Starting phenix.real_space_refine on Mon May 26 15:28:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6d05_7785/05_2025/6d05_7785.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d05_7785/05_2025/6d05_7785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6d05_7785/05_2025/6d05_7785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d05_7785/05_2025/6d05_7785.map" model { file = "/net/cci-nas-00/data/ceres_data/6d05_7785/05_2025/6d05_7785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d05_7785/05_2025/6d05_7785.cif" } resolution = 3.8 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= 0.002 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 S 142 5.16 5 C 18252 2.51 5 N 4850 2.21 5 O 5498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28748 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "B" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "C" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 644} Chain: "D" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 644} Chain: "E" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 458} Chain: "F" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 458} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' FE': 2, 'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' FE': 2, 'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 15.08, per 1000 atoms: 0.52 Number of scatterers: 28748 At special positions: 0 Unit cell: (171.45, 148.5, 163.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 Ca 2 19.99 S 142 16.00 O 5498 8.00 N 4850 7.00 C 18252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 353 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 48 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 158 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 179 " distance=2.02 Simple disulfide: pdb=" SG CYS C 171 " - pdb=" SG CYS C 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 596 " distance=2.03 Simple disulfide: pdb=" SG CYS C 345 " - pdb=" SG CYS C 377 " distance=2.02 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 368 " distance=2.02 Simple disulfide: pdb=" SG CYS C 402 " - pdb=" SG CYS C 674 " distance=2.03 Simple disulfide: pdb=" SG CYS C 418 " - pdb=" SG CYS C 637 " distance=2.04 Simple disulfide: pdb=" SG CYS C 450 " - pdb=" SG CYS C 523 " distance=2.04 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 665 " distance=2.02 Simple disulfide: pdb=" SG CYS C 484 " - pdb=" SG CYS C 498 " distance=2.03 Simple disulfide: pdb=" SG CYS C 495 " - pdb=" SG CYS C 506 " distance=2.03 Simple disulfide: pdb=" SG CYS C 563 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 620 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 48 " distance=2.02 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 118 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 158 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 179 " distance=2.02 Simple disulfide: pdb=" SG CYS D 171 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS D 227 " - pdb=" SG CYS D 241 " distance=2.02 Simple disulfide: pdb=" SG CYS D 339 " - pdb=" SG CYS D 596 " distance=2.03 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 377 " distance=2.02 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 368 " distance=2.02 Simple disulfide: pdb=" SG CYS D 402 " - pdb=" SG CYS D 674 " distance=2.03 Simple disulfide: pdb=" SG CYS D 418 " - pdb=" SG CYS D 637 " distance=2.04 Simple disulfide: pdb=" SG CYS D 450 " - pdb=" SG CYS D 523 " distance=2.04 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 665 " distance=2.02 Simple disulfide: pdb=" SG CYS D 484 " - pdb=" SG CYS D 498 " distance=2.03 Simple disulfide: pdb=" SG CYS D 495 " - pdb=" SG CYS D 506 " distance=2.03 Simple disulfide: pdb=" SG CYS D 563 " - pdb=" SG CYS D 577 " distance=2.02 Simple disulfide: pdb=" SG CYS D 615 " - pdb=" SG CYS D 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 240 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 316 " distance=2.03 Simple disulfide: pdb=" SG CYS F 240 " - pdb=" SG CYS F 284 " distance=2.04 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 802 " - " ASN A 251 " " NAG B 802 " - " ASN B 251 " " NAG C 707 " - " ASN C 611 " " NAG D 707 " - " ASN D 611 " " NAG G 1 " - " ASN A 317 " " NAG H 1 " - " ASN A 727 " " NAG I 1 " - " ASN B 317 " " NAG J 1 " - " ASN B 727 " " NAG K 1 " - " ASN C 413 " " NAG L 1 " - " ASN D 413 " Time building additional restraints: 6.34 Conformation dependent library (CDL) restraints added in 3.3 seconds 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6740 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 28 sheets defined 50.9% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 123 through 138 removed outlier: 3.802A pdb=" N SER A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 159 through 176 Processing helix chain 'A' and resid 239 through 245 removed outlier: 3.530A pdb=" N ASP A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 removed outlier: 3.555A pdb=" N LYS A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 415 through 439 removed outlier: 3.606A pdb=" N SER A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLY A 422 " --> pdb=" O LYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.525A pdb=" N THR A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 583 through 603 removed outlier: 3.697A pdb=" N VAL A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 627 removed outlier: 3.547A pdb=" N GLN A 627 " --> pdb=" O ARG A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 635 removed outlier: 3.503A pdb=" N ILE A 632 " --> pdb=" O TYR A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.674A pdb=" N TYR A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 684 removed outlier: 3.520A pdb=" N LYS A 673 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 674 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU A 682 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR A 683 " --> pdb=" O MET A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 722 removed outlier: 3.846A pdb=" N LYS A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 750 removed outlier: 3.628A pdb=" N SER A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 138 removed outlier: 3.801A pdb=" N SER B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 159 through 176 Processing helix chain 'B' and resid 239 through 245 removed outlier: 3.529A pdb=" N ASP B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 274 removed outlier: 3.555A pdb=" N LYS B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 415 through 439 removed outlier: 3.605A pdb=" N SER B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VAL B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLY B 422 " --> pdb=" O LYS B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.525A pdb=" N THR B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 583 through 603 removed outlier: 3.697A pdb=" N VAL B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 627 removed outlier: 3.546A pdb=" N GLN B 627 " --> pdb=" O ARG B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 635 removed outlier: 3.502A pdb=" N ILE B 632 " --> pdb=" O TYR B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 662 removed outlier: 3.675A pdb=" N TYR B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 684 removed outlier: 3.520A pdb=" N LYS B 673 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 674 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 677 " --> pdb=" O LYS B 673 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU B 682 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR B 683 " --> pdb=" O MET B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 722 removed outlier: 3.846A pdb=" N LYS B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 750 removed outlier: 3.627A pdb=" N SER B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 30 removed outlier: 3.600A pdb=" N ILE C 30 " --> pdb=" O MET C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 63 through 72 removed outlier: 4.123A pdb=" N LEU C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 135 Processing helix chain 'C' and resid 145 through 154 Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 187 through 197 Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.539A pdb=" N LEU C 214 " --> pdb=" O ILE C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 259 through 275 removed outlier: 3.945A pdb=" N ILE C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 316 Processing helix chain 'C' and resid 317 through 329 Processing helix chain 'C' and resid 350 through 362 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 392 through 403 removed outlier: 3.847A pdb=" N ILE C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 472 removed outlier: 3.775A pdb=" N LEU C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 528 Processing helix chain 'C' and resid 536 through 542 removed outlier: 3.732A pdb=" N GLN C 540 " --> pdb=" O GLN C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 553 Processing helix chain 'C' and resid 593 through 609 removed outlier: 3.906A pdb=" N HIS C 606 " --> pdb=" O ARG C 602 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 652 removed outlier: 3.696A pdb=" N TYR C 650 " --> pdb=" O THR C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 663 Processing helix chain 'C' and resid 668 through 677 Processing helix chain 'D' and resid 12 through 30 removed outlier: 3.599A pdb=" N ILE D 30 " --> pdb=" O MET D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 54 Processing helix chain 'D' and resid 63 through 72 removed outlier: 4.123A pdb=" N LEU D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 135 Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 187 through 197 Processing helix chain 'D' and resid 208 through 214 removed outlier: 3.539A pdb=" N LEU D 214 " --> pdb=" O ILE D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 223 Processing helix chain 'D' and resid 259 through 275 removed outlier: 3.945A pdb=" N ILE D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY D 275 " --> pdb=" O GLN D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 316 Processing helix chain 'D' and resid 317 through 329 Processing helix chain 'D' and resid 350 through 362 Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'D' and resid 392 through 403 removed outlier: 3.848A pdb=" N ILE D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 removed outlier: 3.775A pdb=" N LEU D 466 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS D 470 " --> pdb=" O LEU D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 528 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.733A pdb=" N GLN D 540 " --> pdb=" O GLN D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 553 Processing helix chain 'D' and resid 593 through 609 removed outlier: 3.906A pdb=" N HIS D 606 " --> pdb=" O ARG D 602 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 652 removed outlier: 3.695A pdb=" N TYR D 650 " --> pdb=" O THR D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 663 Processing helix chain 'D' and resid 668 through 677 Processing helix chain 'E' and resid 196 through 210 removed outlier: 4.383A pdb=" N TYR E 200 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 256 removed outlier: 4.653A pdb=" N THR E 246 " --> pdb=" O ARG E 242 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU E 250 " --> pdb=" O THR E 246 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN E 256 " --> pdb=" O ASN E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 263 removed outlier: 4.248A pdb=" N GLN E 263 " --> pdb=" O LYS E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 307 removed outlier: 3.568A pdb=" N LYS E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 335 removed outlier: 3.710A pdb=" N MET E 335 " --> pdb=" O ASP E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 365 removed outlier: 3.931A pdb=" N LYS E 363 " --> pdb=" O ARG E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 406 removed outlier: 4.479A pdb=" N ILE E 371 " --> pdb=" O ASN E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 477 removed outlier: 4.174A pdb=" N ASP E 438 " --> pdb=" O LYS E 434 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU E 460 " --> pdb=" O ASN E 456 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLY E 463 " --> pdb=" O GLY E 459 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N HIS E 464 " --> pdb=" O GLU E 460 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP E 474 " --> pdb=" O SER E 470 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER E 475 " --> pdb=" O LYS E 471 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR E 477 " --> pdb=" O ILE E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 513 removed outlier: 3.590A pdb=" N LYS E 505 " --> pdb=" O ASP E 501 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU E 512 " --> pdb=" O GLU E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 567 removed outlier: 3.936A pdb=" N ASN E 566 " --> pdb=" O SER E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 633 removed outlier: 4.036A pdb=" N ASP E 578 " --> pdb=" O GLN E 574 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N PHE E 592 " --> pdb=" O SER E 588 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER E 593 " --> pdb=" O TYR E 589 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 210 removed outlier: 4.383A pdb=" N TYR F 200 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 256 removed outlier: 4.653A pdb=" N THR F 246 " --> pdb=" O ARG F 242 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU F 250 " --> pdb=" O THR F 246 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN F 256 " --> pdb=" O ASN F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 263 removed outlier: 4.248A pdb=" N GLN F 263 " --> pdb=" O LYS F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 307 removed outlier: 3.568A pdb=" N LYS F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 335 removed outlier: 3.710A pdb=" N MET F 335 " --> pdb=" O ASP F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 365 removed outlier: 3.930A pdb=" N LYS F 363 " --> pdb=" O ARG F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 406 removed outlier: 4.479A pdb=" N ILE F 371 " --> pdb=" O ASN F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 477 removed outlier: 4.174A pdb=" N ASP F 438 " --> pdb=" O LYS F 434 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU F 460 " --> pdb=" O ASN F 456 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLY F 463 " --> pdb=" O GLY F 459 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N HIS F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP F 474 " --> pdb=" O SER F 470 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER F 475 " --> pdb=" O LYS F 471 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR F 477 " --> pdb=" O ILE F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 513 removed outlier: 3.591A pdb=" N LYS F 505 " --> pdb=" O ASP F 501 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU F 512 " --> pdb=" O GLU F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 567 removed outlier: 3.936A pdb=" N ASN F 566 " --> pdb=" O SER F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 633 removed outlier: 4.035A pdb=" N ASP F 578 " --> pdb=" O GLN F 574 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N PHE F 592 " --> pdb=" O SER F 588 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER F 593 " --> pdb=" O TYR F 589 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 193 removed outlier: 3.583A pdb=" N VAL A 403 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR A 402 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR A 480 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE A 555 " --> pdb=" O ASN A 483 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 214 removed outlier: 7.411A pdb=" N VAL A 200 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 234 removed outlier: 6.267A pdb=" N VAL A 233 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ARG A 258 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL A 279 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AA6, first strand: chain 'B' and resid 180 through 193 removed outlier: 3.583A pdb=" N VAL B 403 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR B 402 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR B 480 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE B 555 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 210 through 214 removed outlier: 7.411A pdb=" N VAL B 200 " --> pdb=" O VAL B 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'B' and resid 232 through 234 removed outlier: 6.267A pdb=" N VAL B 233 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ARG B 258 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B 279 " --> pdb=" O GLN B 335 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 349 through 350 Processing sheet with id=AB2, first strand: chain 'C' and resid 8 through 10 Processing sheet with id=AB3, first strand: chain 'C' and resid 60 through 62 removed outlier: 6.530A pdb=" N ALA C 253 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 158 removed outlier: 6.427A pdb=" N SER C 117 " --> pdb=" O CYS C 158 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 204 " --> pdb=" O CYS C 118 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ALA C 99 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 225 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 233 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 158 removed outlier: 6.427A pdb=" N SER C 117 " --> pdb=" O CYS C 158 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 204 " --> pdb=" O CYS C 118 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA C 244 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 342 through 347 removed outlier: 6.002A pdb=" N VAL C 342 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL C 369 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TRP C 344 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ALA C 371 " --> pdb=" O TRP C 344 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA C 346 " --> pdb=" O ALA C 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 388 through 391 removed outlier: 3.767A pdb=" N LEU C 408 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR C 589 " --> pdb=" O PRO C 406 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 530 through 534 Processing sheet with id=AB9, first strand: chain 'C' and resid 530 through 534 removed outlier: 3.912A pdb=" N ALA C 580 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 449 through 450 removed outlier: 6.983A pdb=" N SER C 449 " --> pdb=" O CYS C 484 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 8 through 10 Processing sheet with id=AC3, first strand: chain 'D' and resid 60 through 62 removed outlier: 6.531A pdb=" N ALA D 253 " --> pdb=" O PRO D 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 157 through 158 removed outlier: 6.428A pdb=" N SER D 117 " --> pdb=" O CYS D 158 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE D 204 " --> pdb=" O CYS D 118 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ALA D 99 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 225 " --> pdb=" O LYS D 233 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS D 233 " --> pdb=" O LEU D 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 157 through 158 removed outlier: 6.428A pdb=" N SER D 117 " --> pdb=" O CYS D 158 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE D 204 " --> pdb=" O CYS D 118 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA D 244 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 342 through 347 removed outlier: 6.002A pdb=" N VAL D 342 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL D 369 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TRP D 344 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA D 371 " --> pdb=" O TRP D 344 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA D 346 " --> pdb=" O ALA D 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 388 through 391 removed outlier: 3.767A pdb=" N LEU D 408 " --> pdb=" O VAL D 587 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR D 589 " --> pdb=" O PRO D 406 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 530 through 534 Processing sheet with id=AC9, first strand: chain 'D' and resid 530 through 534 removed outlier: 3.914A pdb=" N ALA D 580 " --> pdb=" O ALA D 428 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 449 through 450 removed outlier: 6.983A pdb=" N SER D 449 " --> pdb=" O CYS D 484 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 1492 hydrogen bonds defined for protein. 4386 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: 10.06 Time building geometry restraints manager: 7.55 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: 9261 1.34 - 1.47: 7200 1.47 - 1.59: 12707 1.59 - 1.72: 0 1.72 - 1.84: 192 Bond restraints: 29360 Sorted by residual: bond pdb=" C1 NAG A 802 " pdb=" O5 NAG A 802 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C1 NAG C 707 " pdb=" O5 NAG C 707 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.37e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.29e+00 ... (remaining 29355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 38136 2.57 - 5.14: 1335 5.14 - 7.70: 137 7.70 - 10.27: 44 10.27 - 12.84: 12 Bond angle restraints: 39664 Sorted by residual: angle pdb=" C ASN C 461 " pdb=" N ILE C 462 " pdb=" CA ILE C 462 " ideal model delta sigma weight residual 120.24 123.62 -3.38 6.30e-01 2.52e+00 2.87e+01 angle pdb=" C LEU D 629 " pdb=" N LEU D 630 " pdb=" CA LEU D 630 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 angle pdb=" C LEU C 629 " pdb=" N LEU C 630 " pdb=" CA LEU C 630 " ideal model delta sigma weight residual 121.54 131.73 -10.19 1.91e+00 2.74e-01 2.85e+01 angle pdb=" C ASN D 461 " pdb=" N ILE D 462 " pdb=" CA ILE D 462 " ideal model delta sigma weight residual 120.24 123.60 -3.36 6.30e-01 2.52e+00 2.85e+01 angle pdb=" C ALA C 54 " pdb=" N ASN C 55 " pdb=" CA ASN C 55 " ideal model delta sigma weight residual 122.61 130.74 -8.13 1.56e+00 4.11e-01 2.72e+01 ... (remaining 39659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.62: 17106 22.62 - 45.23: 750 45.23 - 67.85: 101 67.85 - 90.46: 58 90.46 - 113.08: 27 Dihedral angle restraints: 18042 sinusoidal: 7570 harmonic: 10472 Sorted by residual: dihedral pdb=" CA VAL C 1 " pdb=" C VAL C 1 " pdb=" N PRO C 2 " pdb=" CA PRO C 2 " ideal model delta harmonic sigma weight residual -180.00 -93.65 -86.35 0 5.00e+00 4.00e-02 2.98e+02 dihedral pdb=" CA VAL D 1 " pdb=" C VAL D 1 " pdb=" N PRO D 2 " pdb=" CA PRO D 2 " ideal model delta harmonic sigma weight residual -180.00 -93.74 -86.26 0 5.00e+00 4.00e-02 2.98e+02 dihedral pdb=" CA ASP F 407 " pdb=" C ASP F 407 " pdb=" N GLY F 408 " pdb=" CA GLY F 408 " ideal model delta harmonic sigma weight residual -180.00 -105.57 -74.43 0 5.00e+00 4.00e-02 2.22e+02 ... (remaining 18039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 4308 0.180 - 0.359: 42 0.359 - 0.539: 2 0.539 - 0.719: 1 0.719 - 0.899: 1 Chirality restraints: 4354 Sorted by residual: chirality pdb=" C1 NAG D 707 " pdb=" ND2 ASN D 611 " pdb=" C2 NAG D 707 " pdb=" O5 NAG D 707 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.02e+01 chirality pdb=" C1 NAG B 802 " pdb=" ND2 ASN B 251 " pdb=" C2 NAG B 802 " pdb=" O5 NAG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1 NAG C 707 " pdb=" ND2 ASN C 611 " pdb=" C2 NAG C 707 " pdb=" O5 NAG C 707 " both_signs ideal model delta sigma weight residual False -2.40 -2.86 0.46 2.00e-01 2.50e+01 5.18e+00 ... (remaining 4351 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 728 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.46e+00 pdb=" C GLU B 728 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU B 728 " -0.020 2.00e-02 2.50e+03 pdb=" N THR B 729 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 728 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C GLU A 728 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU A 728 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 729 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 727 " 0.028 2.00e-02 2.50e+03 2.62e-02 8.59e+00 pdb=" CG ASN B 727 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 727 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 727 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.031 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 268 2.62 - 3.19: 24748 3.19 - 3.76: 44297 3.76 - 4.33: 59133 4.33 - 4.90: 96973 Nonbonded interactions: 225419 Sorted by model distance: nonbonded pdb=" OH TYR D 95 " pdb="FE FE D 703 " model vdw 2.046 2.260 nonbonded pdb=" OH TYR C 95 " pdb="FE FE C 703 " model vdw 2.051 2.260 nonbonded pdb=" OH TYR D 517 " pdb="FE FE D 701 " model vdw 2.055 2.260 nonbonded pdb=" OH TYR C 517 " pdb="FE FE C 701 " model vdw 2.066 2.260 nonbonded pdb="FE FE D 703 " pdb=" O2 CO3 D 704 " model vdw 2.078 2.260 ... (remaining 225414 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 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: 0.010 Normalize map: mean=0, sd=1: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.960 Check model and map are aligned: 0.190 Set scattering table: 0.270 Process input model: 57.040 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.170 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.009 0.091 29422 Z= 0.396 Angle : 1.172 20.731 39804 Z= 0.646 Chirality : 0.061 0.899 4354 Planarity : 0.007 0.067 5106 Dihedral : 13.781 113.078 11164 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.28 % Allowed : 7.61 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 1.56 % Twisted General : 0.17 % 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: -3.29 (0.11), residues: 3560 helix: -1.98 (0.10), residues: 1720 sheet: -2.10 (0.23), residues: 372 loop : -2.28 (0.13), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP D 358 HIS 0.019 0.003 HIS D 249 PHE 0.039 0.004 PHE A 346 TYR 0.031 0.003 TYR F 552 ARG 0.014 0.002 ARG C 50 Details of bonding type rmsd link_NAG-ASN : bond 0.01696 ( 10) link_NAG-ASN : angle 8.20912 ( 30) link_BETA1-4 : bond 0.01961 ( 6) link_BETA1-4 : angle 7.39746 ( 18) hydrogen bonds : bond 0.16230 ( 1474) hydrogen bonds : angle 8.59687 ( 4386) SS BOND : bond 0.00680 ( 46) SS BOND : angle 2.16811 ( 92) covalent geometry : bond 0.00902 (29360) covalent geometry : angle 1.13652 (39664) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 397 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8645 (tm) REVERT: A 365 MET cc_start: 0.8887 (mmm) cc_final: 0.8678 (mmm) REVERT: A 536 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8249 (p) REVERT: A 671 MET cc_start: 0.8239 (mmm) cc_final: 0.8017 (mmt) REVERT: B 246 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8205 (tm) REVERT: B 349 MET cc_start: 0.8658 (mmt) cc_final: 0.8350 (mmt) REVERT: B 453 TRP cc_start: 0.7613 (m-10) cc_final: 0.7310 (m-10) REVERT: B 655 ARG cc_start: 0.8133 (ttm170) cc_final: 0.7547 (tpp80) REVERT: B 659 ASP cc_start: 0.7798 (m-30) cc_final: 0.7235 (m-30) REVERT: B 671 MET cc_start: 0.8791 (mmm) cc_final: 0.8217 (mmt) REVERT: C 26 MET cc_start: 0.8084 (mmt) cc_final: 0.7740 (tpp) REVERT: C 391 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9025 (pt) REVERT: C 464 MET cc_start: 0.8992 (mmt) cc_final: 0.8681 (mmm) REVERT: D 26 MET cc_start: 0.8084 (mmt) cc_final: 0.7849 (mmt) REVERT: D 464 MET cc_start: 0.8743 (mmt) cc_final: 0.8477 (mmm) REVERT: E 175 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7864 (mp) REVERT: E 306 LEU cc_start: 0.6491 (tt) cc_final: 0.6201 (tp) REVERT: F 306 LEU cc_start: 0.6458 (tt) cc_final: 0.6149 (tp) REVERT: F 324 MET cc_start: 0.6831 (tpp) cc_final: 0.5844 (mmp) REVERT: F 335 MET cc_start: 0.7409 (tmm) cc_final: 0.7109 (tmm) outliers start: 40 outliers final: 5 residues processed: 432 average time/residue: 0.4823 time to fit residues: 314.2917 Evaluate side-chains 165 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 3.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain F residue 175 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 277 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 206 optimal weight: 20.0000 chunk 321 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 150 ASN A 186 HIS A 275 ASN A 401 HIS A 483 ASN A 615 ASN A 626 ASN A 715 ASN A 722 ASN A 743 GLN B 148 ASN B 150 ASN B 186 HIS B 275 ASN B 483 ASN B 626 ASN B 640 GLN B 715 ASN B 722 ASN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 ASN C 111 GLN C 207 HIS C 213 ASN C 273 HIS C 300 HIS C 417 ASN C 443 ASN C 451 HIS D 55 ASN D 111 GLN D 207 HIS D 213 ASN D 273 HIS D 300 HIS D 417 ASN D 451 HIS E 212 HIS E 252 ASN E 263 GLN E 273 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 ASN E 428 ASN E 444 ASN E 449 HIS E 456 ASN E 503 ASN E 528 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 ASN F 212 HIS F 252 ASN F 263 GLN F 273 GLN F 319 ASN F 428 ASN F 444 ASN F 456 ASN F 464 HIS F 528 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 ASN ** F 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.108098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.082627 restraints weight = 65920.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.080721 restraints weight = 68264.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.081938 restraints weight = 74019.942| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 29422 Z= 0.250 Angle : 0.775 12.910 39804 Z= 0.407 Chirality : 0.047 0.378 4354 Planarity : 0.005 0.060 5106 Dihedral : 10.223 112.061 4226 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.32 % Allowed : 9.14 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 1.56 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 3560 helix: 0.15 (0.12), residues: 1742 sheet: -1.76 (0.24), residues: 374 loop : -1.94 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 740 HIS 0.013 0.001 HIS F 222 PHE 0.020 0.002 PHE E 462 TYR 0.041 0.002 TYR F 525 ARG 0.007 0.001 ARG E 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 10) link_NAG-ASN : angle 3.21464 ( 30) link_BETA1-4 : bond 0.00947 ( 6) link_BETA1-4 : angle 4.49326 ( 18) hydrogen bonds : bond 0.07522 ( 1474) hydrogen bonds : angle 5.71025 ( 4386) SS BOND : bond 0.00523 ( 46) SS BOND : angle 1.46493 ( 92) covalent geometry : bond 0.00566 (29360) covalent geometry : angle 0.76230 (39664) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 164 time to evaluate : 3.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8750 (tm) REVERT: A 349 MET cc_start: 0.8308 (mmm) cc_final: 0.7934 (mmm) REVERT: A 366 VAL cc_start: 0.9178 (p) cc_final: 0.8935 (t) REVERT: B 246 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8582 (tm) REVERT: B 671 MET cc_start: 0.9080 (mmm) cc_final: 0.8119 (mmt) REVERT: B 756 ILE cc_start: 0.8922 (mm) cc_final: 0.8672 (tt) REVERT: C 391 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8608 (pp) REVERT: D 374 THR cc_start: 0.9500 (OUTLIER) cc_final: 0.9250 (m) REVERT: D 382 MET cc_start: 0.8936 (mtp) cc_final: 0.8621 (ttm) REVERT: D 389 MET cc_start: 0.8144 (ttp) cc_final: 0.7935 (ttp) REVERT: E 175 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7770 (mp) REVERT: F 324 MET cc_start: 0.6678 (tpp) cc_final: 0.6307 (mmp) REVERT: F 335 MET cc_start: 0.7542 (tmm) cc_final: 0.7318 (tmm) REVERT: F 357 MET cc_start: 0.7154 (ptp) cc_final: 0.6673 (ptp) outliers start: 104 outliers final: 48 residues processed: 254 average time/residue: 0.3592 time to fit residues: 153.2863 Evaluate side-chains 179 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 126 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 726 PHE Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 278 LYS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 578 ASP Chi-restraints excluded: chain F residue 581 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.0588 > 50: distance: 19 - 44: 11.534 distance: 25 - 52: 19.829 distance: 30 - 35: 10.889 distance: 35 - 36: 18.141 distance: 36 - 37: 13.874 distance: 36 - 39: 17.803 distance: 37 - 38: 7.936 distance: 37 - 44: 33.858 distance: 39 - 40: 36.632 distance: 40 - 41: 16.158 distance: 41 - 42: 7.243 distance: 41 - 43: 11.071 distance: 44 - 45: 11.349 distance: 45 - 46: 29.465 distance: 45 - 48: 8.086 distance: 46 - 47: 15.831 distance: 46 - 52: 8.835 distance: 48 - 49: 20.270 distance: 49 - 50: 24.685 distance: 49 - 51: 15.643 distance: 52 - 53: 31.035 distance: 53 - 54: 30.274 distance: 53 - 56: 48.728 distance: 54 - 55: 26.394 distance: 54 - 59: 3.386 distance: 56 - 57: 37.250 distance: 56 - 58: 30.470 distance: 59 - 60: 13.342 distance: 60 - 61: 26.754 distance: 61 - 62: 14.193 distance: 61 - 63: 16.870 distance: 63 - 64: 16.462 distance: 64 - 65: 14.418 distance: 65 - 66: 14.670 distance: 65 - 67: 15.814 distance: 67 - 68: 18.937 distance: 68 - 69: 19.319 distance: 69 - 70: 20.313 distance: 69 - 76: 15.563 distance: 71 - 72: 16.565 distance: 72 - 73: 13.897 distance: 73 - 74: 4.258 distance: 74 - 75: 4.309 distance: 76 - 77: 16.661 distance: 77 - 78: 24.001 distance: 77 - 80: 16.913 distance: 78 - 79: 41.615 distance: 78 - 84: 45.377 distance: 80 - 81: 15.537 distance: 81 - 82: 13.517 distance: 81 - 83: 26.877 distance: 84 - 85: 18.617 distance: 84 - 90: 27.464 distance: 85 - 86: 11.177 distance: 85 - 88: 19.972 distance: 86 - 87: 33.677 distance: 86 - 91: 16.823 distance: 88 - 89: 34.559 distance: 89 - 90: 4.259 distance: 91 - 92: 34.672 distance: 92 - 93: 51.993 distance: 92 - 95: 27.352 distance: 93 - 94: 29.755 distance: 93 - 99: 48.376 distance: 94 - 122: 6.902 distance: 95 - 96: 24.506 distance: 96 - 97: 9.814 distance: 96 - 98: 33.534 distance: 99 - 100: 30.987 distance: 99 - 105: 37.645 distance: 100 - 101: 16.274 distance: 100 - 103: 28.048 distance: 101 - 102: 27.557 distance: 101 - 106: 28.208 distance: 102 - 131: 26.018 distance: 103 - 104: 19.662 distance: 104 - 105: 20.436