Starting phenix.real_space_refine on Sun Jul 5 09:04:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mvz_48675/07_2026/9mvz_48675.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mvz_48675/07_2026/9mvz_48675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mvz_48675/07_2026/9mvz_48675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mvz_48675/07_2026/9mvz_48675.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mvz_48675/07_2026/9mvz_48675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mvz_48675/07_2026/9mvz_48675.map" } resolution = 2.81 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= -0.001 sd= 0.025 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 P 3 5.49 5 S 180 5.16 5 C 16812 2.51 5 N 4401 2.21 5 O 5019 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26415 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 7151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7151 Classifications: {'peptide': 938} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 894} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1025 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 7151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7151 Classifications: {'peptide': 938} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 894} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 7151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7151 Classifications: {'peptide': 938} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 894} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1025 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1025 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.91, per 1000 atoms: 0.19 Number of scatterers: 26415 At special positions: 0 Unit cell: (126.26, 118.77, 257.87, 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 180 16.00 P 3 15.00 O 5019 8.00 N 4401 7.00 C 16812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 593 " - pdb=" SG CYS D 599 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 133 " distance=2.04 Simple disulfide: pdb=" SG CYS E 593 " - pdb=" SG CYS E 599 " distance=2.03 Simple disulfide: pdb=" SG CYS F 593 " - pdb=" SG CYS F 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 133 " distance=2.04 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 133 " 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 Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 993.2 milliseconds 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6486 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 12 sheets defined 69.9% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'D' and resid 24 through 33 Processing helix chain 'D' and resid 33 through 52 removed outlier: 4.033A pdb=" N VAL D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'D' and resid 71 through 84 Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 137 through 142 removed outlier: 3.777A pdb=" N ALA D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 137 through 142' Processing helix chain 'D' and resid 161 through 177 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 205 through 226 Processing helix chain 'D' and resid 227 through 255 removed outlier: 3.629A pdb=" N TYR D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 294 Processing helix chain 'D' and resid 296 through 325 removed outlier: 5.338A pdb=" N HIS D 310 " --> pdb=" O HIS D 306 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 329 Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 337 through 366 Proline residue: D 357 - end of helix removed outlier: 3.764A pdb=" N ARG D 365 " --> pdb=" O SER D 361 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE D 366 " --> pdb=" O VAL D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 391 Processing helix chain 'D' and resid 391 through 405 removed outlier: 3.603A pdb=" N ILE D 395 " --> pdb=" O TRP D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 418 through 423 removed outlier: 3.824A pdb=" N LEU D 423 " --> pdb=" O ARG D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 440 removed outlier: 3.890A pdb=" N HIS D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 Processing helix chain 'D' and resid 460 through 476 removed outlier: 3.730A pdb=" N VAL D 466 " --> pdb=" O ALA D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 505 Processing helix chain 'D' and resid 507 through 513 Processing helix chain 'D' and resid 513 through 576 Processing helix chain 'D' and resid 580 through 590 Processing helix chain 'D' and resid 598 through 673 Proline residue: D 624 - end of helix removed outlier: 3.602A pdb=" N MET D 633 " --> pdb=" O MET D 629 " (cutoff:3.500A) Proline residue: D 634 - end of helix Proline residue: D 641 - end of helix removed outlier: 3.640A pdb=" N ILE D 644 " --> pdb=" O MET D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 685 Processing helix chain 'D' and resid 694 through 699 Processing helix chain 'D' and resid 700 through 711 removed outlier: 3.611A pdb=" N LYS D 708 " --> pdb=" O GLN D 704 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET D 711 " --> pdb=" O MET D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 749 removed outlier: 4.307A pdb=" N MET D 737 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP D 738 " --> pdb=" O THR D 734 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 798 Processing helix chain 'D' and resid 799 through 827 removed outlier: 3.974A pdb=" N ALA D 803 " --> pdb=" O ALA D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 836 through 864 removed outlier: 4.195A pdb=" N MET D 840 " --> pdb=" O MET D 836 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL D 844 " --> pdb=" O MET D 840 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA D 847 " --> pdb=" O ILE D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 896 removed outlier: 5.177A pdb=" N ALA D 881 " --> pdb=" O VAL D 877 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL D 882 " --> pdb=" O GLY D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 900 Processing helix chain 'D' and resid 902 through 923 removed outlier: 3.658A pdb=" N GLY D 906 " --> pdb=" O LEU D 902 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 936 Processing helix chain 'D' and resid 937 through 941 removed outlier: 3.524A pdb=" N TRP D 940 " --> pdb=" O ARG D 937 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 20 Processing helix chain 'G' and resid 23 through 27 Processing helix chain 'G' and resid 40 through 56 Processing helix chain 'G' and resid 60 through 67 removed outlier: 3.511A pdb=" N GLY G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 82 Processing helix chain 'C' and resid 5 through 27 removed outlier: 3.959A pdb=" N THR C 27 " --> pdb=" O MET C 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 33 Processing helix chain 'E' and resid 33 through 52 removed outlier: 4.056A pdb=" N VAL E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 62 Processing helix chain 'E' and resid 71 through 84 Processing helix chain 'E' and resid 104 through 121 Processing helix chain 'E' and resid 137 through 142 removed outlier: 3.719A pdb=" N ALA E 141 " --> pdb=" O THR E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 177 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 205 through 226 Processing helix chain 'E' and resid 227 through 255 removed outlier: 3.647A pdb=" N TYR E 255 " --> pdb=" O PHE E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 294 Processing helix chain 'E' and resid 296 through 325 removed outlier: 5.347A pdb=" N HIS E 310 " --> pdb=" O HIS E 306 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL E 311 " --> pdb=" O GLY E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 329 Processing helix chain 'E' and resid 331 through 336 Processing helix chain 'E' and resid 337 through 366 removed outlier: 3.544A pdb=" N GLY E 356 " --> pdb=" O ALA E 352 " (cutoff:3.500A) Proline residue: E 357 - end of helix removed outlier: 3.735A pdb=" N ARG E 365 " --> pdb=" O SER E 361 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE E 366 " --> pdb=" O VAL E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 391 Processing helix chain 'E' and resid 391 through 405 removed outlier: 3.595A pdb=" N ILE E 395 " --> pdb=" O TRP E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 413 Proline residue: E 411 - end of helix Processing helix chain 'E' and resid 418 through 423 removed outlier: 3.808A pdb=" N LEU E 423 " --> pdb=" O ARG E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 440 removed outlier: 3.877A pdb=" N HIS E 439 " --> pdb=" O ALA E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 446 Processing helix chain 'E' and resid 460 through 476 removed outlier: 3.709A pdb=" N VAL E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 505 Processing helix chain 'E' and resid 507 through 513 Processing helix chain 'E' and resid 513 through 576 Processing helix chain 'E' and resid 580 through 590 Processing helix chain 'E' and resid 598 through 673 Proline residue: E 624 - end of helix Proline residue: E 634 - end of helix removed outlier: 3.681A pdb=" N MET E 640 " --> pdb=" O MET E 636 " (cutoff:3.500A) Proline residue: E 641 - end of helix removed outlier: 3.680A pdb=" N ILE E 644 " --> pdb=" O MET E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 676 through 685 Processing helix chain 'E' and resid 694 through 699 Processing helix chain 'E' and resid 700 through 711 removed outlier: 3.578A pdb=" N LYS E 708 " --> pdb=" O GLN E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 730 through 735 Processing helix chain 'E' and resid 736 through 749 Processing helix chain 'E' and resid 763 through 798 Processing helix chain 'E' and resid 799 through 827 removed outlier: 3.974A pdb=" N ALA E 803 " --> pdb=" O ALA E 799 " (cutoff:3.500A) Processing helix chain 'E' and resid 836 through 864 removed outlier: 4.133A pdb=" N MET E 840 " --> pdb=" O MET E 836 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL E 844 " --> pdb=" O MET E 840 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA E 847 " --> pdb=" O ILE E 843 " (cutoff:3.500A) Processing helix chain 'E' and resid 867 through 896 removed outlier: 5.216A pdb=" N ALA E 881 " --> pdb=" O VAL E 877 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL E 882 " --> pdb=" O GLY E 878 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 900 Processing helix chain 'E' and resid 902 through 923 removed outlier: 3.536A pdb=" N GLY E 906 " --> pdb=" O LEU E 902 " (cutoff:3.500A) Processing helix chain 'E' and resid 926 through 936 Processing helix chain 'E' and resid 937 through 941 removed outlier: 3.506A pdb=" N TRP E 940 " --> pdb=" O ARG E 937 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 33 Processing helix chain 'F' and resid 33 through 52 removed outlier: 4.079A pdb=" N VAL F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 62 Processing helix chain 'F' and resid 71 through 84 Processing helix chain 'F' and resid 104 through 121 Processing helix chain 'F' and resid 137 through 142 removed outlier: 3.773A pdb=" N ALA F 141 " --> pdb=" O THR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 177 Processing helix chain 'F' and resid 190 through 205 Processing helix chain 'F' and resid 205 through 226 Processing helix chain 'F' and resid 227 through 255 removed outlier: 3.625A pdb=" N TYR F 255 " --> pdb=" O PHE F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 294 Processing helix chain 'F' and resid 296 through 325 removed outlier: 5.351A pdb=" N HIS F 310 " --> pdb=" O HIS F 306 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N VAL F 311 " --> pdb=" O GLY F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 329 Processing helix chain 'F' and resid 331 through 336 Processing helix chain 'F' and resid 337 through 366 Proline residue: F 357 - end of helix removed outlier: 3.722A pdb=" N ARG F 365 " --> pdb=" O SER F 361 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE F 366 " --> pdb=" O VAL F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 391 Processing helix chain 'F' and resid 391 through 405 removed outlier: 3.594A pdb=" N ILE F 395 " --> pdb=" O TRP F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 410 Processing helix chain 'F' and resid 418 through 423 removed outlier: 3.829A pdb=" N LEU F 423 " --> pdb=" O ARG F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 438 Processing helix chain 'F' and resid 441 through 446 Processing helix chain 'F' and resid 460 through 476 removed outlier: 3.706A pdb=" N VAL F 466 " --> pdb=" O ALA F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 505 Processing helix chain 'F' and resid 507 through 513 Processing helix chain 'F' and resid 513 through 576 Processing helix chain 'F' and resid 580 through 590 Processing helix chain 'F' and resid 598 through 640 Proline residue: F 624 - end of helix Proline residue: F 634 - end of helix removed outlier: 3.747A pdb=" N MET F 640 " --> pdb=" O MET F 636 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 673 removed outlier: 3.725A pdb=" N ILE F 644 " --> pdb=" O MET F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 676 through 685 Processing helix chain 'F' and resid 694 through 699 Processing helix chain 'F' and resid 700 through 711 removed outlier: 3.602A pdb=" N LYS F 708 " --> pdb=" O GLN F 704 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET F 711 " --> pdb=" O MET F 707 " (cutoff:3.500A) Processing helix chain 'F' and resid 730 through 735 Processing helix chain 'F' and resid 736 through 749 Processing helix chain 'F' and resid 763 through 798 Processing helix chain 'F' and resid 799 through 827 removed outlier: 3.931A pdb=" N ALA F 803 " --> pdb=" O ALA F 799 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 864 removed outlier: 4.140A pdb=" N MET F 840 " --> pdb=" O MET F 836 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL F 844 " --> pdb=" O MET F 840 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA F 847 " --> pdb=" O ILE F 843 " (cutoff:3.500A) Processing helix chain 'F' and resid 867 through 896 removed outlier: 5.194A pdb=" N ALA F 881 " --> pdb=" O VAL F 877 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL F 882 " --> pdb=" O GLY F 878 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 900 Processing helix chain 'F' and resid 902 through 923 removed outlier: 3.657A pdb=" N GLY F 906 " --> pdb=" O LEU F 902 " (cutoff:3.500A) Processing helix chain 'F' and resid 926 through 936 Processing helix chain 'F' and resid 937 through 941 Processing helix chain 'H' and resid 4 through 20 Processing helix chain 'H' and resid 23 through 27 Processing helix chain 'H' and resid 40 through 56 Processing helix chain 'H' and resid 60 through 67 removed outlier: 3.517A pdb=" N GLY H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 82 Processing helix chain 'I' and resid 4 through 21 Processing helix chain 'I' and resid 23 through 27 Processing helix chain 'I' and resid 40 through 56 Processing helix chain 'I' and resid 60 through 67 removed outlier: 3.537A pdb=" N GLY I 66 " --> pdb=" O GLU I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 82 Processing helix chain 'A' and resid 5 through 29 removed outlier: 3.506A pdb=" N VAL A 9 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 27 " --> pdb=" O MET A 23 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 29 removed outlier: 3.662A pdb=" N THR B 27 " --> pdb=" O MET B 23 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 29 " --> pdb=" O VAL B 25 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.501A pdb=" N HIS D 127 " --> pdb=" O TYR D 154 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN D 152 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N SER D 91 " --> pdb=" O ILE D 155 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 480 through 484 removed outlier: 7.017A pdb=" N ILE D 723 " --> pdb=" O ALA D 481 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL D 483 " --> pdb=" O THR D 721 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR D 721 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 35 " --> pdb=" O ILE D 758 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 35 through 36 removed outlier: 3.550A pdb=" N VAL C 35 " --> pdb=" O ILE F 758 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR F 721 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL F 483 " --> pdb=" O THR F 721 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE F 723 " --> pdb=" O ALA F 481 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 90 removed outlier: 6.795A pdb=" N ILE C 108 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR C 123 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N CYS C 110 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU C 121 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL C 112 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 74 through 81 removed outlier: 3.533A pdb=" N ILE C 65 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER C 79 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA C 63 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N HIS C 98 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.504A pdb=" N HIS E 127 " --> pdb=" O TYR E 154 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN E 152 " --> pdb=" O GLN E 129 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER E 91 " --> pdb=" O ILE E 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 480 through 484 removed outlier: 7.059A pdb=" N ILE E 723 " --> pdb=" O ALA E 481 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL E 483 " --> pdb=" O THR E 721 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR E 721 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 35 " --> pdb=" O ILE E 758 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 125 through 129 removed outlier: 4.295A pdb=" N GLN F 152 " --> pdb=" O GLN F 129 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER F 91 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 90 removed outlier: 6.803A pdb=" N ILE A 108 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR A 123 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS A 110 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU A 121 " --> pdb=" O CYS A 110 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 112 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 74 through 81 removed outlier: 3.527A pdb=" N ILE A 65 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER A 79 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA A 63 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N HIS A 98 " --> pdb=" O MET A 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 84 through 90 removed outlier: 6.820A pdb=" N ILE B 108 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR B 123 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N CYS B 110 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU B 121 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 112 " --> pdb=" O LYS B 119 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 74 through 81 removed outlier: 4.320A pdb=" N SER B 79 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA B 63 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N HIS B 98 " --> pdb=" O MET B 68 " (cutoff:3.500A) 1953 hydrogen bonds defined for protein. 5682 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.84 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8700 1.34 - 1.46: 5814 1.46 - 1.58: 12064 1.58 - 1.71: 2 1.71 - 1.83: 342 Bond restraints: 26922 Sorted by residual: bond pdb=" O27 PNS I 101 " pdb=" P24 PNS I 101 " ideal model delta sigma weight residual 1.704 1.829 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" O27 PNS G 101 " pdb=" P24 PNS G 101 " ideal model delta sigma weight residual 1.704 1.829 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" O27 PNS H 101 " pdb=" P24 PNS H 101 " ideal model delta sigma weight residual 1.704 1.828 -0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" C34 PNS H 101 " pdb=" N36 PNS H 101 " ideal model delta sigma weight residual 1.337 1.410 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C34 PNS G 101 " pdb=" N36 PNS G 101 " ideal model delta sigma weight residual 1.337 1.409 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 26917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 36039 1.59 - 3.18: 524 3.18 - 4.76: 100 4.76 - 6.35: 37 6.35 - 7.94: 5 Bond angle restraints: 36705 Sorted by residual: angle pdb=" C THR E 498 " pdb=" N ILE E 499 " pdb=" CA ILE E 499 " ideal model delta sigma weight residual 120.24 122.87 -2.63 6.30e-01 2.52e+00 1.75e+01 angle pdb=" C THR F 498 " pdb=" N ILE F 499 " pdb=" CA ILE F 499 " ideal model delta sigma weight residual 120.24 122.85 -2.61 6.30e-01 2.52e+00 1.71e+01 angle pdb=" N ILE A 5 " pdb=" CA ILE A 5 " pdb=" C ILE A 5 " ideal model delta sigma weight residual 113.53 109.84 3.69 9.80e-01 1.04e+00 1.42e+01 angle pdb=" C THR D 498 " pdb=" N ILE D 499 " pdb=" CA ILE D 499 " ideal model delta sigma weight residual 120.33 122.79 -2.46 8.00e-01 1.56e+00 9.49e+00 angle pdb=" C ILE E 499 " pdb=" CA ILE E 499 " pdb=" CB ILE E 499 " ideal model delta sigma weight residual 114.35 111.33 3.02 1.06e+00 8.90e-01 8.11e+00 ... (remaining 36700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 15313 16.62 - 33.24: 660 33.24 - 49.85: 138 49.85 - 66.47: 46 66.47 - 83.09: 4 Dihedral angle restraints: 16161 sinusoidal: 6120 harmonic: 10041 Sorted by residual: dihedral pdb=" CA ILE E 596 " pdb=" C ILE E 596 " pdb=" N PRO E 597 " pdb=" CA PRO E 597 " ideal model delta harmonic sigma weight residual 180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ASP D 565 " pdb=" CB ASP D 565 " pdb=" CG ASP D 565 " pdb=" OD1 ASP D 565 " ideal model delta sinusoidal sigma weight residual -30.00 -86.03 56.03 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CA ILE F 596 " pdb=" C ILE F 596 " pdb=" N PRO F 597 " pdb=" CA PRO F 597 " ideal model delta harmonic sigma weight residual -180.00 -164.29 -15.71 0 5.00e+00 4.00e-02 9.88e+00 ... (remaining 16158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2885 0.034 - 0.067: 1061 0.067 - 0.101: 279 0.101 - 0.135: 140 0.135 - 0.168: 6 Chirality restraints: 4371 Sorted by residual: chirality pdb=" C32 PNS G 101 " pdb=" C29 PNS G 101 " pdb=" C34 PNS G 101 " pdb=" O33 PNS G 101 " both_signs ideal model delta sigma weight residual False 2.33 2.50 -0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" C32 PNS I 101 " pdb=" C29 PNS I 101 " pdb=" C34 PNS I 101 " pdb=" O33 PNS I 101 " both_signs ideal model delta sigma weight residual False 2.33 2.49 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" C32 PNS H 101 " pdb=" C29 PNS H 101 " pdb=" C34 PNS H 101 " pdb=" O33 PNS H 101 " both_signs ideal model delta sigma weight residual False 2.33 2.49 -0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 4368 not shown) Planarity restraints: 4707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 356 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO D 357 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 357 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 357 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 52 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.06e+00 pdb=" N PRO D 53 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 53 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 53 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 71 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO F 72 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO F 72 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 72 " 0.019 5.00e-02 4.00e+02 ... (remaining 4704 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 5543 2.78 - 3.31: 26177 3.31 - 3.84: 44310 3.84 - 4.37: 50544 4.37 - 4.90: 90316 Nonbonded interactions: 216890 Sorted by model distance: nonbonded pdb=" OH TYR D 111 " pdb=" OD1 ASP D 130 " model vdw 2.244 3.040 nonbonded pdb=" O ILE E 748 " pdb=" OG1 THR E 751 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR E 111 " pdb=" OD1 ASP E 130 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR F 111 " pdb=" OD1 ASP F 130 " model vdw 2.260 3.040 nonbonded pdb=" O ILE D 748 " pdb=" OG1 THR D 751 " model vdw 2.273 3.040 ... (remaining 216885 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.430 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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:5.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.005 0.125 26928 Z= 0.219 Angle : 0.545 7.941 36717 Z= 0.297 Chirality : 0.041 0.168 4371 Planarity : 0.004 0.037 4707 Dihedral : 10.487 83.091 9657 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.42 % Allowed : 3.13 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 3.03 (0.14), residues: 3450 helix: 2.68 (0.11), residues: 2196 sheet: 1.90 (0.30), residues: 324 loop : 0.41 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 23 TYR 0.012 0.001 TYR D 767 PHE 0.010 0.001 PHE E 720 TRP 0.013 0.001 TRP E 381 HIS 0.002 0.001 HIS F 827 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (26922) covalent geometry : angle 0.54461 / 0.30 (36705) SS BOND : bond 0.00379 / 0.24 ( 6) SS BOND : angle 1.32766 / 0.96 ( 12) hydrogen bonds : bond 0.14508 / 9.67 ( 1953) hydrogen bonds : angle 5.25616 / 3.77 ( 5682) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 611 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 VAL cc_start: 0.9164 (t) cc_final: 0.8919 (m) REVERT: D 335 GLN cc_start: 0.8230 (tt0) cc_final: 0.7840 (tm-30) REVERT: D 544 ILE cc_start: 0.8920 (mt) cc_final: 0.8718 (mp) REVERT: D 577 ASP cc_start: 0.1808 (OUTLIER) cc_final: 0.1400 (m-30) REVERT: D 925 SER cc_start: 0.9243 (m) cc_final: 0.8949 (p) REVERT: G 31 LYS cc_start: 0.8810 (mmtp) cc_final: 0.8441 (mmmm) REVERT: C 62 SER cc_start: 0.8499 (p) cc_final: 0.7920 (t) REVERT: C 100 MET cc_start: 0.8621 (mtp) cc_final: 0.8412 (mtp) REVERT: C 119 LYS cc_start: 0.9272 (mmtt) cc_final: 0.9021 (mmtm) REVERT: C 127 MET cc_start: 0.7093 (ttm) cc_final: 0.5940 (ttm) REVERT: E 577 ASP cc_start: 0.4108 (OUTLIER) cc_final: 0.2505 (m-30) REVERT: E 777 ASP cc_start: 0.7707 (m-30) cc_final: 0.7484 (m-30) REVERT: E 794 MET cc_start: 0.8409 (ttp) cc_final: 0.8141 (ttp) REVERT: E 814 LEU cc_start: 0.8859 (tp) cc_final: 0.8649 (tp) REVERT: E 925 SER cc_start: 0.9237 (m) cc_final: 0.9031 (p) REVERT: F 112 ASP cc_start: 0.7772 (m-30) cc_final: 0.7524 (m-30) REVERT: F 541 MET cc_start: 0.8433 (tpt) cc_final: 0.8011 (tpt) REVERT: F 699 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7304 (mm-30) REVERT: F 777 ASP cc_start: 0.7811 (m-30) cc_final: 0.7437 (m-30) REVERT: H 31 LYS cc_start: 0.8873 (mmtp) cc_final: 0.8473 (mmmm) REVERT: H 36 ASP cc_start: 0.8573 (m-30) cc_final: 0.8372 (m-30) REVERT: H 62 GLU cc_start: 0.8603 (mp0) cc_final: 0.8338 (mp0) REVERT: H 69 THR cc_start: 0.8961 (p) cc_final: 0.8344 (p) REVERT: I 25 SER cc_start: 0.9435 (p) cc_final: 0.7852 (p) REVERT: I 26 GLU cc_start: 0.8429 (tp30) cc_final: 0.8178 (tp30) REVERT: I 31 LYS cc_start: 0.9012 (mmtp) cc_final: 0.8381 (mmmm) REVERT: I 62 GLU cc_start: 0.8611 (mp0) cc_final: 0.8358 (mp0) REVERT: A 28 VAL cc_start: 0.7801 (t) cc_final: 0.7488 (t) REVERT: A 62 SER cc_start: 0.8481 (p) cc_final: 0.7989 (t) REVERT: B 62 SER cc_start: 0.8675 (p) cc_final: 0.8106 (t) outliers start: 68 outliers final: 11 residues processed: 667 average time/residue: 0.5970 time to fit residues: 460.1493 Evaluate side-chains 483 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 470 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 577 ASP Chi-restraints excluded: chain F residue 779 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.0050 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 82 GLN D 496 HIS D 645 GLN D 652 GLN D 674 ASN C 128 ASN E 82 GLN E 496 HIS E 652 GLN E 674 ASN F 82 GLN F 496 HIS A 128 ASN B 128 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.104542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.073318 restraints weight = 43039.531| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.42 r_work: 0.2785 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26928 Z= 0.146 Angle : 0.542 8.811 36717 Z= 0.284 Chirality : 0.041 0.154 4371 Planarity : 0.004 0.052 4707 Dihedral : 4.931 58.521 3756 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.31 % Allowed : 10.92 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 3.17 (0.14), residues: 3450 helix: 2.82 (0.11), residues: 2187 sheet: 1.71 (0.30), residues: 306 loop : 0.55 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 68 TYR 0.019 0.001 TYR I 76 PHE 0.014 0.001 PHE F 580 TRP 0.011 0.001 TRP D 600 HIS 0.015 0.001 HIS E 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (26922) covalent geometry : angle 0.54019 / 0.28 (36705) SS BOND : bond 0.00185 / 0.15 ( 6) SS BOND : angle 2.48321 / 1.84 ( 12) hydrogen bonds : bond 0.05633 / 3.90 ( 1953) hydrogen bonds : angle 4.31289 / 3.11 ( 5682) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 514 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 25 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7460 (mpp-170) REVERT: D 64 VAL cc_start: 0.9319 (t) cc_final: 0.8963 (m) REVERT: D 237 MET cc_start: 0.9012 (mtm) cc_final: 0.8716 (mtm) REVERT: D 335 GLN cc_start: 0.8689 (tt0) cc_final: 0.8160 (tm-30) REVERT: D 541 MET cc_start: 0.8464 (tpp) cc_final: 0.8042 (tpt) REVERT: D 544 ILE cc_start: 0.8545 (mt) cc_final: 0.8339 (mp) REVERT: D 602 MET cc_start: 0.2671 (ptp) cc_final: 0.2397 (mtm) REVERT: D 709 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8435 (mp) REVERT: D 777 ASP cc_start: 0.8527 (m-30) cc_final: 0.8240 (m-30) REVERT: G 7 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8594 (mt-10) REVERT: G 18 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: G 26 GLU cc_start: 0.8757 (tp30) cc_final: 0.8232 (tp30) REVERT: G 31 LYS cc_start: 0.8914 (mmtp) cc_final: 0.8337 (mmmm) REVERT: G 36 ASP cc_start: 0.8807 (m-30) cc_final: 0.8605 (m-30) REVERT: C 23 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8253 (mpp) REVERT: C 62 SER cc_start: 0.8659 (p) cc_final: 0.7991 (t) REVERT: C 121 GLU cc_start: 0.9268 (tt0) cc_final: 0.8866 (tt0) REVERT: C 122 ARG cc_start: 0.8591 (mtp85) cc_final: 0.8291 (mtp-110) REVERT: E 25 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8088 (pmt-80) REVERT: E 295 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: E 335 GLN cc_start: 0.8727 (tt0) cc_final: 0.8463 (tm-30) REVERT: E 559 MET cc_start: 0.6825 (tmm) cc_final: 0.6121 (tmt) REVERT: E 577 ASP cc_start: 0.2613 (OUTLIER) cc_final: 0.2173 (m-30) REVERT: E 777 ASP cc_start: 0.8541 (m-30) cc_final: 0.8334 (m-30) REVERT: E 824 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8908 (tp) REVERT: F 25 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7654 (mpp-170) REVERT: F 112 ASP cc_start: 0.8752 (m-30) cc_final: 0.8427 (m-30) REVERT: F 541 MET cc_start: 0.8578 (tpt) cc_final: 0.8322 (tpt) REVERT: F 544 ILE cc_start: 0.8232 (mt) cc_final: 0.7940 (mp) REVERT: F 555 MET cc_start: 0.8577 (mtt) cc_final: 0.8260 (ppp) REVERT: F 688 ASP cc_start: 0.9132 (p0) cc_final: 0.8838 (p0) REVERT: F 699 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8343 (mm-30) REVERT: F 777 ASP cc_start: 0.8461 (m-30) cc_final: 0.8168 (m-30) REVERT: H 17 GLU cc_start: 0.8787 (tp30) cc_final: 0.8412 (tp30) REVERT: H 18 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8407 (tm-30) REVERT: H 25 SER cc_start: 0.9114 (p) cc_final: 0.8831 (p) REVERT: H 26 GLU cc_start: 0.8785 (tp30) cc_final: 0.8455 (tp30) REVERT: H 31 LYS cc_start: 0.8986 (mmtp) cc_final: 0.8538 (mmmm) REVERT: H 36 ASP cc_start: 0.8526 (m-30) cc_final: 0.8285 (m-30) REVERT: I 7 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8429 (mp0) REVERT: I 25 SER cc_start: 0.9079 (p) cc_final: 0.8789 (p) REVERT: I 26 GLU cc_start: 0.9009 (tp30) cc_final: 0.8508 (tp30) REVERT: I 31 LYS cc_start: 0.8812 (mmtp) cc_final: 0.8398 (mmmm) REVERT: A 23 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7506 (mpt) REVERT: A 62 SER cc_start: 0.8793 (p) cc_final: 0.8079 (t) REVERT: B 62 SER cc_start: 0.8769 (p) cc_final: 0.8092 (t) REVERT: B 71 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8308 (pt0) REVERT: B 127 MET cc_start: 0.8451 (ttm) cc_final: 0.8156 (ttp) outliers start: 93 outliers final: 28 residues processed: 555 average time/residue: 0.5606 time to fit residues: 363.1252 Evaluate side-chains 508 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 469 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 791 ILE Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 919 ASP Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 577 ASP Chi-restraints excluded: chain F residue 779 ILE Chi-restraints excluded: chain F residue 791 ILE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 92 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 169 optimal weight: 7.9990 chunk 313 optimal weight: 6.9990 chunk 182 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 84 optimal weight: 0.3980 chunk 240 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 652 GLN D 680 GLN F 652 GLN A 66 ASN B 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.103573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.072297 restraints weight = 43243.443| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.43 r_work: 0.2766 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26928 Z= 0.172 Angle : 0.547 11.249 36717 Z= 0.282 Chirality : 0.041 0.141 4371 Planarity : 0.004 0.044 4707 Dihedral : 4.715 57.875 3754 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.17 % Allowed : 13.16 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 3.12 (0.14), residues: 3450 helix: 2.79 (0.11), residues: 2187 sheet: 1.60 (0.31), residues: 306 loop : 0.53 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 456 TYR 0.014 0.001 TYR E 516 PHE 0.013 0.001 PHE D 110 TRP 0.010 0.001 TRP E 381 HIS 0.011 0.001 HIS E 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (26922) covalent geometry : angle 0.54526 / 0.28 (36705) SS BOND : bond 0.00546 / 0.33 ( 6) SS BOND : angle 2.52693 / 1.97 ( 12) hydrogen bonds : bond 0.05593 / 3.88 ( 1953) hydrogen bonds : angle 4.20580 / 3.04 ( 5682) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 473 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 129 GLN cc_start: 0.8628 (pt0) cc_final: 0.8345 (tt0) REVERT: D 237 MET cc_start: 0.9032 (mtm) cc_final: 0.8480 (mtt) REVERT: D 335 GLN cc_start: 0.8712 (tt0) cc_final: 0.8199 (tm-30) REVERT: D 598 MET cc_start: 0.3517 (OUTLIER) cc_final: 0.2004 (mtm) REVERT: D 602 MET cc_start: 0.2637 (ptp) cc_final: 0.2422 (mtm) REVERT: D 629 MET cc_start: 0.7595 (tmm) cc_final: 0.7384 (tmm) REVERT: D 709 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8468 (mp) REVERT: D 777 ASP cc_start: 0.8542 (m-30) cc_final: 0.8236 (m-30) REVERT: D 824 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8907 (tp) REVERT: G 26 GLU cc_start: 0.8655 (tp30) cc_final: 0.8152 (tp30) REVERT: G 31 LYS cc_start: 0.8941 (mmtp) cc_final: 0.8421 (mmmm) REVERT: G 36 ASP cc_start: 0.8811 (m-30) cc_final: 0.8539 (m-30) REVERT: C 62 SER cc_start: 0.8695 (p) cc_final: 0.8029 (t) REVERT: C 121 GLU cc_start: 0.9242 (tt0) cc_final: 0.8909 (tt0) REVERT: E 295 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: E 577 ASP cc_start: 0.2701 (OUTLIER) cc_final: 0.2239 (m-30) REVERT: E 777 ASP cc_start: 0.8560 (m-30) cc_final: 0.8346 (m-30) REVERT: E 824 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8876 (tp) REVERT: F 112 ASP cc_start: 0.8787 (m-30) cc_final: 0.8457 (m-30) REVERT: F 555 MET cc_start: 0.8495 (mtt) cc_final: 0.8274 (pp-130) REVERT: F 559 MET cc_start: 0.5488 (tmt) cc_final: 0.5106 (tmt) REVERT: F 602 MET cc_start: 0.2824 (ptp) cc_final: 0.1570 (mpp) REVERT: F 688 ASP cc_start: 0.9121 (p0) cc_final: 0.8854 (p0) REVERT: F 699 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8401 (mm-30) REVERT: H 17 GLU cc_start: 0.8806 (tp30) cc_final: 0.8465 (tp30) REVERT: H 25 SER cc_start: 0.9107 (p) cc_final: 0.8803 (p) REVERT: H 26 GLU cc_start: 0.8801 (tp30) cc_final: 0.8329 (tp30) REVERT: H 31 LYS cc_start: 0.9007 (mmtp) cc_final: 0.8468 (mmmm) REVERT: H 36 ASP cc_start: 0.8603 (m-30) cc_final: 0.8318 (m-30) REVERT: I 25 SER cc_start: 0.9094 (p) cc_final: 0.8809 (p) REVERT: I 26 GLU cc_start: 0.9032 (tp30) cc_final: 0.8436 (tp30) REVERT: I 31 LYS cc_start: 0.8843 (mmtp) cc_final: 0.8314 (mmmm) REVERT: A 23 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7464 (mpt) REVERT: A 55 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8622 (mt-10) REVERT: A 62 SER cc_start: 0.8827 (p) cc_final: 0.8127 (t) REVERT: B 62 SER cc_start: 0.8775 (p) cc_final: 0.8106 (t) REVERT: B 120 GLU cc_start: 0.9096 (tp30) cc_final: 0.8850 (tp30) REVERT: B 127 MET cc_start: 0.8455 (ttm) cc_final: 0.8201 (tmm) outliers start: 89 outliers final: 41 residues processed: 521 average time/residue: 0.5587 time to fit residues: 341.3017 Evaluate side-chains 493 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 445 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 598 MET Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 791 ILE Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain E residue 796 LEU Chi-restraints excluded: chain E residue 816 SER Chi-restraints excluded: chain E residue 823 LEU Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 919 ASP Chi-restraints excluded: chain E residue 925 SER Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 577 ASP Chi-restraints excluded: chain F residue 781 VAL Chi-restraints excluded: chain F residue 791 ILE Chi-restraints excluded: chain F residue 816 SER Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 92 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.0184 > 50: distance: 8 - 29: 13.691 distance: 12 - 34: 16.753 distance: 25 - 29: 10.971 distance: 29 - 30: 11.313 distance: 30 - 31: 11.735 distance: 30 - 33: 20.570 distance: 31 - 32: 13.307 distance: 31 - 34: 17.263 distance: 34 - 35: 26.870 distance: 35 - 36: 5.068 distance: 35 - 38: 27.643 distance: 36 - 37: 11.481 distance: 36 - 39: 19.094 distance: 39 - 40: 21.209 distance: 39 - 45: 33.288 distance: 40 - 41: 21.574 distance: 40 - 43: 28.167 distance: 41 - 42: 13.726 distance: 41 - 46: 16.947 distance: 43 - 44: 32.440 distance: 44 - 45: 16.856 distance: 46 - 47: 20.332 distance: 47 - 48: 10.778 distance: 48 - 49: 15.390 distance: 48 - 56: 10.852 distance: 50 - 51: 11.164 distance: 51 - 52: 7.646 distance: 51 - 53: 23.701 distance: 52 - 54: 5.669 distance: 53 - 55: 20.796 distance: 54 - 55: 28.179 distance: 56 - 57: 25.563 distance: 57 - 58: 20.826 distance: 57 - 60: 27.918 distance: 58 - 59: 23.070 distance: 58 - 62: 16.726 distance: 60 - 61: 11.587 distance: 61 - 103: 21.589 distance: 62 - 63: 5.995 distance: 63 - 64: 3.763 distance: 63 - 66: 14.502 distance: 64 - 65: 9.551 distance: 64 - 67: 9.390 distance: 67 - 68: 10.984 distance: 68 - 69: 20.033 distance: 68 - 71: 9.051 distance: 69 - 70: 19.660 distance: 69 - 75: 23.194 distance: 71 - 72: 12.571 distance: 72 - 73: 13.164 distance: 72 - 74: 33.378 distance: 75 - 76: 28.874 distance: 76 - 77: 17.236 distance: 76 - 79: 12.376 distance: 77 - 78: 12.340 distance: 77 - 83: 10.332 distance: 79 - 80: 7.618 distance: 79 - 81: 5.073 distance: 80 - 82: 38.811 distance: 83 - 84: 47.751 distance: 83 - 89: 6.046 distance: 84 - 85: 32.669 distance: 84 - 87: 37.393 distance: 85 - 86: 13.566 distance: 85 - 90: 39.040 distance: 88 - 89: 44.217 distance: 90 - 91: 27.826 distance: 91 - 92: 18.849 distance: 91 - 94: 46.234 distance: 92 - 93: 17.523 distance: 92 - 98: 20.334 distance: 93 - 120: 21.717 distance: 94 - 95: 7.655 distance: 95 - 96: 39.665