Starting phenix.real_space_refine on Tue May 13 11:10:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wi6_32526/05_2025/7wi6_32526.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wi6_32526/05_2025/7wi6_32526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wi6_32526/05_2025/7wi6_32526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wi6_32526/05_2025/7wi6_32526.map" model { file = "/net/cci-nas-00/data/ceres_data/7wi6_32526/05_2025/7wi6_32526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wi6_32526/05_2025/7wi6_32526.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 104 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6206 2.51 5 N 1638 2.21 5 O 1786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9696 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 4808 Classifications: {'peptide': 723} Incomplete info: {'truncation_to_alanine': 232} Link IDs: {'PTRANS': 28, 'TRANS': 694} Chain breaks: 6 Unresolved non-hydrogen bonds: 945 Unresolved non-hydrogen angles: 1197 Unresolved non-hydrogen dihedrals: 794 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 12, 'ASN:plan1': 13, 'TRP:plan': 5, 'ASP:plan': 28, 'PHE:plan': 11, 'GLU:plan': 30, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 608 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 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 Restraints were copied for chains: B Time building chain proxies: 9.58, per 1000 atoms: 0.99 Number of scatterers: 9696 At special positions: 0 Unit cell: (95.95, 97.97, 181.8, 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 66 16.00 O 1786 8.00 N 1638 7.00 C 6206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 527 " distance=2.03 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 373 " distance=2.02 Simple disulfide: pdb=" SG CYS A 412 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 509 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 513 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 546 " distance=2.04 Simple disulfide: pdb=" SG CYS A 549 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 373 " distance=2.02 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 509 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 513 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 546 " distance=2.04 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 562 " 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 NAG-ASN " NAG A 902 " - " ASN A 209 " " NAG B 902 " - " ASN B 209 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.5 seconds 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2732 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 32.4% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 65 through 80 removed outlier: 4.073A pdb=" N ALA A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 removed outlier: 4.508A pdb=" N GLU A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.568A pdb=" N SER A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 238 removed outlier: 4.748A pdb=" N GLU A 231 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLN A 232 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ARG A 235 " --> pdb=" O GLN A 232 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU A 236 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN A 238 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.929A pdb=" N ASP A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 399 through 409 removed outlier: 4.383A pdb=" N HIS A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 removed outlier: 3.925A pdb=" N LYS A 423 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.950A pdb=" N ASP A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 577 through 588 removed outlier: 3.864A pdb=" N VAL A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 598 removed outlier: 3.623A pdb=" N VAL A 597 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 Processing helix chain 'A' and resid 615 through 625 removed outlier: 4.243A pdb=" N GLY A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 624 " --> pdb=" O PHE A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 632 removed outlier: 5.996A pdb=" N THR A 629 " --> pdb=" O TYR A 626 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 631 " --> pdb=" O MET A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 646 removed outlier: 3.681A pdb=" N ARG A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 657 through 665 removed outlier: 3.773A pdb=" N THR A 661 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LYS A 662 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N THR A 663 " --> pdb=" O LEU A 660 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 664 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS A 665 " --> pdb=" O LYS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 699 removed outlier: 3.820A pdb=" N LEU A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN A 699 " --> pdb=" O LEU A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.529A pdb=" N ILE A 746 " --> pdb=" O TYR A 743 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 747 " --> pdb=" O ASP A 744 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 748 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 776 removed outlier: 3.606A pdb=" N MET A 775 " --> pdb=" O GLY A 772 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR A 776 " --> pdb=" O PHE A 773 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 772 through 776' Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 786 through 792 removed outlier: 4.046A pdb=" N TYR A 790 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 792 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 802 removed outlier: 4.078A pdb=" N THR A 802 " --> pdb=" O VAL A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 811 Processing helix chain 'A' and resid 816 through 820 removed outlier: 3.649A pdb=" N PHE A 819 " --> pdb=" O GLY A 816 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 820 " --> pdb=" O CYS A 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 816 through 820' Processing helix chain 'B' and resid 65 through 80 removed outlier: 4.074A pdb=" N ALA B 71 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 removed outlier: 4.508A pdb=" N GLU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.569A pdb=" N SER B 179 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 238 removed outlier: 4.749A pdb=" N GLU B 231 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN B 232 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ARG B 235 " --> pdb=" O GLN B 232 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 236 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN B 238 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.928A pdb=" N ASP B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B 338 " --> pdb=" O ASP B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 399 through 409 removed outlier: 4.383A pdb=" N HIS B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 423 removed outlier: 3.924A pdb=" N LYS B 423 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 removed outlier: 3.951A pdb=" N ASP B 433 " --> pdb=" O LYS B 429 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU B 435 " --> pdb=" O TYR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 Processing helix chain 'B' and resid 577 through 588 removed outlier: 3.864A pdb=" N VAL B 581 " --> pdb=" O ALA B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 598 removed outlier: 3.622A pdb=" N VAL B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 608 Processing helix chain 'B' and resid 615 through 625 removed outlier: 4.244A pdb=" N GLY B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 624 " --> pdb=" O PHE B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 632 removed outlier: 5.996A pdb=" N THR B 629 " --> pdb=" O TYR B 626 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 631 " --> pdb=" O MET B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 646 removed outlier: 3.681A pdb=" N ARG B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 654 Processing helix chain 'B' and resid 657 through 665 removed outlier: 3.774A pdb=" N THR B 661 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LYS B 662 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N THR B 663 " --> pdb=" O LEU B 660 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN B 664 " --> pdb=" O THR B 661 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS B 665 " --> pdb=" O LYS B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 699 removed outlier: 3.820A pdb=" N LEU B 695 " --> pdb=" O ILE B 691 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN B 699 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 709 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.528A pdb=" N ILE B 746 " --> pdb=" O TYR B 743 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 747 " --> pdb=" O ASP B 744 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 748 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 776 removed outlier: 3.606A pdb=" N MET B 775 " --> pdb=" O GLY B 772 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR B 776 " --> pdb=" O PHE B 773 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 772 through 776' Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'B' and resid 786 through 792 removed outlier: 4.046A pdb=" N TYR B 790 " --> pdb=" O LEU B 786 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR B 792 " --> pdb=" O ILE B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 802 removed outlier: 4.078A pdb=" N THR B 802 " --> pdb=" O VAL B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 811 Processing helix chain 'B' and resid 816 through 820 removed outlier: 3.649A pdb=" N PHE B 819 " --> pdb=" O GLY B 816 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA B 820 " --> pdb=" O CYS B 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 816 through 820' Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 3.710A pdb=" N ILE A 33 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A 39 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N HIS A 94 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 41 " --> pdb=" O HIS A 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU A 96 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY A 43 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ILE A 146 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY A 42 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 218 removed outlier: 5.946A pdb=" N VAL A 213 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR A 243 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 245 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL A 247 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 274 removed outlier: 3.779A pdb=" N VAL A 272 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TRP A 297 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N LEU A 323 " --> pdb=" O TRP A 297 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA A 299 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N LEU A 325 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 484 through 485 removed outlier: 3.744A pdb=" N HIS A 485 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.367A pdb=" N THR A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 718 through 720 Processing sheet with id=AA7, first strand: chain 'B' and resid 33 through 35 removed outlier: 3.710A pdb=" N ILE B 33 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 39 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N HIS B 94 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 41 " --> pdb=" O HIS B 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU B 96 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY B 43 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ILE B 146 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLY B 42 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 145 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 212 through 218 removed outlier: 5.947A pdb=" N VAL B 213 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR B 243 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 245 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL B 247 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 271 through 274 removed outlier: 3.777A pdb=" N VAL B 272 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP B 297 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N LEU B 323 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ALA B 299 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N LEU B 325 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 484 through 485 removed outlier: 3.744A pdb=" N HIS B 485 " --> pdb=" O SER B 491 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.368A pdb=" N THR B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 718 through 720 210 hydrogen bonds defined for protein. 516 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: 2.63 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2487 1.33 - 1.45: 2165 1.45 - 1.58: 5148 1.58 - 1.70: 2 1.70 - 1.82: 84 Bond restraints: 9886 Sorted by residual: bond pdb=" CAT Z99 B 901 " pdb=" OAP Z99 B 901 " ideal model delta sigma weight residual 1.364 1.492 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" CAT Z99 A 901 " pdb=" OAP Z99 A 901 " ideal model delta sigma weight residual 1.364 1.492 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" CAS Z99 A 901 " pdb=" OAP Z99 A 901 " ideal model delta sigma weight residual 1.369 1.494 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" CAS Z99 B 901 " pdb=" OAP Z99 B 901 " ideal model delta sigma weight residual 1.369 1.493 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C LEU B 340 " pdb=" N ASN B 341 " ideal model delta sigma weight residual 1.331 1.264 0.067 2.07e-02 2.33e+03 1.04e+01 ... (remaining 9881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 12511 1.69 - 3.38: 856 3.38 - 5.07: 161 5.07 - 6.76: 26 6.76 - 8.45: 26 Bond angle restraints: 13580 Sorted by residual: angle pdb=" N ILE A 155 " pdb=" CA ILE A 155 " pdb=" C ILE A 155 " ideal model delta sigma weight residual 113.20 105.06 8.14 9.60e-01 1.09e+00 7.20e+01 angle pdb=" N ILE B 155 " pdb=" CA ILE B 155 " pdb=" C ILE B 155 " ideal model delta sigma weight residual 113.20 105.10 8.10 9.60e-01 1.09e+00 7.12e+01 angle pdb=" C GLY A 713 " pdb=" N THR A 714 " pdb=" CA THR A 714 " ideal model delta sigma weight residual 122.46 128.34 -5.88 1.41e+00 5.03e-01 1.74e+01 angle pdb=" C GLY B 713 " pdb=" N THR B 714 " pdb=" CA THR B 714 " ideal model delta sigma weight residual 122.46 128.25 -5.79 1.41e+00 5.03e-01 1.69e+01 angle pdb=" N VAL B 701 " pdb=" CA VAL B 701 " pdb=" C VAL B 701 " ideal model delta sigma weight residual 113.20 109.32 3.88 9.60e-01 1.09e+00 1.63e+01 ... (remaining 13575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.34: 5244 18.34 - 36.67: 488 36.67 - 55.01: 98 55.01 - 73.34: 12 73.34 - 91.68: 18 Dihedral angle restraints: 5860 sinusoidal: 1654 harmonic: 4206 Sorted by residual: dihedral pdb=" CB CYS B 513 " pdb=" SG CYS B 513 " pdb=" SG CYS B 531 " pdb=" CB CYS B 531 " ideal model delta sinusoidal sigma weight residual -86.00 -169.15 83.15 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS A 513 " pdb=" SG CYS A 513 " pdb=" SG CYS A 531 " pdb=" CB CYS A 531 " ideal model delta sinusoidal sigma weight residual -86.00 -169.13 83.13 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CB CYS B 534 " pdb=" SG CYS B 534 " pdb=" SG CYS B 546 " pdb=" CB CYS B 546 " ideal model delta sinusoidal sigma weight residual 93.00 170.72 -77.72 1 1.00e+01 1.00e-02 7.56e+01 ... (remaining 5857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1410 0.077 - 0.153: 250 0.153 - 0.230: 14 0.230 - 0.307: 8 0.307 - 0.383: 6 Chirality restraints: 1688 Sorted by residual: chirality pdb=" CAW Z99 B 901 " pdb=" CAN Z99 B 901 " pdb=" CAU Z99 B 901 " pdb=" CAV Z99 B 901 " both_signs ideal model delta sigma weight residual False 2.61 2.23 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CAW Z99 A 901 " pdb=" CAN Z99 A 901 " pdb=" CAU Z99 A 901 " pdb=" CAV Z99 A 901 " both_signs ideal model delta sigma weight residual False 2.61 2.23 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CAY Z99 B 901 " pdb=" CAN Z99 B 901 " pdb=" CAR Z99 B 901 " pdb=" CAZ Z99 B 901 " both_signs ideal model delta sigma weight residual False -2.97 -2.62 -0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 1685 not shown) Planarity restraints: 1738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 146 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.88e+00 pdb=" C ILE B 146 " -0.049 2.00e-02 2.50e+03 pdb=" O ILE B 146 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY B 147 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 146 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.83e+00 pdb=" C ILE A 146 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE A 146 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY A 147 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 390 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C ILE A 390 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE A 390 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 391 " -0.014 2.00e-02 2.50e+03 ... (remaining 1735 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3322 2.81 - 3.33: 8182 3.33 - 3.86: 14819 3.86 - 4.38: 15446 4.38 - 4.90: 26121 Nonbonded interactions: 67890 Sorted by model distance: nonbonded pdb=" OE1 GLN B 165 " pdb=" OH TYR B 186 " model vdw 2.290 3.040 nonbonded pdb=" OE1 GLN A 165 " pdb=" OH TYR A 186 " model vdw 2.290 3.040 nonbonded pdb=" O SER B 179 " pdb=" OG SER B 179 " model vdw 2.295 3.040 nonbonded pdb=" O SER A 179 " pdb=" OG SER A 179 " model vdw 2.295 3.040 nonbonded pdb=" O THR A 296 " pdb=" OG1 THR A 296 " model vdw 2.298 3.040 ... (remaining 67885 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.920 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 0.128 9902 Z= 0.418 Angle : 1.035 11.779 13614 Z= 0.558 Chirality : 0.063 0.383 1688 Planarity : 0.006 0.056 1736 Dihedral : 15.694 91.675 3086 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.46 % Favored : 85.54 % Rotamer: Outliers : 1.54 % Allowed : 14.10 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.21 (0.16), residues: 1418 helix: -4.83 (0.09), residues: 512 sheet: -3.65 (0.35), residues: 154 loop : -3.75 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 297 HIS 0.007 0.002 HIS B 498 PHE 0.025 0.002 PHE B 456 TYR 0.021 0.002 TYR A 434 ARG 0.005 0.001 ARG B 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 2) link_NAG-ASN : angle 8.43257 ( 6) hydrogen bonds : bond 0.29210 ( 210) hydrogen bonds : angle 11.16083 ( 516) SS BOND : bond 0.00601 ( 14) SS BOND : angle 2.10475 ( 28) covalent geometry : bond 0.00916 ( 9886) covalent geometry : angle 1.01700 (13580) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 1.059 Fit side-chains REVERT: A 266 LYS cc_start: 0.8849 (mptt) cc_final: 0.8628 (mptt) REVERT: B 266 LYS cc_start: 0.8826 (mptt) cc_final: 0.8600 (mptt) REVERT: B 754 TYR cc_start: 0.6736 (t80) cc_final: 0.5443 (t80) outliers start: 12 outliers final: 4 residues processed: 110 average time/residue: 0.1836 time to fit residues: 30.0385 Evaluate side-chains 87 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 747 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 0.0670 chunk 37 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 58 optimal weight: 0.0010 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 overall best weight: 0.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 156 GLN A 386 GLN B 108 GLN B 156 GLN B 386 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.156998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.098068 restraints weight = 17286.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.100604 restraints weight = 9506.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.102294 restraints weight = 6607.023| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9902 Z= 0.118 Angle : 0.633 8.144 13614 Z= 0.341 Chirality : 0.042 0.165 1688 Planarity : 0.004 0.038 1736 Dihedral : 10.495 95.272 1598 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 1.79 % Allowed : 21.03 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.53 (0.18), residues: 1418 helix: -4.13 (0.13), residues: 496 sheet: -3.37 (0.37), residues: 154 loop : -3.47 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 297 HIS 0.003 0.001 HIS A 498 PHE 0.009 0.001 PHE B 620 TYR 0.018 0.001 TYR B 434 ARG 0.004 0.000 ARG A 162 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 2) link_NAG-ASN : angle 5.41174 ( 6) hydrogen bonds : bond 0.04093 ( 210) hydrogen bonds : angle 6.43459 ( 516) SS BOND : bond 0.00357 ( 14) SS BOND : angle 1.57897 ( 28) covalent geometry : bond 0.00262 ( 9886) covalent geometry : angle 0.61905 (13580) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 1.132 Fit side-chains REVERT: A 340 LEU cc_start: 0.9505 (mm) cc_final: 0.9256 (mm) REVERT: A 355 TRP cc_start: 0.8991 (t-100) cc_final: 0.8146 (t-100) REVERT: A 391 MET cc_start: 0.8393 (tmm) cc_final: 0.8150 (tmm) REVERT: B 340 LEU cc_start: 0.9496 (mm) cc_final: 0.9258 (mm) REVERT: B 355 TRP cc_start: 0.8967 (t-100) cc_final: 0.8106 (t-100) REVERT: B 391 MET cc_start: 0.8388 (tmm) cc_final: 0.8144 (tmm) REVERT: B 754 TYR cc_start: 0.6487 (t80) cc_final: 0.5093 (t80) outliers start: 14 outliers final: 8 residues processed: 103 average time/residue: 0.1802 time to fit residues: 28.5462 Evaluate side-chains 81 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 95 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 0.4980 chunk 48 optimal weight: 20.0000 chunk 126 optimal weight: 0.0970 chunk 124 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 101 optimal weight: 0.0000 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS B 402 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.156179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.096598 restraints weight = 17478.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099068 restraints weight = 9620.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.100707 restraints weight = 6730.537| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9902 Z= 0.145 Angle : 0.596 6.807 13614 Z= 0.319 Chirality : 0.043 0.173 1688 Planarity : 0.004 0.036 1736 Dihedral : 10.141 96.251 1596 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 4.10 % Allowed : 22.05 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.05 (0.19), residues: 1418 helix: -3.63 (0.16), residues: 522 sheet: -3.00 (0.41), residues: 112 loop : -3.28 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 529 HIS 0.003 0.001 HIS A 485 PHE 0.010 0.001 PHE A 456 TYR 0.020 0.001 TYR B 434 ARG 0.004 0.000 ARG B 162 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 2) link_NAG-ASN : angle 4.68127 ( 6) hydrogen bonds : bond 0.03716 ( 210) hydrogen bonds : angle 5.59786 ( 516) SS BOND : bond 0.00423 ( 14) SS BOND : angle 1.42357 ( 28) covalent geometry : bond 0.00331 ( 9886) covalent geometry : angle 0.58515 (13580) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 1.119 Fit side-chains REVERT: A 194 ASP cc_start: 0.8460 (m-30) cc_final: 0.8195 (m-30) REVERT: A 407 MET cc_start: 0.7953 (tpp) cc_final: 0.7523 (tpt) REVERT: B 194 ASP cc_start: 0.8456 (m-30) cc_final: 0.8181 (m-30) REVERT: B 407 MET cc_start: 0.7864 (tpp) cc_final: 0.7378 (tpt) outliers start: 32 outliers final: 10 residues processed: 108 average time/residue: 0.1575 time to fit residues: 26.8146 Evaluate side-chains 86 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 86 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 106 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.156486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.097016 restraints weight = 17138.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099469 restraints weight = 9495.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.101117 restraints weight = 6655.167| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9902 Z= 0.134 Angle : 0.571 6.755 13614 Z= 0.302 Chirality : 0.042 0.160 1688 Planarity : 0.004 0.037 1736 Dihedral : 9.847 96.516 1594 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.21 % Allowed : 24.62 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.20), residues: 1418 helix: -3.30 (0.18), residues: 510 sheet: -2.97 (0.40), residues: 132 loop : -3.05 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 529 HIS 0.002 0.001 HIS A 485 PHE 0.009 0.001 PHE B 456 TYR 0.021 0.001 TYR A 434 ARG 0.003 0.000 ARG A 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 2) link_NAG-ASN : angle 4.48250 ( 6) hydrogen bonds : bond 0.03255 ( 210) hydrogen bonds : angle 5.26577 ( 516) SS BOND : bond 0.00329 ( 14) SS BOND : angle 1.33678 ( 28) covalent geometry : bond 0.00312 ( 9886) covalent geometry : angle 0.56061 (13580) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 1.006 Fit side-chains REVERT: A 407 MET cc_start: 0.7657 (tpp) cc_final: 0.7224 (tpt) REVERT: B 407 MET cc_start: 0.7657 (tpp) cc_final: 0.7261 (tpt) outliers start: 25 outliers final: 22 residues processed: 109 average time/residue: 0.1394 time to fit residues: 24.8697 Evaluate side-chains 97 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 TRP Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 498 HIS Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 69 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 30.0000 chunk 130 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.158581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.100784 restraints weight = 17308.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.103309 restraints weight = 9424.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.104955 restraints weight = 6519.818| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9902 Z= 0.122 Angle : 0.558 7.344 13614 Z= 0.292 Chirality : 0.042 0.143 1688 Planarity : 0.004 0.037 1736 Dihedral : 9.568 97.050 1594 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 3.59 % Allowed : 24.36 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.20), residues: 1418 helix: -3.10 (0.19), residues: 506 sheet: -2.71 (0.42), residues: 132 loop : -2.80 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 529 HIS 0.002 0.001 HIS B 498 PHE 0.010 0.001 PHE B 632 TYR 0.015 0.001 TYR B 434 ARG 0.003 0.000 ARG A 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 2) link_NAG-ASN : angle 4.35365 ( 6) hydrogen bonds : bond 0.02991 ( 210) hydrogen bonds : angle 4.99940 ( 516) SS BOND : bond 0.00336 ( 14) SS BOND : angle 1.23407 ( 28) covalent geometry : bond 0.00285 ( 9886) covalent geometry : angle 0.54839 (13580) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 1.131 Fit side-chains REVERT: A 407 MET cc_start: 0.7696 (tpp) cc_final: 0.7160 (tpt) REVERT: B 407 MET cc_start: 0.7752 (tpp) cc_final: 0.7238 (tpt) outliers start: 28 outliers final: 21 residues processed: 110 average time/residue: 0.1688 time to fit residues: 29.6807 Evaluate side-chains 100 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 TRP Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 498 HIS Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 108 optimal weight: 3.9990 chunk 132 optimal weight: 0.0050 chunk 76 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 0.0030 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 142 optimal weight: 0.0020 chunk 80 optimal weight: 0.8980 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN B 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.168885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.110678 restraints weight = 17094.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.113493 restraints weight = 9112.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.115282 restraints weight = 6240.162| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9902 Z= 0.087 Angle : 0.529 6.773 13614 Z= 0.277 Chirality : 0.041 0.175 1688 Planarity : 0.003 0.035 1736 Dihedral : 8.961 97.738 1594 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.95 % Allowed : 25.13 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.21), residues: 1418 helix: -2.88 (0.20), residues: 504 sheet: -2.42 (0.43), residues: 146 loop : -2.63 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 529 HIS 0.003 0.001 HIS A 498 PHE 0.007 0.001 PHE A 632 TYR 0.012 0.001 TYR B 434 ARG 0.003 0.000 ARG A 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 2) link_NAG-ASN : angle 4.21874 ( 6) hydrogen bonds : bond 0.02488 ( 210) hydrogen bonds : angle 4.64264 ( 516) SS BOND : bond 0.00335 ( 14) SS BOND : angle 1.05329 ( 28) covalent geometry : bond 0.00200 ( 9886) covalent geometry : angle 0.52010 (13580) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.180 Fit side-chains REVERT: A 407 MET cc_start: 0.7841 (tpp) cc_final: 0.7365 (tpt) REVERT: B 355 TRP cc_start: 0.9081 (t-100) cc_final: 0.8418 (t-100) REVERT: B 407 MET cc_start: 0.7838 (tpp) cc_final: 0.7410 (tpt) outliers start: 23 outliers final: 16 residues processed: 108 average time/residue: 0.1497 time to fit residues: 25.5654 Evaluate side-chains 95 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 TRP Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 498 HIS Chi-restraints excluded: chain B residue 732 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 68.0255 > 50: distance: 107 - 113: 16.327 distance: 113 - 114: 20.460 distance: 114 - 115: 20.924 distance: 114 - 117: 45.934 distance: 115 - 116: 33.446 distance: 115 - 118: 15.250 distance: 118 - 119: 14.724 distance: 119 - 120: 17.235 distance: 119 - 122: 48.106 distance: 120 - 121: 14.356 distance: 120 - 124: 19.293 distance: 122 - 123: 10.928 distance: 124 - 125: 7.455 distance: 125 - 126: 15.789 distance: 125 - 128: 12.499 distance: 126 - 135: 7.817 distance: 128 - 129: 3.938 distance: 129 - 130: 15.927 distance: 130 - 131: 5.785 distance: 131 - 132: 3.908 distance: 132 - 133: 12.024 distance: 132 - 134: 5.820 distance: 135 - 136: 12.666 distance: 136 - 137: 34.157 distance: 136 - 139: 7.692 distance: 137 - 138: 13.973 distance: 137 - 147: 31.554 distance: 139 - 140: 18.000 distance: 140 - 141: 4.949 distance: 140 - 142: 13.113 distance: 141 - 143: 8.659 distance: 142 - 144: 8.741 distance: 143 - 145: 14.351 distance: 144 - 145: 8.910 distance: 145 - 146: 13.885 distance: 147 - 148: 4.461 distance: 148 - 149: 9.220 distance: 148 - 151: 13.924 distance: 149 - 150: 12.308 distance: 152 - 153: 16.015 distance: 153 - 154: 14.825 distance: 153 - 156: 6.714 distance: 154 - 155: 15.354 distance: 154 - 164: 6.187 distance: 156 - 157: 8.250 distance: 157 - 158: 6.213 distance: 157 - 159: 5.451 distance: 158 - 160: 6.895 distance: 159 - 161: 10.091 distance: 160 - 162: 4.830 distance: 161 - 162: 5.737 distance: 162 - 163: 4.856 distance: 164 - 165: 6.252 distance: 165 - 166: 13.587 distance: 165 - 168: 13.783 distance: 166 - 167: 15.225 distance: 166 - 175: 9.443 distance: 168 - 169: 10.460 distance: 169 - 170: 14.466 distance: 169 - 171: 4.811 distance: 170 - 172: 5.924 distance: 171 - 173: 9.325 distance: 172 - 174: 5.769 distance: 173 - 174: 13.673 distance: 175 - 176: 4.087 distance: 176 - 177: 31.722 distance: 176 - 179: 34.831 distance: 177 - 178: 11.016 distance: 177 - 180: 33.378 distance: 180 - 181: 11.399 distance: 181 - 182: 14.302 distance: 181 - 184: 14.286 distance: 182 - 183: 11.331 distance: 182 - 191: 12.825 distance: 184 - 185: 4.941 distance: 185 - 186: 22.347 distance: 186 - 187: 17.284 distance: 187 - 188: 10.747 distance: 188 - 189: 16.110 distance: 188 - 190: 17.197 distance: 191 - 192: 8.127 distance: 192 - 193: 15.550 distance: 192 - 195: 12.274 distance: 193 - 194: 12.852 distance: 193 - 198: 11.317 distance: 195 - 196: 9.001 distance: 195 - 197: 23.903