Starting phenix.real_space_refine on Sun Aug 24 20:05:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mit_23864/08_2025/7mit_23864_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mit_23864/08_2025/7mit_23864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mit_23864/08_2025/7mit_23864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mit_23864/08_2025/7mit_23864.map" model { file = "/net/cci-nas-00/data/ceres_data/7mit_23864/08_2025/7mit_23864_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mit_23864/08_2025/7mit_23864_neut.cif" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 1.000 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 37 5.49 5 S 104 5.16 5 Cl 1 4.86 5 C 13871 2.51 5 N 3594 2.21 5 O 3836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21447 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2696 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 12, 'TRANS': 351} Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 99 Chain: "B" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2564 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 10, 'TRANS': 326} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2546 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 10, 'TRANS': 325} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 9, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2558 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 10, 'TRANS': 326} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 4, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 9995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1438, 9995 Classifications: {'peptide': 1438} Incomplete info: {'truncation_to_alanine': 414} Link IDs: {'PTRANS': 47, 'TRANS': 1390} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1440 Unresolved non-hydrogen angles: 1828 Unresolved non-hydrogen dihedrals: 1165 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 13, 'ASN:plan1': 22, 'ASP:plan': 46, 'GLU:plan': 43, 'ARG:plan': 24, 'PHE:plan': 12, 'TYR:plan': 9, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 817 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 192 Unusual residues: {' K': 3, 'ATP': 1, 'POV': 2, 'PTY': 1} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 152 Unusual residues: {'ATP': 2, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 193 Unusual residues: {'ATP': 1, 'POV': 3} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 127 Unusual residues: {' K': 1, 'POV': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 396 Unusual residues: {'ATP': 1, 'GBM': 1, 'PTY': 7} Classifications: {'peptide': 2, 'undetermined': 9} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 126 Time building chain proxies: 4.44, per 1000 atoms: 0.21 Number of scatterers: 21447 At special positions: 0 Unit cell: (125.54, 168.224, 154.414, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 Cl 1 17.00 S 104 16.00 P 37 15.00 O 3836 8.00 N 3594 7.00 C 13871 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 120 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 120 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 24 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG N 1 " - " ASN E 9 " Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5332 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 27 sheets defined 51.6% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.776A pdb=" N PHE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 98 removed outlier: 3.607A pdb=" N LEU A 73 " --> pdb=" O TRP A 69 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 110 removed outlier: 3.743A pdb=" N THR A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 139 Processing helix chain 'A' and resid 152 through 183 removed outlier: 3.714A pdb=" N ILE A 156 " --> pdb=" O CYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 4.505A pdb=" N ASP A 279 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE A 280 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.685A pdb=" N ASP A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 66 removed outlier: 3.732A pdb=" N ILE B 60 " --> pdb=" O PHE B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 98 removed outlier: 4.014A pdb=" N VAL B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 111 removed outlier: 4.178A pdb=" N GLY B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE B 109 " --> pdb=" O MET B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 140 Processing helix chain 'B' and resid 152 through 183 removed outlier: 3.574A pdb=" N ILE B 156 " --> pdb=" O CYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.722A pdb=" N LEU B 285 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 286 " --> pdb=" O THR B 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 282 through 286' Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 339 through 342 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 361 through 366 removed outlier: 4.245A pdb=" N LEU B 365 " --> pdb=" O LYS B 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.868A pdb=" N PHE C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 98 removed outlier: 4.484A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 107 Processing helix chain 'C' and resid 114 through 119 removed outlier: 4.154A pdb=" N ALA C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 114 through 119' Processing helix chain 'C' and resid 126 through 140 removed outlier: 3.688A pdb=" N ALA C 130 " --> pdb=" O SER C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 183 removed outlier: 3.765A pdb=" N ILE C 156 " --> pdb=" O CYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 354 through 361 removed outlier: 3.678A pdb=" N ASP C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 66 removed outlier: 3.744A pdb=" N PHE D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 98 removed outlier: 4.128A pdb=" N VAL D 74 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE D 80 " --> pdb=" O PHE D 76 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS D 98 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 110 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 126 through 139 Processing helix chain 'D' and resid 152 through 183 removed outlier: 3.758A pdb=" N ILE D 156 " --> pdb=" O CYS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 186 No H-bonds generated for 'chain 'D' and resid 184 through 186' Processing helix chain 'D' and resid 275 through 280 removed outlier: 4.210A pdb=" N ASP D 279 " --> pdb=" O PRO D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'E' and resid 9 through 14 removed outlier: 3.769A pdb=" N ASN E 14 " --> pdb=" O SER E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 48 Proline residue: E 33 - end of helix Proline residue: E 43 - end of helix Processing helix chain 'E' and resid 69 through 96 removed outlier: 3.580A pdb=" N GLN E 96 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 128 removed outlier: 4.027A pdb=" N SER E 128 " --> pdb=" O ASN E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 133 Processing helix chain 'E' and resid 134 through 158 removed outlier: 3.703A pdb=" N LEU E 158 " --> pdb=" O LYS E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 192 removed outlier: 3.518A pdb=" N CYS E 168 " --> pdb=" O ASP E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 210 removed outlier: 3.820A pdb=" N GLN E 209 " --> pdb=" O PRO E 205 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP E 210 " --> pdb=" O GLU E 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 205 through 210' Processing helix chain 'E' and resid 216 through 220 removed outlier: 3.777A pdb=" N VAL E 220 " --> pdb=" O GLN E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 231 through 237 Processing helix chain 'E' and resid 256 through 278 removed outlier: 3.589A pdb=" N ASN E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 294 through 312 removed outlier: 3.992A pdb=" N PHE E 312 " --> pdb=" O ASP E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 326 removed outlier: 3.557A pdb=" N LEU E 316 " --> pdb=" O PHE E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 394 removed outlier: 3.731A pdb=" N VAL E 353 " --> pdb=" O HIS E 349 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR E 364 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG E 394 " --> pdb=" O ASN E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 416 Processing helix chain 'E' and resid 416 through 427 removed outlier: 3.738A pdb=" N LEU E 427 " --> pdb=" O TRP E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 432 Processing helix chain 'E' and resid 433 through 450 Processing helix chain 'E' and resid 451 through 462 removed outlier: 3.797A pdb=" N VAL E 455 " --> pdb=" O SER E 451 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU E 462 " --> pdb=" O ALA E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 498 removed outlier: 3.925A pdb=" N GLY E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 505 Processing helix chain 'E' and resid 509 through 559 removed outlier: 4.248A pdb=" N SER E 514 " --> pdb=" O ILE E 510 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL E 515 " --> pdb=" O PHE E 511 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR E 528 " --> pdb=" O SER E 524 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE E 529 " --> pdb=" O SER E 525 " (cutoff:3.500A) Proline residue: E 544 - end of helix removed outlier: 3.924A pdb=" N HIS E 555 " --> pdb=" O THR E 551 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA E 556 " --> pdb=" O PHE E 552 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR E 557 " --> pdb=" O VAL E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 607 removed outlier: 4.242A pdb=" N ALA E 570 " --> pdb=" O ALA E 566 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR E 580 " --> pdb=" O HIS E 576 " (cutoff:3.500A) Proline residue: E 581 - end of helix removed outlier: 4.408A pdb=" N SER E 586 " --> pdb=" O LEU E 582 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR E 587 " --> pdb=" O PHE E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 716 Processing helix chain 'E' and resid 761 through 768 Processing helix chain 'E' and resid 773 through 785 Processing helix chain 'E' and resid 786 through 793 Processing helix chain 'E' and resid 795 through 799 Processing helix chain 'E' and resid 809 through 823 Processing helix chain 'E' and resid 840 through 855 Processing helix chain 'E' and resid 891 through 896 Processing helix chain 'E' and resid 900 through 910 removed outlier: 4.080A pdb=" N GLU E 904 " --> pdb=" O VAL E 900 " (cutoff:3.500A) Processing helix chain 'E' and resid 965 through 972 Processing helix chain 'E' and resid 976 through 983 Processing helix chain 'E' and resid 990 through 1018 removed outlier: 3.784A pdb=" N ASP E1008 " --> pdb=" O ILE E1004 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR E1018 " --> pdb=" O TRP E1014 " (cutoff:3.500A) Processing helix chain 'E' and resid 1029 through 1073 removed outlier: 3.750A pdb=" N SER E1050 " --> pdb=" O CYS E1046 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU E1051 " --> pdb=" O LEU E1047 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE E1073 " --> pdb=" O LEU E1069 " (cutoff:3.500A) Processing helix chain 'E' and resid 1076 through 1083 Processing helix chain 'E' and resid 1084 through 1102 removed outlier: 3.846A pdb=" N ILE E1088 " --> pdb=" O PRO E1084 " (cutoff:3.500A) Processing helix chain 'E' and resid 1102 through 1128 Processing helix chain 'E' and resid 1129 through 1134 removed outlier: 4.061A pdb=" N ILE E1133 " --> pdb=" O PRO E1129 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA E1134 " --> pdb=" O VAL E1130 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1129 through 1134' Processing helix chain 'E' and resid 1134 through 1177 removed outlier: 3.844A pdb=" N LEU E1138 " --> pdb=" O ALA E1134 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG E1150 " --> pdb=" O GLN E1146 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS E1154 " --> pdb=" O ARG E1150 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP E1155 " --> pdb=" O VAL E1151 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER E1162 " --> pdb=" O GLU E1158 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU E1165 " --> pdb=" O ASP E1161 " (cutoff:3.500A) Proline residue: E1166 - end of helix removed outlier: 3.752A pdb=" N PHE E1171 " --> pdb=" O LEU E1167 " (cutoff:3.500A) Processing helix chain 'E' and resid 1177 through 1185 Processing helix chain 'E' and resid 1186 through 1236 removed outlier: 3.877A pdb=" N ARG E1193 " --> pdb=" O ARG E1189 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU E1196 " --> pdb=" O GLN E1192 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA E1233 " --> pdb=" O THR E1229 " (cutoff:3.500A) Processing helix chain 'E' and resid 1241 through 1258 removed outlier: 3.873A pdb=" N GLY E1247 " --> pdb=" O LEU E1243 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR E1255 " --> pdb=" O ALA E1251 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN E1256 " --> pdb=" O LEU E1252 " (cutoff:3.500A) Processing helix chain 'E' and resid 1259 through 1284 removed outlier: 4.132A pdb=" N LYS E1277 " --> pdb=" O GLY E1273 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL E1278 " --> pdb=" O ALA E1274 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR E1283 " --> pdb=" O ASN E1279 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET E1284 " --> pdb=" O SER E1280 " (cutoff:3.500A) Processing helix chain 'E' and resid 1294 through 1298 Processing helix chain 'E' and resid 1301 through 1305 removed outlier: 3.789A pdb=" N GLN E1304 " --> pdb=" O HIS E1301 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU E1305 " --> pdb=" O TRP E1302 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1301 through 1305' Processing helix chain 'E' and resid 1348 through 1356 removed outlier: 4.292A pdb=" N PHE E1356 " --> pdb=" O SER E1352 " (cutoff:3.500A) Processing helix chain 'E' and resid 1377 through 1383 Processing helix chain 'E' and resid 1407 through 1414 Processing helix chain 'E' and resid 1416 through 1423 removed outlier: 4.250A pdb=" N GLN E1422 " --> pdb=" O LEU E1418 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E1423 " --> pdb=" O GLU E1419 " (cutoff:3.500A) Processing helix chain 'E' and resid 1425 through 1430 removed outlier: 3.734A pdb=" N SER E1429 " --> pdb=" O ASN E1425 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU E1430 " --> pdb=" O MET E1426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1425 through 1430' Processing helix chain 'E' and resid 1442 through 1461 removed outlier: 4.556A pdb=" N GLY E1448 " --> pdb=" O ASN E1444 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN E1451 " --> pdb=" O VAL E1447 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG E1461 " --> pdb=" O ARG E1457 " (cutoff:3.500A) Processing helix chain 'E' and resid 1475 through 1489 Processing helix chain 'E' and resid 1526 through 1534 Processing helix chain 'E' and resid 1534 through 1541 removed outlier: 4.280A pdb=" N VAL E1541 " --> pdb=" O PHE E1537 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 193 Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.523A pdb=" N ILE A 199 " --> pdb=" O GLN A 319 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 247 removed outlier: 5.486A pdb=" N THR A 233 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA A 223 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 247 removed outlier: 5.486A pdb=" N THR A 233 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER A 222 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL A 299 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 291 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA7, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AA9, first strand: chain 'B' and resid 191 through 193 Processing sheet with id=AB1, first strand: chain 'B' and resid 191 through 193 removed outlier: 6.769A pdb=" N ALA B 197 " --> pdb=" O GLN B 319 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 248 removed outlier: 4.900A pdb=" N THR B 233 " --> pdb=" O PRO B 242 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE B 227 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N SER B 222 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL B 299 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 322 through 324 Processing sheet with id=AB4, first strand: chain 'B' and resid 328 through 330 removed outlier: 3.584A pdb=" N THR B 329 " --> pdb=" O SER B 336 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 47 through 48 Processing sheet with id=AB6, first strand: chain 'C' and resid 191 through 192 Processing sheet with id=AB7, first strand: chain 'C' and resid 191 through 192 Processing sheet with id=AB8, first strand: chain 'C' and resid 244 through 248 removed outlier: 4.325A pdb=" N ILE C 227 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA C 223 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU C 297 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL C 225 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 295 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE C 227 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE C 293 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL C 229 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU C 291 " --> pdb=" O VAL C 229 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 191 through 193 Processing sheet with id=AC1, first strand: chain 'D' and resid 191 through 193 Processing sheet with id=AC2, first strand: chain 'D' and resid 241 through 248 removed outlier: 5.286A pdb=" N THR D 233 " --> pdb=" O PRO D 242 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE D 227 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA D 223 " --> pdb=" O GLU D 297 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU D 297 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL D 225 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE D 295 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE D 227 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE D 293 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL D 229 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU D 291 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY D 298 " --> pdb=" O THR D 307 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 322 through 324 Processing sheet with id=AC4, first strand: chain 'E' and resid 669 through 670 removed outlier: 3.660A pdb=" N VAL E 670 " --> pdb=" O ILE E 689 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 675 through 676 Processing sheet with id=AC6, first strand: chain 'E' and resid 700 through 701 removed outlier: 7.042A pdb=" N VAL E 700 " --> pdb=" O MET E 881 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 1338 through 1339 removed outlier: 6.426A pdb=" N VAL E1338 " --> pdb=" O THR E1498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 1367 through 1368 Processing sheet with id=AC9, first strand: chain 'E' and resid 1512 through 1514 removed outlier: 6.129A pdb=" N VAL E1512 " --> pdb=" O TYR E1523 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 3264 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: 3.40 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3271 1.31 - 1.44: 5742 1.44 - 1.57: 12596 1.57 - 1.69: 71 1.69 - 1.82: 163 Bond restraints: 21843 Sorted by residual: bond pdb=" C29 POV D 504 " pdb="C210 POV D 504 " ideal model delta sigma weight residual 1.333 1.544 -0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C29 POV D 503 " pdb="C210 POV D 503 " ideal model delta sigma weight residual 1.333 1.544 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C29 POV C 505 " pdb="C210 POV C 505 " ideal model delta sigma weight residual 1.333 1.543 -0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C29 POV C 504 " pdb="C210 POV C 504 " ideal model delta sigma weight residual 1.333 1.543 -0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C29 POV A 507 " pdb="C210 POV A 507 " ideal model delta sigma weight residual 1.333 1.543 -0.210 2.00e-02 2.50e+03 1.10e+02 ... (remaining 21838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 29285 3.80 - 7.60: 269 7.60 - 11.40: 80 11.40 - 15.20: 36 15.20 - 19.01: 26 Bond angle restraints: 29696 Sorted by residual: angle pdb=" PB ATP E1601 " pdb=" O3B ATP E1601 " pdb=" PG ATP E1601 " ideal model delta sigma weight residual 139.87 121.12 18.75 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 121.28 18.59 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 122.02 17.85 1.00e+00 1.00e+00 3.18e+02 angle pdb=" PB ATP B 502 " pdb=" O3B ATP B 502 " pdb=" PG ATP B 502 " ideal model delta sigma weight residual 139.87 122.21 17.66 1.00e+00 1.00e+00 3.12e+02 angle pdb=" PB ATP A 504 " pdb=" O3B ATP A 504 " pdb=" PG ATP A 504 " ideal model delta sigma weight residual 139.87 122.45 17.42 1.00e+00 1.00e+00 3.04e+02 ... (remaining 29691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 12715 35.44 - 70.89: 423 70.89 - 106.33: 79 106.33 - 141.78: 20 141.78 - 177.22: 19 Dihedral angle restraints: 13256 sinusoidal: 5060 harmonic: 8196 Sorted by residual: dihedral pdb=" CA ASP E1469 " pdb=" C ASP E1469 " pdb=" N GLU E1470 " pdb=" CA GLU E1470 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" C27 P5S E1609 " pdb=" C28 P5S E1609 " pdb=" C29 P5S E1609 " pdb=" C30 P5S E1609 " ideal model delta sinusoidal sigma weight residual 298.90 121.68 177.22 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB P5S C 503 " pdb=" OG P5S C 503 " pdb=" P12 P5S C 503 " pdb=" O15 P5S C 503 " ideal model delta sinusoidal sigma weight residual 180.41 8.87 171.54 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 13253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2673 0.052 - 0.104: 679 0.104 - 0.156: 159 0.156 - 0.208: 5 0.208 - 0.259: 2 Chirality restraints: 3518 Sorted by residual: chirality pdb=" C5 NAG N 2 " pdb=" C4 NAG N 2 " pdb=" C6 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.41 -2.67 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 9 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB THR D 128 " pdb=" CA THR D 128 " pdb=" OG1 THR D 128 " pdb=" CG2 THR D 128 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3515 not shown) Planarity restraints: 3636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 P5S E1607 " -0.366 2.00e-02 2.50e+03 2.11e-01 4.47e+02 pdb=" C20 P5S E1607 " 0.114 2.00e-02 2.50e+03 pdb=" O18 P5S E1607 " 0.124 2.00e-02 2.50e+03 pdb=" O19 P5S E1607 " 0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 P5S A 508 " -0.365 2.00e-02 2.50e+03 2.11e-01 4.43e+02 pdb=" C20 P5S A 508 " 0.112 2.00e-02 2.50e+03 pdb=" O18 P5S A 508 " 0.127 2.00e-02 2.50e+03 pdb=" O19 P5S A 508 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 P5S B 504 " -0.362 2.00e-02 2.50e+03 2.09e-01 4.38e+02 pdb=" C20 P5S B 504 " 0.113 2.00e-02 2.50e+03 pdb=" O18 P5S B 504 " 0.124 2.00e-02 2.50e+03 pdb=" O19 P5S B 504 " 0.126 2.00e-02 2.50e+03 ... (remaining 3633 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.67: 373 2.67 - 3.29: 23630 3.29 - 3.91: 38451 3.91 - 4.52: 51093 4.52 - 5.14: 83003 Nonbonded interactions: 196550 Sorted by model distance: nonbonded pdb=" OE1 GLU B 150 " pdb=" OG SER C 129 " model vdw 2.057 3.040 nonbonded pdb=" O TRP E 980 " pdb=" OG SER E 984 " model vdw 2.155 3.040 nonbonded pdb=" OE1 GLU C 150 " pdb=" OG SER D 129 " model vdw 2.155 3.040 nonbonded pdb=" OG SER E 708 " pdb=" OE1 GLN E 753 " model vdw 2.163 3.040 nonbonded pdb=" O VAL C 139 " pdb=" OG1 THR C 140 " model vdw 2.174 3.040 ... (remaining 196545 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 30 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 through 51 or (resid 52 through 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 56 or (resid 57 and (n \ ame N or name CA or name C or name O or name CB )) or resid 58 through 64 or (re \ sid 65 through 66 and (name N or name CA or name C or name O or name CB )) or re \ sid 67 through 74 or (resid 75 and (name N or name CA or name C or name O or nam \ e CB )) or resid 76 through 100 or (resid 101 and (name N or name CA or name C o \ r name O or name CB )) or resid 102 through 104 or (resid 105 through 107 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 108 through 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 125 o \ r (resid 126 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 27 through 160 or (resid 161 and (name N or name CA or name C or name O or name \ CB )) or resid 162 through 186 or (resid 187 through 189 and (name N or name CA \ or name C or name O or name CB )) or resid 190 through 216 or (resid 217 and (na \ me N or name CA or name C or name O or name CB )) or resid 218 or (resid 219 and \ (name N or name CA or name C or name O or name CB )) or resid 220 through 242 o \ r (resid 243 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 44 through 246 or (resid 247 through 248 and (name N or name CA or name C or nam \ e O or name CB )) or resid 249 through 261 or (resid 262 through 263 and (name N \ or name CA or name C or name O or name CB )) or resid 264 through 272 or (resid \ 273 and (name N or name CA or name C or name O or name CB )) or resid 274 throu \ gh 300 or (resid 301 and (name N or name CA or name C or name O or name CB )) or \ resid 302 or (resid 303 and (name N or name CA or name C or name O or name CB ) \ ) or resid 304 or (resid 305 and (name N or name CA or name C or name O or name \ CB )) or resid 306 through 316 or (resid 317 and (name N or name CA or name C or \ name O or name CB )) or resid 318 through 358 or (resid 359 through 361 and (na \ me N or name CA or name C or name O or name CB )) or resid 362 through 364 or re \ sid 505)) selection = (chain 'B' and (resid 30 through 36 or (resid 37 through 38 and (name N or name \ CA or name C or name O or name CB )) or resid 39 through 51 or (resid 52 through \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) or res \ id 58 or (resid 59 and (name N or name CA or name C or name O or name CB )) or r \ esid 60 through 100 or (resid 101 and (name N or name CA or name C or name O or \ name CB )) or resid 102 through 104 or (resid 105 through 107 and (name N or nam \ e CA or name C or name O or name CB )) or resid 108 through 149 or (resid 150 an \ d (name N or name CA or name C or name O or name CB )) or resid 151 through 160 \ or (resid 161 and (name N or name CA or name C or name O or name CB )) or resid \ 162 through 186 or (resid 187 through 189 and (name N or name CA or name C or na \ me O or name CB )) or resid 190 through 218 or (resid 219 and (name N or name CA \ or name C or name O or name CB )) or resid 220 through 239 or (resid 240 and (n \ ame N or name CA or name C or name O or name CB )) or resid 241 through 242 or ( \ resid 243 and (name N or name CA or name C or name O or name CB )) or resid 244 \ through 246 or (resid 247 through 248 and (name N or name CA or name C or name O \ or name CB )) or resid 249 through 254 or (resid 255 and (name N or name CA or \ name C or name O or name CB )) or resid 256 through 261 or (resid 262 through 26 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 264 through \ 265 or (resid 266 and (name N or name CA or name C or name O or name CB )) or re \ sid 267 through 272 or (resid 273 and (name N or name CA or name C or name O or \ name CB )) or resid 274 or (resid 275 and (name N or name CA or name C or name O \ or name CB )) or resid 276 through 285 or (resid 286 through 287 and (name N or \ name CA or name C or name O or name CB )) or resid 288 or (resid 289 and (name \ N or name CA or name C or name O or name CB )) or resid 290 through 300 or (resi \ d 301 and (name N or name CA or name C or name O or name CB )) or resid 302 or ( \ resid 303 and (name N or name CA or name C or name O or name CB )) or resid 304 \ through 316 or (resid 317 and (name N or name CA or name C or name O or name CB \ )) or resid 318 through 326 or (resid 327 and (name N or name CA or name C or na \ me O or name CB )) or resid 328 or (resid 329 and (name N or name CA or name C o \ r name O or name CB )) or resid 330 or (resid 331 through 332 and (name N or nam \ e CA or name C or name O or name CB )) or resid 333 through 345 or (resid 346 an \ d (name N or name CA or name C or name O or name CB )) or resid 347 through 356 \ or (resid 357 and (name N or name CA or name C or name O or name CB )) or resid \ 358 or (resid 359 through 361 and (name N or name CA or name C or name O or name \ CB )) or resid 362 through 364 or resid 503)) selection = (chain 'C' and (resid 30 through 36 or (resid 37 through 38 and (name N or name \ CA or name C or name O or name CB )) or resid 39 through 52 or (resid 53 and (na \ me N or name CA or name C or name O or name CB )) or resid 54 through 56 or (res \ id 57 and (name N or name CA or name C or name O or name CB )) or resid 58 or (r \ esid 59 and (name N or name CA or name C or name O or name CB )) or resid 60 thr \ ough 64 or (resid 65 through 66 and (name N or name CA or name C or name O or na \ me CB )) or resid 67 through 74 or (resid 75 and (name N or name CA or name C or \ name O or name CB )) or resid 76 through 116 or (resid 117 through 119 and (nam \ e N or name CA or name C or name O or name CB )) or resid 120 through 125 or (re \ sid 126 and (name N or name CA or name C or name O or name CB )) or resid 127 th \ rough 149 or (resid 150 and (name N or name CA or name C or name O or name CB )) \ or resid 151 through 188 or (resid 189 and (name N or name CA or name C or name \ O or name CB )) or resid 190 through 216 or (resid 217 and (name N or name CA o \ r name C or name O or name CB )) or resid 218 through 239 or (resid 240 and (nam \ e N or name CA or name C or name O or name CB )) or resid 241 through 242 or (re \ sid 243 and (name N or name CA or name C or name O or name CB )) or resid 244 th \ rough 246 or (resid 247 through 248 and (name N or name CA or name C or name O o \ r name CB )) or resid 249 through 258 or (resid 259 and (name N or name CA or na \ me C or name O or name CB )) or resid 260 through 261 or (resid 262 through 263 \ and (name N or name CA or name C or name O or name CB )) or resid 264 through 26 \ 5 or (resid 266 and (name N or name CA or name C or name O or name CB )) or resi \ d 267 through 274 or (resid 275 and (name N or name CA or name C or name O or na \ me CB )) or resid 276 through 285 or (resid 286 through 287 and (name N or name \ CA or name C or name O or name CB )) or resid 288 or (resid 289 and (name N or n \ ame CA or name C or name O or name CB )) or resid 290 through 304 or (resid 305 \ and (name N or name CA or name C or name O or name CB )) or resid 306 through 31 \ 6 or (resid 317 and (name N or name CA or name C or name O or name CB )) or resi \ d 318 through 326 or (resid 327 and (name N or name CA or name C or name O or na \ me CB )) or resid 328 or (resid 329 and (name N or name CA or name C or name O o \ r name CB )) or resid 330 or (resid 331 through 332 and (name N or name CA or na \ me C or name O or name CB )) or resid 333 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB )) or resid 347 through 358 or (resid \ 359 through 361 and (name N or name CA or name C or name O or name CB )) or resi \ d 362 through 364 or resid 504)) selection = (chain 'D' and (resid 30 through 36 or (resid 37 through 38 and (name N or name \ CA or name C or name O or name CB )) or resid 39 through 51 or (resid 52 through \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 64 or (resid 65 through 66 and (name N or name CA or name C or name O or name C \ B )) or resid 67 through 74 or (resid 75 and (name N or name CA or name C or nam \ e O or name CB )) or resid 76 through 100 or (resid 101 and (name N or name CA o \ r name C or name O or name CB )) or resid 102 through 104 or (resid 105 through \ 107 and (name N or name CA or name C or name O or name CB )) or (resid 108 throu \ gh 119 and (name N or name CA or name C or name O or name CB )) or resid 120 thr \ ough 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) \ or resid 127 through 149 or (resid 150 and (name N or name CA or name C or name \ O or name CB )) or resid 151 through 160 or (resid 161 and (name N or name CA or \ name C or name O or name CB )) or resid 162 through 186 or (resid 187 through 1 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 190 through \ 216 or (resid 217 and (name N or name CA or name C or name O or name CB )) or r \ esid 218 through 239 or (resid 240 and (name N or name CA or name C or name O or \ name CB )) or resid 241 through 254 or (resid 255 and (name N or name CA or nam \ e C or name O or name CB )) or resid 256 through 258 or (resid 259 and (name N o \ r name CA or name C or name O or name CB )) or resid 260 through 265 or (resid 2 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 267 through \ 272 or (resid 273 and (name N or name CA or name C or name O or name CB )) or r \ esid 274 or (resid 275 and (name N or name CA or name C or name O or name CB )) \ or resid 276 through 285 or (resid 286 through 287 and (name N or name CA or nam \ e C or name O or name CB )) or resid 288 or (resid 289 and (name N or name CA or \ name C or name O or name CB )) or resid 290 through 302 or (resid 303 and (name \ N or name CA or name C or name O or name CB )) or resid 304 or (resid 305 and ( \ name N or name CA or name C or name O or name CB )) or resid 306 through 326 or \ (resid 327 and (name N or name CA or name C or name O or name CB )) or resid 328 \ or (resid 329 and (name N or name CA or name C or name O or name CB )) or resid \ 330 or (resid 331 through 332 and (name N or name CA or name C or name O or nam \ e CB )) or resid 333 through 345 or (resid 346 and (name N or name CA or name C \ or name O or name CB )) or resid 347 through 356 or (resid 357 and (name N or na \ me CA or name C or name O or name CB )) or resid 358 through 364 or resid 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.920 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.211 21850 Z= 0.517 Angle : 1.159 19.005 29712 Z= 0.586 Chirality : 0.048 0.259 3518 Planarity : 0.010 0.211 3635 Dihedral : 20.208 177.223 7909 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % 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 aren not related in a simple way. whole: -0.87 (0.16), residues: 2796 helix: 0.95 (0.15), residues: 1288 sheet: -0.75 (0.32), residues: 239 loop : -2.24 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 323 TYR 0.016 0.002 TYR E 228 PHE 0.020 0.002 PHE C 76 TRP 0.016 0.002 TRP E1214 HIS 0.009 0.001 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.01012 (21843) covalent geometry : angle 1.15810 (29696) SS BOND : bond 0.00334 ( 5) SS BOND : angle 1.20663 ( 10) hydrogen bonds : bond 0.13538 ( 1114) hydrogen bonds : angle 6.00611 ( 3264) link_BETA1-4 : bond 0.00395 ( 1) link_BETA1-4 : angle 3.86344 ( 3) link_NAG-ASN : bond 0.00052 ( 1) link_NAG-ASN : angle 1.91389 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 614 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.8790 (ptp-170) cc_final: 0.8438 (ptp90) REVERT: A 151 GLU cc_start: 0.8538 (tp30) cc_final: 0.8290 (tp30) REVERT: A 205 LYS cc_start: 0.8850 (mmpt) cc_final: 0.8638 (mmtt) REVERT: B 48 LYS cc_start: 0.8246 (ptpt) cc_final: 0.7981 (ptpp) REVERT: B 185 HIS cc_start: 0.7950 (t-90) cc_final: 0.7691 (t-90) REVERT: B 216 ARG cc_start: 0.7428 (ttp80) cc_final: 0.7040 (ttp-170) REVERT: B 222 SER cc_start: 0.8980 (m) cc_final: 0.8240 (p) REVERT: B 232 LYS cc_start: 0.8810 (tttt) cc_final: 0.8576 (tttm) REVERT: B 288 GLN cc_start: 0.7846 (tp40) cc_final: 0.7453 (tp40) REVERT: B 325 VAL cc_start: 0.9154 (p) cc_final: 0.8943 (m) REVERT: C 125 ARG cc_start: 0.8401 (ptp-170) cc_final: 0.8152 (ptp90) REVERT: C 163 ASN cc_start: 0.8608 (m-40) cc_final: 0.8238 (m110) REVERT: C 195 ARG cc_start: 0.7702 (ttp-110) cc_final: 0.7390 (ttp-110) REVERT: C 222 SER cc_start: 0.9188 (m) cc_final: 0.8812 (p) REVERT: C 231 LYS cc_start: 0.8270 (mttm) cc_final: 0.7995 (mmmt) REVERT: C 284 ASP cc_start: 0.7068 (m-30) cc_final: 0.6838 (m-30) REVERT: C 319 GLN cc_start: 0.8685 (pt0) cc_final: 0.8226 (pt0) REVERT: D 37 ILE cc_start: 0.9449 (pt) cc_final: 0.9217 (pt) REVERT: D 217 LYS cc_start: 0.8424 (tttt) cc_final: 0.7768 (mtmm) REVERT: D 273 LYS cc_start: 0.8768 (mttt) cc_final: 0.8154 (mtmm) REVERT: D 287 ASN cc_start: 0.8653 (t0) cc_final: 0.8433 (t0) REVERT: D 338 ASP cc_start: 0.8239 (t70) cc_final: 0.7689 (t0) REVERT: E 110 MET cc_start: 0.8049 (mmm) cc_final: 0.7695 (mmt) REVERT: E 156 TRP cc_start: 0.7307 (t-100) cc_final: 0.6852 (t60) REVERT: E 211 LEU cc_start: 0.8272 (tp) cc_final: 0.8042 (tp) REVERT: E 285 ILE cc_start: 0.8779 (mm) cc_final: 0.8431 (mm) REVERT: E 346 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7173 (tm-30) REVERT: E 360 ILE cc_start: 0.9156 (pt) cc_final: 0.8908 (mt) REVERT: E 434 MET cc_start: 0.7478 (mtt) cc_final: 0.7221 (mtp) REVERT: E 479 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7902 (tptm) REVERT: E 497 LYS cc_start: 0.7845 (ttmt) cc_final: 0.7491 (tttm) REVERT: E 527 LYS cc_start: 0.8513 (ttpt) cc_final: 0.8294 (ttpp) REVERT: E 972 LYS cc_start: 0.5979 (tptp) cc_final: 0.4969 (ptpt) REVERT: E 976 LYS cc_start: 0.7774 (mmtt) cc_final: 0.7219 (mmtm) REVERT: E 1108 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7674 (tm-30) REVERT: E 1395 PHE cc_start: 0.8295 (m-80) cc_final: 0.7898 (m-80) outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 0.1404 time to fit residues: 130.0478 Evaluate side-chains 533 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 533 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 228 GLN B 203 ASN B 344 ASN D 183 GLN ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 467 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.161128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.127550 restraints weight = 26625.271| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.75 r_work: 0.3117 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21850 Z= 0.193 Angle : 0.609 10.679 29712 Z= 0.312 Chirality : 0.046 0.237 3518 Planarity : 0.004 0.048 3635 Dihedral : 21.765 177.053 3977 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.01 % Allowed : 16.75 % Favored : 80.23 % 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 aren not related in a simple way. whole: -0.36 (0.16), residues: 2796 helix: 1.45 (0.15), residues: 1308 sheet: -0.83 (0.32), residues: 244 loop : -2.05 (0.16), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 202 TYR 0.018 0.002 TYR E 121 PHE 0.020 0.002 PHE C 76 TRP 0.015 0.001 TRP E1214 HIS 0.006 0.001 HIS C 98 Details of bonding type rmsd covalent geometry : bond 0.00448 (21843) covalent geometry : angle 0.60727 (29696) SS BOND : bond 0.00563 ( 5) SS BOND : angle 1.06082 ( 10) hydrogen bonds : bond 0.05683 ( 1114) hydrogen bonds : angle 4.46630 ( 3264) link_BETA1-4 : bond 0.00607 ( 1) link_BETA1-4 : angle 3.59156 ( 3) link_NAG-ASN : bond 0.00074 ( 1) link_NAG-ASN : angle 2.15878 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 558 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9046 (mmtt) cc_final: 0.8696 (tptt) REVERT: A 125 ARG cc_start: 0.9107 (ptp-170) cc_final: 0.8725 (ptp90) REVERT: B 48 LYS cc_start: 0.8557 (ptpt) cc_final: 0.8286 (ptpp) REVERT: B 150 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8063 (pt0) REVERT: B 174 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8768 (tp) REVERT: B 205 LYS cc_start: 0.7541 (mtpt) cc_final: 0.6966 (tptp) REVERT: B 288 GLN cc_start: 0.7982 (tp40) cc_final: 0.7688 (tp40) REVERT: C 78 MET cc_start: 0.8158 (mmt) cc_final: 0.7164 (ttt) REVERT: C 125 ARG cc_start: 0.9086 (ptp-170) cc_final: 0.8703 (ptp90) REVERT: C 163 ASN cc_start: 0.8830 (m-40) cc_final: 0.8451 (m110) REVERT: C 195 ARG cc_start: 0.8262 (ttp-110) cc_final: 0.7676 (ttp-110) REVERT: C 222 SER cc_start: 0.9331 (m) cc_final: 0.9005 (p) REVERT: C 231 LYS cc_start: 0.8563 (mttm) cc_final: 0.8326 (mmmt) REVERT: D 37 ILE cc_start: 0.9404 (pt) cc_final: 0.9203 (pt) REVERT: D 217 LYS cc_start: 0.8669 (tttt) cc_final: 0.7804 (mtmm) REVERT: D 258 ASN cc_start: 0.8911 (m110) cc_final: 0.8697 (m-40) REVERT: D 269 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.7720 (t-90) REVERT: D 273 LYS cc_start: 0.9013 (mttt) cc_final: 0.8436 (mtmt) REVERT: D 287 ASN cc_start: 0.8513 (t0) cc_final: 0.8184 (t0) REVERT: D 338 ASP cc_start: 0.8841 (t70) cc_final: 0.8508 (t0) REVERT: D 357 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7944 (tt0) REVERT: E 110 MET cc_start: 0.8893 (mmm) cc_final: 0.8577 (mmt) REVERT: E 156 TRP cc_start: 0.7495 (t-100) cc_final: 0.6937 (t60) REVERT: E 324 ARG cc_start: 0.8287 (tpp80) cc_final: 0.7167 (tpt-90) REVERT: E 344 PHE cc_start: 0.8766 (t80) cc_final: 0.8320 (t80) REVERT: E 346 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7424 (tm-30) REVERT: E 434 MET cc_start: 0.8187 (mtt) cc_final: 0.7892 (mtp) REVERT: E 479 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7804 (tptm) REVERT: E 497 LYS cc_start: 0.7969 (ttmt) cc_final: 0.7593 (tttm) REVERT: E 527 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8346 (ttpp) REVERT: E 972 LYS cc_start: 0.6143 (tptp) cc_final: 0.4842 (ptpt) REVERT: E 976 LYS cc_start: 0.7901 (mmtt) cc_final: 0.7356 (mmtp) REVERT: E 1216 GLU cc_start: 0.8500 (tt0) cc_final: 0.8266 (tt0) REVERT: E 1395 PHE cc_start: 0.8387 (m-80) cc_final: 0.7974 (m-80) outliers start: 57 outliers final: 40 residues processed: 590 average time/residue: 0.1277 time to fit residues: 115.4499 Evaluate side-chains 568 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 525 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 269 HIS Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 467 GLN Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 786 LEU Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 998 LEU Chi-restraints excluded: chain E residue 1013 THR Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1198 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 257 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 chunk 204 optimal weight: 40.0000 chunk 66 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN B 344 ASN D 183 GLN D 288 GLN ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 467 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.165525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.131548 restraints weight = 26706.107| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.90 r_work: 0.3089 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 0.054 21850 Z= 0.186 Angle : 0.585 11.363 29712 Z= 0.301 Chirality : 0.045 0.211 3518 Planarity : 0.004 0.047 3635 Dihedral : 20.685 176.985 3977 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.02 % Allowed : 18.08 % Favored : 77.91 % 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 aren not related in a simple way. whole: -0.13 (0.16), residues: 2796 helix: 1.64 (0.15), residues: 1308 sheet: -0.70 (0.32), residues: 244 loop : -1.94 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 226 TYR 0.017 0.001 TYR E 121 PHE 0.019 0.002 PHE D 208 TRP 0.015 0.001 TRP E1214 HIS 0.004 0.001 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00432 (21843) covalent geometry : angle 0.58204 (29696) SS BOND : bond 0.00430 ( 5) SS BOND : angle 2.20627 ( 10) hydrogen bonds : bond 0.05440 ( 1114) hydrogen bonds : angle 4.28040 ( 3264) link_BETA1-4 : bond 0.00512 ( 1) link_BETA1-4 : angle 3.56843 ( 3) link_NAG-ASN : bond 0.00493 ( 1) link_NAG-ASN : angle 2.89311 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 546 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASN cc_start: 0.8849 (m-40) cc_final: 0.8515 (m110) REVERT: A 186 ARG cc_start: 0.6746 (ttp80) cc_final: 0.6527 (ttp80) REVERT: B 48 LYS cc_start: 0.8588 (ptpt) cc_final: 0.8340 (ptpp) REVERT: B 150 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8064 (pt0) REVERT: B 231 LYS cc_start: 0.8612 (tttt) cc_final: 0.8246 (tttp) REVERT: B 288 GLN cc_start: 0.7913 (tp40) cc_final: 0.7511 (tp40) REVERT: C 78 MET cc_start: 0.8320 (mmt) cc_final: 0.7199 (ttt) REVERT: C 163 ASN cc_start: 0.8847 (m-40) cc_final: 0.8469 (m110) REVERT: C 195 ARG cc_start: 0.8250 (ttp-110) cc_final: 0.7711 (ttp-110) REVERT: C 222 SER cc_start: 0.9278 (m) cc_final: 0.8842 (p) REVERT: C 231 LYS cc_start: 0.8617 (mttm) cc_final: 0.8389 (mmmt) REVERT: D 37 ILE cc_start: 0.9424 (pt) cc_final: 0.9198 (pt) REVERT: D 217 LYS cc_start: 0.8675 (tttt) cc_final: 0.7817 (mtmm) REVERT: D 269 HIS cc_start: 0.8515 (OUTLIER) cc_final: 0.7836 (t-90) REVERT: D 273 LYS cc_start: 0.9017 (mttt) cc_final: 0.8581 (mtmt) REVERT: D 287 ASN cc_start: 0.8412 (t0) cc_final: 0.8180 (t0) REVERT: D 338 ASP cc_start: 0.8885 (t70) cc_final: 0.8509 (t0) REVERT: D 357 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8078 (tt0) REVERT: E 110 MET cc_start: 0.8980 (mmm) cc_final: 0.8661 (mmt) REVERT: E 156 TRP cc_start: 0.7541 (t-100) cc_final: 0.7019 (t60) REVERT: E 200 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8224 (tp40) REVERT: E 246 LYS cc_start: 0.9183 (mppt) cc_final: 0.8937 (mptt) REVERT: E 344 PHE cc_start: 0.8786 (t80) cc_final: 0.8342 (t80) REVERT: E 346 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8086 (tm-30) REVERT: E 347 ASN cc_start: 0.9287 (t0) cc_final: 0.8993 (t0) REVERT: E 434 MET cc_start: 0.8257 (mtt) cc_final: 0.7941 (mtp) REVERT: E 479 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7943 (tptm) REVERT: E 497 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7652 (tttm) REVERT: E 527 LYS cc_start: 0.8577 (ttpt) cc_final: 0.8347 (ttpp) REVERT: E 539 MET cc_start: 0.8640 (tpp) cc_final: 0.8416 (mmm) REVERT: E 972 LYS cc_start: 0.6259 (tptp) cc_final: 0.4857 (ptpt) REVERT: E 976 LYS cc_start: 0.7914 (mmtt) cc_final: 0.7406 (mmtm) REVERT: E 1395 PHE cc_start: 0.8410 (m-80) cc_final: 0.8009 (m-10) outliers start: 76 outliers final: 56 residues processed: 587 average time/residue: 0.1278 time to fit residues: 115.1767 Evaluate side-chains 587 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 528 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 268 CYS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 269 HIS Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 467 GLN Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 577 ILE Chi-restraints excluded: chain E residue 785 SER Chi-restraints excluded: chain E residue 786 LEU Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 1013 THR Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1198 THR Chi-restraints excluded: chain E residue 1315 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 205 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 chunk 1 optimal weight: 50.0000 chunk 171 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN B 344 ASN ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 GLN ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 65 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 467 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.169409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.135748 restraints weight = 26420.743| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.91 r_work: 0.3118 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21850 Z= 0.121 Angle : 0.532 11.992 29712 Z= 0.273 Chirality : 0.044 0.236 3518 Planarity : 0.004 0.043 3635 Dihedral : 19.509 175.159 3977 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.01 % Allowed : 19.71 % Favored : 77.27 % 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 aren not related in a simple way. whole: 0.24 (0.16), residues: 2796 helix: 1.93 (0.15), residues: 1318 sheet: -0.52 (0.32), residues: 243 loop : -1.77 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 394 TYR 0.017 0.001 TYR E 121 PHE 0.017 0.001 PHE A 76 TRP 0.011 0.001 TRP E1214 HIS 0.003 0.001 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00262 (21843) covalent geometry : angle 0.52870 (29696) SS BOND : bond 0.00383 ( 5) SS BOND : angle 1.89558 ( 10) hydrogen bonds : bond 0.04768 ( 1114) hydrogen bonds : angle 4.04121 ( 3264) link_BETA1-4 : bond 0.00734 ( 1) link_BETA1-4 : angle 3.20470 ( 3) link_NAG-ASN : bond 0.00438 ( 1) link_NAG-ASN : angle 3.61201 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 561 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASN cc_start: 0.8890 (m110) cc_final: 0.8419 (m110) REVERT: A 81 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8713 (mp) REVERT: A 317 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7844 (mm-30) REVERT: B 203 ASN cc_start: 0.8649 (m-40) cc_final: 0.8394 (m-40) REVERT: B 231 LYS cc_start: 0.8515 (tttt) cc_final: 0.8067 (mtpp) REVERT: B 232 LYS cc_start: 0.9138 (tttm) cc_final: 0.8936 (tptp) REVERT: B 288 GLN cc_start: 0.7752 (tp40) cc_final: 0.7340 (tp40) REVERT: B 319 GLN cc_start: 0.8359 (mt0) cc_final: 0.7966 (mt0) REVERT: C 78 MET cc_start: 0.8085 (mmt) cc_final: 0.7214 (ttt) REVERT: C 195 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7572 (ttp-110) REVERT: C 222 SER cc_start: 0.9246 (m) cc_final: 0.8827 (p) REVERT: D 37 ILE cc_start: 0.9348 (pt) cc_final: 0.9132 (pt) REVERT: D 179 MET cc_start: 0.7631 (mmm) cc_final: 0.7375 (mmm) REVERT: D 186 ARG cc_start: 0.7956 (mmm160) cc_final: 0.7730 (mmm-85) REVERT: D 217 LYS cc_start: 0.8599 (tttt) cc_final: 0.7782 (mtmm) REVERT: D 273 LYS cc_start: 0.8950 (mttt) cc_final: 0.8479 (mtmt) REVERT: D 338 ASP cc_start: 0.8727 (t70) cc_final: 0.8330 (t0) REVERT: D 357 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8029 (tt0) REVERT: E 110 MET cc_start: 0.8707 (mmm) cc_final: 0.8372 (mmt) REVERT: E 130 PHE cc_start: 0.8739 (t80) cc_final: 0.8392 (t80) REVERT: E 156 TRP cc_start: 0.7395 (t-100) cc_final: 0.7014 (t60) REVERT: E 200 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8206 (tp40) REVERT: E 228 TYR cc_start: 0.9317 (m-80) cc_final: 0.8860 (m-80) REVERT: E 344 PHE cc_start: 0.8746 (t80) cc_final: 0.8334 (t80) REVERT: E 346 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7941 (tm-30) REVERT: E 347 ASN cc_start: 0.9253 (t0) cc_final: 0.8962 (t0) REVERT: E 434 MET cc_start: 0.7972 (mtt) cc_final: 0.7667 (mtp) REVERT: E 438 ILE cc_start: 0.8654 (mt) cc_final: 0.8424 (mt) REVERT: E 479 LYS cc_start: 0.8267 (ttmt) cc_final: 0.7877 (tptm) REVERT: E 497 LYS cc_start: 0.7901 (ttmt) cc_final: 0.7512 (tttm) REVERT: E 539 MET cc_start: 0.8474 (tpp) cc_final: 0.8254 (mmm) REVERT: E 972 LYS cc_start: 0.6141 (tptp) cc_final: 0.4906 (ptpt) REVERT: E 976 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7405 (mmtm) REVERT: E 988 PHE cc_start: 0.6292 (OUTLIER) cc_final: 0.6025 (t80) REVERT: E 999 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8012 (mp) REVERT: E 1395 PHE cc_start: 0.8503 (m-80) cc_final: 0.8077 (m-80) outliers start: 57 outliers final: 34 residues processed: 596 average time/residue: 0.1259 time to fit residues: 115.7439 Evaluate side-chains 566 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 527 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 786 LEU Chi-restraints excluded: chain E residue 988 PHE Chi-restraints excluded: chain E residue 999 LEU Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1315 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9392 > 50: distance: 15 - 18: 35.186 distance: 18 - 19: 41.412 distance: 18 - 24: 56.290 distance: 19 - 20: 50.813 distance: 19 - 22: 68.222 distance: 20 - 21: 47.228 distance: 20 - 25: 41.710 distance: 22 - 23: 56.885 distance: 23 - 24: 40.511 distance: 25 - 26: 4.471 distance: 26 - 29: 37.500 distance: 27 - 28: 51.020 distance: 27 - 30: 61.345 distance: 30 - 31: 17.265 distance: 31 - 32: 33.647 distance: 31 - 34: 56.636 distance: 32 - 33: 55.063 distance: 32 - 35: 17.419 distance: 36 - 37: 59.368 distance: 37 - 38: 49.886 distance: 37 - 39: 49.991 distance: 39 - 40: 22.295 distance: 40 - 41: 22.386 distance: 40 - 43: 41.757 distance: 41 - 42: 26.245 distance: 41 - 44: 58.770 distance: 44 - 45: 40.913 distance: 45 - 46: 41.656 distance: 45 - 48: 57.094 distance: 46 - 47: 46.684 distance: 46 - 49: 43.132 distance: 49 - 50: 41.020 distance: 50 - 51: 66.948 distance: 50 - 53: 39.684 distance: 51 - 52: 62.657 distance: 51 - 54: 39.179 distance: 54 - 55: 41.801 distance: 55 - 56: 45.034 distance: 55 - 58: 47.257 distance: 56 - 57: 53.137 distance: 56 - 59: 57.981 distance: 59 - 60: 38.767 distance: 60 - 61: 69.939 distance: 60 - 63: 55.082 distance: 61 - 62: 69.924 distance: 61 - 64: 39.529 distance: 64 - 65: 57.025 distance: 65 - 66: 49.089 distance: 65 - 68: 35.576 distance: 66 - 67: 65.587 distance: 66 - 69: 33.709