Starting phenix.real_space_refine on Sun May 3 10:09:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0b_37973/05_2026/8x0b_37973.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0b_37973/05_2026/8x0b_37973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x0b_37973/05_2026/8x0b_37973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0b_37973/05_2026/8x0b_37973.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x0b_37973/05_2026/8x0b_37973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0b_37973/05_2026/8x0b_37973.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.028 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: 5 Type Number sf(0) Gaussians S 118 5.16 5 C 7964 2.51 5 N 2056 2.21 5 O 2275 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12415 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6140 Classifications: {'peptide': 780} Link IDs: {'PTRANS': 33, 'TRANS': 746} Chain breaks: 1 Chain: "B" Number of atoms: 6140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6140 Classifications: {'peptide': 780} Link IDs: {'PTRANS': 33, 'TRANS': 746} Chain breaks: 1 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'NAG': 1, 'QUS': 1, 'XQT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'NAG': 1, 'QUS': 1, 'XQT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 2.68, per 1000 atoms: 0.22 Number of scatterers: 12415 At special positions: 0 Unit cell: (103.32, 83.16, 183.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 118 16.00 F 2 9.00 O 2275 8.00 N 2056 7.00 C 7964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.08 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 278 " distance=2.05 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.04 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.02 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.04 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.02 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.04 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 278 " distance=2.06 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.02 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.04 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.04 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 901 " - " ASN A 210 " " NAG B 901 " - " ASN B 210 " Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 553.7 milliseconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 16 sheets defined 47.4% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 65 through 82 removed outlier: 3.735A pdb=" N GLU A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 113 Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.674A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.523A pdb=" N ASP A 181 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 222 through 239 removed outlier: 3.855A pdb=" N GLU A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 317 through 322 removed outlier: 3.803A pdb=" N ALA A 321 " --> pdb=" O TYR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.794A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 396 through 419 removed outlier: 4.081A pdb=" N VAL A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 577 through 602 Processing helix chain 'A' and resid 614 through 636 removed outlier: 3.675A pdb=" N THR A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 675 removed outlier: 3.642A pdb=" N LEU A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG A 648 " --> pdb=" O CYS A 644 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE A 649 " --> pdb=" O TYR A 645 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 3.518A pdb=" N TYR A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 673 " --> pdb=" O ILE A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 715 removed outlier: 3.626A pdb=" N VAL A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 762 removed outlier: 3.556A pdb=" N VAL A 740 " --> pdb=" O THR A 736 " (cutoff:3.500A) Proline residue: A 743 - end of helix Processing helix chain 'A' and resid 769 through 788 removed outlier: 3.529A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 797 through 817 Processing helix chain 'A' and resid 818 through 824 removed outlier: 3.608A pdb=" N TYR A 823 " --> pdb=" O VAL A 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 removed outlier: 3.802A pdb=" N GLU B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.721A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 176 through 181 removed outlier: 3.507A pdb=" N ASP B 181 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 209 removed outlier: 3.566A pdb=" N TYR B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 239 removed outlier: 3.881A pdb=" N GLU B 238 " --> pdb=" O MET B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 317 through 322 removed outlier: 3.760A pdb=" N ALA B 321 " --> pdb=" O TYR B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 342 removed outlier: 3.794A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR B 340 " --> pdb=" O TRP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 363 Processing helix chain 'B' and resid 396 through 419 Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.749A pdb=" N LYS B 430 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 560 through 563 removed outlier: 3.501A pdb=" N THR B 563 " --> pdb=" O ASP B 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 560 through 563' Processing helix chain 'B' and resid 577 through 604 removed outlier: 3.783A pdb=" N ILE B 581 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 582 " --> pdb=" O PRO B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 634 removed outlier: 5.441A pdb=" N LEU B 622 " --> pdb=" O CYS B 618 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 679 removed outlier: 3.596A pdb=" N TYR B 645 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG B 648 " --> pdb=" O CYS B 644 " (cutoff:3.500A) Proline residue: B 655 - end of helix removed outlier: 4.276A pdb=" N ARG B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU B 673 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 676 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS B 678 " --> pdb=" O ALA B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 715 removed outlier: 4.446A pdb=" N VAL B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 762 removed outlier: 3.757A pdb=" N ALA B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Proline residue: B 743 - end of helix Processing helix chain 'B' and resid 769 through 788 removed outlier: 4.407A pdb=" N TYR B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 783 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 786 " --> pdb=" O CYS B 782 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE B 788 " --> pdb=" O ILE B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 removed outlier: 4.377A pdb=" N GLY B 794 " --> pdb=" O PRO B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 815 Processing helix chain 'B' and resid 817 through 824 removed outlier: 4.240A pdb=" N LYS B 821 " --> pdb=" O MET B 817 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE B 824 " --> pdb=" O PRO B 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.044A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLU A 94 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE A 36 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY A 145 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 248 removed outlier: 8.291A pdb=" N VAL A 214 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N SER A 245 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA A 216 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LYS A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N HIS A 218 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TYR A 213 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ALA A 275 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER A 215 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 277 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 217 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 274 " --> pdb=" O LEU A 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 329 removed outlier: 6.743A pdb=" N TYR A 466 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER A 486 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE A 468 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 523 Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 545 removed outlier: 3.898A pdb=" N PHE A 544 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N THR A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA8, first strand: chain 'A' and resid 719 through 720 Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.352A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE B 36 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY B 145 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLN B 169 " --> pdb=" O MET B 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 241 through 248 removed outlier: 8.026A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LYS B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N HIS B 218 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N TYR B 213 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ALA B 275 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER B 215 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE B 277 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL B 217 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 274 " --> pdb=" O LEU B 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 329 removed outlier: 6.738A pdb=" N TYR B 466 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER B 486 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 468 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 445 through 447 Processing sheet with id=AB4, first strand: chain 'B' and resid 523 through 524 Processing sheet with id=AB5, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AB6, first strand: chain 'B' and resid 557 through 558 Processing sheet with id=AB7, first strand: chain 'B' and resid 719 through 720 551 hydrogen bonds defined for protein. 1608 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: 2.03 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2059 1.32 - 1.45: 3397 1.45 - 1.58: 7040 1.58 - 1.71: 0 1.71 - 1.84: 170 Bond restraints: 12666 Sorted by residual: bond pdb=" CA SER B 462 " pdb=" CB SER B 462 " ideal model delta sigma weight residual 1.537 1.501 0.036 1.38e-02 5.25e+03 6.88e+00 bond pdb=" CA SER B 795 " pdb=" CB SER B 795 " ideal model delta sigma weight residual 1.538 1.507 0.032 1.22e-02 6.72e+03 6.70e+00 bond pdb=" CA SER A 462 " pdb=" CB SER A 462 " ideal model delta sigma weight residual 1.537 1.503 0.034 1.38e-02 5.25e+03 6.02e+00 bond pdb=" CA PRO A 685 " pdb=" CB PRO A 685 " ideal model delta sigma weight residual 1.531 1.546 -0.014 6.20e-03 2.60e+04 5.44e+00 bond pdb=" CA ALA A 39 " pdb=" CB ALA A 39 " ideal model delta sigma weight residual 1.534 1.492 0.041 1.78e-02 3.16e+03 5.36e+00 ... (remaining 12661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 16316 2.07 - 4.15: 817 4.15 - 6.22: 20 6.22 - 8.30: 3 8.30 - 10.37: 2 Bond angle restraints: 17158 Sorted by residual: angle pdb=" N PRO A 716 " pdb=" CA PRO A 716 " pdb=" CB PRO A 716 " ideal model delta sigma weight residual 103.22 105.90 -2.68 5.20e-01 3.70e+00 2.65e+01 angle pdb=" N VAL A 819 " pdb=" CA VAL A 819 " pdb=" CB VAL A 819 " ideal model delta sigma weight residual 110.52 113.71 -3.19 6.70e-01 2.23e+00 2.26e+01 angle pdb=" N TYR B 619 " pdb=" CA TYR B 619 " pdb=" C TYR B 619 " ideal model delta sigma weight residual 113.18 107.93 5.25 1.33e+00 5.65e-01 1.56e+01 angle pdb=" CA ASP B 195 " pdb=" CB ASP B 195 " pdb=" CG ASP B 195 " ideal model delta sigma weight residual 112.60 116.11 -3.51 1.00e+00 1.00e+00 1.23e+01 angle pdb=" C03 QUS B 902 " pdb=" N14 QUS B 902 " pdb=" O20 QUS B 902 " ideal model delta sigma weight residual 112.77 123.14 -10.37 3.00e+00 1.11e-01 1.19e+01 ... (remaining 17153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 7400 35.21 - 70.41: 234 70.41 - 105.62: 22 105.62 - 140.83: 3 140.83 - 176.04: 1 Dihedral angle restraints: 7660 sinusoidal: 3118 harmonic: 4542 Sorted by residual: dihedral pdb=" CB CYS A 57 " pdb=" SG CYS A 57 " pdb=" SG CYS A 99 " pdb=" CB CYS A 99 " ideal model delta sinusoidal sigma weight residual -86.00 2.95 -88.95 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS B 644 " pdb=" SG CYS B 644 " pdb=" SG CYS B 733 " pdb=" CB CYS B 733 " ideal model delta sinusoidal sigma weight residual -86.00 -168.09 82.09 1 1.00e+01 1.00e-02 8.28e+01 dihedral pdb=" CB CYS B 515 " pdb=" SG CYS B 515 " pdb=" SG CYS B 534 " pdb=" CB CYS B 534 " ideal model delta sinusoidal sigma weight residual 93.00 167.63 -74.63 1 1.00e+01 1.00e-02 7.06e+01 ... (remaining 7657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1582 0.093 - 0.187: 331 0.187 - 0.280: 5 0.280 - 0.374: 1 0.374 - 0.467: 1 Chirality restraints: 1920 Sorted by residual: chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 210 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 210 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C2 XQT B 903 " pdb=" C1 XQT B 903 " pdb=" C3 XQT B 903 " pdb=" N1 XQT B 903 " both_signs ideal model delta sigma weight residual False 2.66 2.44 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1917 not shown) Planarity restraints: 2158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 XQT B 903 " 0.076 2.00e-02 2.50e+03 6.32e-02 5.00e+01 pdb=" C6 XQT B 903 " -0.029 2.00e-02 2.50e+03 pdb=" C7 XQT B 903 " 0.061 2.00e-02 2.50e+03 pdb=" N1 XQT B 903 " -0.098 2.00e-02 2.50e+03 pdb=" O2 XQT B 903 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 901 " -0.048 2.00e-02 2.50e+03 3.93e-02 1.93e+01 pdb=" C7 NAG B 901 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG B 901 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG B 901 " 0.063 2.00e-02 2.50e+03 pdb=" O7 NAG B 901 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 XQT B 903 " -0.041 2.00e-02 2.50e+03 2.01e-02 9.07e+00 pdb=" C12 XQT B 903 " 0.029 2.00e-02 2.50e+03 pdb=" C13 XQT B 903 " 0.023 2.00e-02 2.50e+03 pdb=" C14 XQT B 903 " 0.012 2.00e-02 2.50e+03 pdb=" C15 XQT B 903 " -0.002 2.00e-02 2.50e+03 pdb=" C16 XQT B 903 " -0.015 2.00e-02 2.50e+03 pdb=" C17 XQT B 903 " -0.009 2.00e-02 2.50e+03 pdb=" C18 XQT B 903 " 0.009 2.00e-02 2.50e+03 pdb=" F1 XQT B 903 " -0.005 2.00e-02 2.50e+03 ... (remaining 2155 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 476 2.71 - 3.26: 12762 3.26 - 3.81: 19984 3.81 - 4.35: 25918 4.35 - 4.90: 42142 Nonbonded interactions: 101282 Sorted by model distance: nonbonded pdb=" O TYR B 629 " pdb=" OG1 THR B 632 " model vdw 2.166 3.040 nonbonded pdb=" OE1 GLN B 519 " pdb=" O CYS B 537 " model vdw 2.201 3.040 nonbonded pdb=" O LYS A 263 " pdb=" OG SER A 266 " model vdw 2.212 3.040 nonbonded pdb=" OG SER B 331 " pdb=" O SER B 395 " model vdw 2.214 3.040 nonbonded pdb=" O ALA B 656 " pdb=" OG SER B 660 " model vdw 2.232 3.040 ... (remaining 101277 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: 0.02 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.960 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.550 Find NCS groups from input model: 0.230 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 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 : 0.007 0.046 12688 Z= 0.450 Angle : 1.041 10.370 17204 Z= 0.701 Chirality : 0.066 0.467 1920 Planarity : 0.007 0.093 2156 Dihedral : 16.956 176.036 4688 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.60 % Favored : 91.88 % Rotamer: Outliers : 0.89 % Allowed : 19.29 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.20), residues: 1552 helix: 0.32 (0.19), residues: 693 sheet: -0.27 (0.41), residues: 155 loop : -2.28 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.003 ARG A 668 TYR 0.031 0.004 TYR B 645 PHE 0.019 0.003 PHE A 544 TRP 0.018 0.005 TRP B 487 HIS 0.014 0.003 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00689 (12666) covalent geometry : angle 1.03795 (17158) SS BOND : bond 0.01361 ( 20) SS BOND : angle 1.68381 ( 40) hydrogen bonds : bond 0.15939 ( 551) hydrogen bonds : angle 5.53694 ( 1608) link_NAG-ASN : bond 0.00734 ( 2) link_NAG-ASN : angle 2.55269 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.9313 (mmt) cc_final: 0.9059 (mmt) REVERT: A 693 GLN cc_start: 0.8535 (mp10) cc_final: 0.8211 (mp10) REVERT: A 779 TYR cc_start: 0.8786 (m-10) cc_final: 0.8343 (m-80) REVERT: A 817 MET cc_start: 0.8146 (mmm) cc_final: 0.7854 (mmm) REVERT: B 465 ARG cc_start: 0.9090 (ptp90) cc_final: 0.8880 (ptp90) outliers start: 12 outliers final: 5 residues processed: 162 average time/residue: 0.1072 time to fit residues: 25.2102 Evaluate side-chains 139 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 530 CYS Chi-restraints excluded: chain B residue 813 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0020 chunk 149 optimal weight: 0.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN B 88 ASN ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.103653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.070898 restraints weight = 28628.769| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.59 r_work: 0.2973 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12688 Z= 0.146 Angle : 0.616 9.146 17204 Z= 0.313 Chirality : 0.044 0.231 1920 Planarity : 0.004 0.047 2156 Dihedral : 9.526 97.713 1791 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.31 % Favored : 93.49 % Rotamer: Outliers : 2.97 % Allowed : 20.03 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.21), residues: 1552 helix: 0.95 (0.20), residues: 692 sheet: -0.41 (0.42), residues: 160 loop : -1.88 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 25 TYR 0.013 0.001 TYR A 547 PHE 0.047 0.001 PHE A 776 TRP 0.014 0.001 TRP A 575 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00327 (12666) covalent geometry : angle 0.61360 (17158) SS BOND : bond 0.00471 ( 20) SS BOND : angle 1.15565 ( 40) hydrogen bonds : bond 0.04762 ( 551) hydrogen bonds : angle 4.54615 ( 1608) link_NAG-ASN : bond 0.00379 ( 2) link_NAG-ASN : angle 2.01279 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 693 GLN cc_start: 0.8110 (mp10) cc_final: 0.7733 (mp10) REVERT: A 714 MET cc_start: 0.7364 (ptm) cc_final: 0.7162 (mtm) REVERT: A 776 PHE cc_start: 0.8922 (m-80) cc_final: 0.8676 (m-80) REVERT: A 779 TYR cc_start: 0.8765 (m-10) cc_final: 0.8226 (m-80) REVERT: B 31 MET cc_start: 0.8743 (mtp) cc_final: 0.8520 (ttp) REVERT: B 88 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8383 (t0) REVERT: B 277 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.8366 (t80) REVERT: B 429 MET cc_start: 0.7533 (ttt) cc_final: 0.7274 (ttt) outliers start: 40 outliers final: 14 residues processed: 173 average time/residue: 0.0904 time to fit residues: 23.9034 Evaluate side-chains 152 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 733 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 85 optimal weight: 2.9990 chunk 118 optimal weight: 0.0370 chunk 34 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN B 88 ASN B 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.103402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.070537 restraints weight = 28867.812| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.43 r_work: 0.2984 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12688 Z= 0.154 Angle : 0.613 10.137 17204 Z= 0.305 Chirality : 0.044 0.229 1920 Planarity : 0.004 0.052 2156 Dihedral : 8.184 89.274 1783 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.70 % Favored : 93.17 % Rotamer: Outliers : 3.56 % Allowed : 19.88 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.21), residues: 1552 helix: 1.10 (0.20), residues: 690 sheet: -0.41 (0.42), residues: 159 loop : -1.69 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 25 TYR 0.011 0.001 TYR B 659 PHE 0.037 0.001 PHE A 776 TRP 0.015 0.001 TRP A 575 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00358 (12666) covalent geometry : angle 0.61001 (17158) SS BOND : bond 0.00339 ( 20) SS BOND : angle 1.15095 ( 40) hydrogen bonds : bond 0.04355 ( 551) hydrogen bonds : angle 4.37268 ( 1608) link_NAG-ASN : bond 0.00347 ( 2) link_NAG-ASN : angle 2.34419 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.9345 (mmt) cc_final: 0.9084 (mmt) REVERT: A 693 GLN cc_start: 0.8078 (mp10) cc_final: 0.7684 (mp10) REVERT: A 722 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8134 (p0) REVERT: A 776 PHE cc_start: 0.8886 (m-80) cc_final: 0.8629 (m-80) REVERT: B 31 MET cc_start: 0.8717 (mtp) cc_final: 0.8509 (ttp) REVERT: B 88 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.7812 (t0) REVERT: B 277 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8386 (t80) REVERT: B 720 MET cc_start: 0.7371 (mtt) cc_final: 0.7137 (mpp) outliers start: 48 outliers final: 27 residues processed: 179 average time/residue: 0.0883 time to fit residues: 24.5672 Evaluate side-chains 169 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 733 CYS Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 747 ASN Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.9052 > 50: distance: 2 - 20: 24.646 distance: 6 - 25: 26.991 distance: 10 - 31: 33.634 distance: 14 - 20: 22.873 distance: 15 - 39: 25.060 distance: 20 - 21: 25.782 distance: 21 - 22: 31.221 distance: 21 - 24: 17.219 distance: 22 - 23: 5.924 distance: 22 - 25: 42.941 distance: 23 - 43: 50.646 distance: 25 - 26: 19.347 distance: 26 - 27: 47.097 distance: 27 - 28: 15.185 distance: 27 - 31: 16.358 distance: 28 - 51: 55.939 distance: 31 - 32: 4.965 distance: 32 - 33: 38.047 distance: 32 - 35: 36.197 distance: 33 - 34: 31.524 distance: 33 - 39: 29.683 distance: 34 - 59: 50.419 distance: 35 - 36: 39.849 distance: 39 - 40: 32.178 distance: 41 - 42: 39.739 distance: 42 - 64: 67.525 distance: 44 - 45: 27.258 distance: 44 - 47: 29.057 distance: 45 - 46: 11.726 distance: 45 - 51: 48.036 distance: 46 - 71: 38.644 distance: 47 - 48: 19.134 distance: 48 - 49: 17.810 distance: 48 - 50: 19.253 distance: 51 - 52: 35.425 distance: 52 - 53: 6.974 distance: 52 - 55: 10.034 distance: 53 - 54: 33.184 distance: 53 - 59: 22.372 distance: 54 - 79: 58.869 distance: 55 - 56: 8.501 distance: 56 - 58: 34.234 distance: 59 - 60: 42.919 distance: 60 - 61: 33.174 distance: 60 - 63: 10.579 distance: 61 - 62: 22.345 distance: 61 - 64: 43.895 distance: 62 - 90: 35.752 distance: 65 - 66: 37.153 distance: 66 - 67: 54.756 distance: 66 - 71: 39.716 distance: 67 - 97: 35.454 distance: 68 - 69: 41.935 distance: 68 - 70: 39.132 distance: 71 - 72: 38.327 distance: 72 - 73: 38.292 distance: 72 - 75: 23.175 distance: 73 - 79: 40.396 distance: 74 - 104: 36.708 distance: 75 - 76: 44.275 distance: 76 - 77: 68.034 distance: 76 - 78: 61.167 distance: 79 - 80: 51.471 distance: 80 - 81: 41.440 distance: 80 - 83: 17.396 distance: 81 - 82: 16.696 distance: 81 - 90: 32.580 distance: 82 - 111: 26.512 distance: 83 - 84: 33.491 distance: 84 - 85: 24.473 distance: 84 - 86: 32.857 distance: 85 - 87: 48.592 distance: 86 - 88: 50.202 distance: 87 - 89: 8.454 distance: 88 - 89: 13.517