET D 295 " ideal model delta sigma weight residual 121.70 128.56 -6.86 1.80e+00 3.09e-01 1.45e+01 ... (remaining 20779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 8572 15.83 - 31.65: 224 31.65 - 47.48: 72 47.48 - 63.30: 16 63.30 - 79.13: 12 Dihedral angle restraints: 8896 sinusoidal: 3412 harmonic: 5484 Sorted by residual: dihedral pdb=" CA ASN B 432 " pdb=" C ASN B 432 " pdb=" N ILE B 433 " pdb=" CA ILE B 433 " ideal model delta harmonic sigma weight residual 180.00 148.04 31.96 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA ASN D 432 " pdb=" C ASN D 432 " pdb=" N ILE D 433 " pdb=" CA ILE D 433 " ideal model delta harmonic sigma weight residual 180.00 148.04 31.96 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA ASN A 432 " pdb=" C ASN A 432 " pdb=" N ILE A 433 " pdb=" CA ILE A 433 " ideal model delta harmonic sigma weight residual 180.00 148.08 31.92 0 5.00e+00 4.00e-02 4.08e+01 ... (remaining 8893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1277 0.034 - 0.068: 799 0.068 - 0.103: 235 0.103 - 0.137: 95 0.137 - 0.171: 22 Chirality restraints: 2428 Sorted by residual: chirality pdb=" CG LEU D 677 " pdb=" CB LEU D 677 " pdb=" CD1 LEU D 677 " pdb=" CD2 LEU D 677 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CG LEU B 677 " pdb=" CB LEU B 677 " pdb=" CD1 LEU B 677 " pdb=" CD2 LEU B 677 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CG LEU A 314 " pdb=" CB LEU A 314 " pdb=" CD1 LEU A 314 " pdb=" CD2 LEU A 314 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 2425 not shown) Planarity restraints: 2564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 380 " 0.018 2.00e-02 2.50e+03 1.50e-02 5.60e+00 pdb=" CG TRP B 380 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 380 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 380 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 380 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 380 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 380 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 380 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 380 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 380 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 380 " 0.018 2.00e-02 2.50e+03 1.50e-02 5.59e+00 pdb=" CG TRP D 380 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP D 380 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP D 380 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 380 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 380 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 380 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 380 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 380 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 380 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 380 " 0.018 2.00e-02 2.50e+03 1.49e-02 5.52e+00 pdb=" CG TRP A 380 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 380 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 380 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 380 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 380 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 380 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 380 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 380 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 380 " 0.002 2.00e-02 2.50e+03 ... (remaining 2561 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 279 2.68 - 3.23: 16182 3.23 - 3.79: 24255 3.79 - 4.34: 31807 4.34 - 4.90: 52246 Nonbonded interactions: 124769 Sorted by model distance: nonbonded pdb=" OH TYR B 227 " pdb=" O VAL B 569 " model vdw 2.120 2.440 nonbonded pdb=" OH TYR A 227 " pdb=" O VAL A 569 " model vdw 2.120 2.440 nonbonded pdb=" OH TYR C 227 " pdb=" O VAL C 569 " model vdw 2.120 2.440 nonbonded pdb=" OH TYR D 227 " pdb=" O VAL D 569 " model vdw 2.121 2.440 nonbonded pdb=" O LEU A 586 " pdb=" OG1 THR A 589 " model vdw 2.216 2.440 ... (remaining 124764 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 'B' selection = chain 'C' selection = chain 'D' } 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: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.360 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 41.890 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.100 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:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 0.051 15264 Z= 0.673 Angle : 0.809 10.994 20784 Z= 0.446 Chirality : 0.049 0.171 2428 Planarity : 0.005 0.052 2552 Dihedral : 9.476 79.127 5332 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.26 % Allowed : 1.58 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.69 (0.17), residues: 1828 helix: -2.42 (0.12), residues: 1004 sheet: 0.11 (0.31), residues: 192 loop : -0.88 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.005 TRP D 380 HIS 0.005 0.003 HIS A 379 PHE 0.025 0.002 PHE C 310 TYR 0.026 0.002 TYR D 249 ARG 0.009 0.001 ARG D 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 359 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ASN cc_start: 0.7875 (m-40) cc_final: 0.7657 (m-40) REVERT: A 410 LYS cc_start: 0.8414 (tttm) cc_final: 0.8109 (tttm) REVERT: A 508 ASN cc_start: 0.7052 (m110) cc_final: 0.6776 (m-40) REVERT: B 269 ASN cc_start: 0.7879 (m-40) cc_final: 0.7667 (m-40) REVERT: B 410 LYS cc_start: 0.8414 (tttm) cc_final: 0.8107 (tttm) REVERT: B 508 ASN cc_start: 0.7048 (m110) cc_final: 0.6770 (m-40) REVERT: C 410 LYS cc_start: 0.8429 (tttm) cc_final: 0.8119 (tttp) REVERT: C 508 ASN cc_start: 0.7127 (m110) cc_final: 0.6822 (m-40) REVERT: D 269 ASN cc_start: 0.7871 (m-40) cc_final: 0.7658 (m-40) REVERT: D 410 LYS cc_start: 0.8412 (tttm) cc_final: 0.8107 (tttp) REVERT: D 508 ASN cc_start: 0.7056 (m110) cc_final: 0.6778 (m-40) outliers start: 4 outliers final: 0 residues processed: 359 average time/residue: 1.1268 time to fit residues: 449.7955 Evaluate side-chains 196 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.2345 > 50: distance: 67 - 101: 8.962 distance: 80 - 81: 5.103 distance: 81 - 82: 4.741 distance: 81 - 84: 5.996 distance: 82 - 83: 4.911 distance: 82 - 92: 3.910 distance: 84 - 85: 5.575 distance: 85 - 86: 4.656 distance: 85 - 87: 11.471 distance: 86 - 88: 3.248 distance: 87 - 89: 5.444 distance: 88 - 90: 10.510 distance: 89 - 90: 7.713 distance: 90 - 91: 3.655 distance: 93 - 94: 3.190 distance: 93 - 96: 5.822 distance: 94 - 95: 11.542 distance: 94 - 101: 6.297 distance: 96 - 97: 6.950 distance: 97 - 98: 9.088 distance: 98 - 99: 11.663 distance: 98 - 100: 7.852 distance: 101 - 102: 3.553 distance: 102 - 103: 4.969 distance: 105 - 106: 3.509 distance: 106 - 108: 5.248 distance: 109 - 110: 3.436 distance: 110 - 111: 3.105 distance: 110 - 113: 6.322 distance: 111 - 112: 4.476 distance: 113 - 114: 7.213 distance: 114 - 115: 7.072 distance: 114 - 116: 3.208 distance: 117 - 118: 3.147 distance: 118 - 119: 6.006 distance: 118 - 121: 5.152 distance: 119 - 120: 11.971 distance: 119 - 125: 9.960 distance: 121 - 122: 7.940 distance: 122 - 123: 12.790 distance: 122 - 124: 11.555 distance: 125 - 126: 8.264 distance: 126 - 127: 15.068 distance: 126 - 129: 10.398 distance: 127 - 128: 11.564 distance: 127 - 133: 14.896 distance: 129 - 130: 8.351 distance: 130 - 131: 9.681 distance: 130 - 132: 10.672 distance: 133 - 134: 35.318 distance: 134 - 135: 30.709 distance: 135 - 136: 21.333 distance: 135 - 137: 8.597 distance: 137 - 138: 9.675 distance: 138 - 139: 3.966 distance: 138 - 141: 7.403 distance: 139 - 140: 6.727 distance: 139 - 144: 4.569 distance: 141 - 142: 6.413 distance: 141 - 143: 4.627 distance: 144 - 145: 3.275 distance: 144 - 150: 4.435 distance: 145 - 148: 4.964 distance: 146 - 147: 3.791 distance: 148 - 149: 4.004 distance: 149 - 150: 5.322 distance: 151 - 152: 3.159 distance: 151 - 218: 4.167 distance: 153 - 154: 5.844 distance: 154 - 215: 6.035 distance: 157 - 158: 3.611 distance: 159 - 161: 3.573