Starting phenix.real_space_refine on Sun Sep 29 05:47:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyt_26194/09_2024/7tyt_26194.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyt_26194/09_2024/7tyt_26194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyt_26194/09_2024/7tyt_26194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyt_26194/09_2024/7tyt_26194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyt_26194/09_2024/7tyt_26194.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyt_26194/09_2024/7tyt_26194.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 6 Type Number sf(0) Gaussians K 1 8.98 5 P 28 5.49 5 S 93 5.16 5 C 13171 2.51 5 N 3452 2.21 5 O 3604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20349 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2535 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 16, 'TRANS': 339} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 13, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 164 Chain: "B" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2349 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 13, 'TRANS': 312} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 9, 'ASN:plan1': 2, 'HIS:plan': 4, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 147 Chain: "C" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2370 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 13, 'TRANS': 312} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 138 Chain: "D" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2395 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 13, 'TRANS': 312} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 102 Chain: "E" Number of atoms: 10003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1425, 10003 Classifications: {'peptide': 1425} Incomplete info: {'truncation_to_alanine': 366} Link IDs: {'PTRANS': 48, 'TRANS': 1376} Chain breaks: 6 Unresolved non-hydrogen bonds: 1285 Unresolved non-hydrogen angles: 1612 Unresolved non-hydrogen dihedrals: 1025 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 21, 'ASP:plan': 37, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 15, 'GLU:plan': 39, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 687 Chain: "F" 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: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {' K': 1, 'ATP': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "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: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} 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: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "E" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 346 Unusual residues: {'ATP': 1, 'BJX': 1, 'POV': 1, 'PTY': 6} Classifications: {'peptide': 1, 'undetermined': 9} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 124 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 12.54, per 1000 atoms: 0.62 Number of scatterers: 20349 At special positions: 0 Unit cell: (163.02, 107.635, 149.435, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 1 19.00 S 93 16.00 P 28 15.00 O 3604 8.00 N 3452 7.00 C 13171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 26 " 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 F 1 " - " NAG F 2 " NAG-ASN " NAG F 1 " - " ASN E 10 " Time building additional restraints: 6.06 Conformation dependent library (CDL) restraints added in 2.8 seconds 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5204 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 30 sheets defined 52.7% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 removed outlier: 4.372A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 65 removed outlier: 3.871A pdb=" N VAL A 59 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 97 Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 142 through 174 removed outlier: 3.569A pdb=" N ALA A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.996A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 4.040A pdb=" N HIS A 276 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 345 through 356 removed outlier: 3.623A pdb=" N ASP A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 65 removed outlier: 4.051A pdb=" N PHE B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR B 61 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 97 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 142 through 177 removed outlier: 3.779A pdb=" N ILE B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 173 " --> pdb=" O MET B 169 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG B 177 " --> pdb=" O GLN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 removed outlier: 4.047A pdb=" N ASP B 269 " --> pdb=" O PRO B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 356 removed outlier: 4.025A pdb=" N SER B 354 " --> pdb=" O ASP B 350 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 65 removed outlier: 4.190A pdb=" N THR C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 98 Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 142 through 176 removed outlier: 3.923A pdb=" N HIS C 175 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 removed outlier: 4.380A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 345 through 356 Processing helix chain 'D' and resid 55 through 65 removed outlier: 3.509A pdb=" N VAL D 59 " --> pdb=" O PHE D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 97 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 142 through 176 removed outlier: 3.896A pdb=" N ARG D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 removed outlier: 4.152A pdb=" N ASP D 269 " --> pdb=" O PRO D 266 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU D 270 " --> pdb=" O LEU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 346 through 356 removed outlier: 3.567A pdb=" N GLU D 351 " --> pdb=" O ARG D 347 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER D 354 " --> pdb=" O ASP D 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 16 removed outlier: 3.929A pdb=" N HIS E 11 " --> pdb=" O THR E 8 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ALA E 14 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR E 15 " --> pdb=" O SER E 12 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG E 16 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 51 removed outlier: 3.543A pdb=" N VAL E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Proline residue: E 35 - end of helix Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 60 through 65 Processing helix chain 'E' and resid 70 through 96 removed outlier: 4.161A pdb=" N TRP E 75 " --> pdb=" O HIS E 71 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 106 Processing helix chain 'E' and resid 107 through 130 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 160 removed outlier: 3.779A pdb=" N LEU E 145 " --> pdb=" O ILE E 141 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS E 150 " --> pdb=" O ALA E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 194 removed outlier: 3.520A pdb=" N CYS E 170 " --> pdb=" O GLN E 166 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 212 removed outlier: 3.652A pdb=" N GLN E 211 " --> pdb=" O PRO E 207 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP E 212 " --> pdb=" O GLU E 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 207 through 212' Processing helix chain 'E' and resid 223 through 230 Processing helix chain 'E' and resid 232 through 241 removed outlier: 4.168A pdb=" N PHE E 236 " --> pdb=" O TRP E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 276 removed outlier: 3.950A pdb=" N LYS E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 329 removed outlier: 5.346A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU E 301 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE E 314 " --> pdb=" O ASP E 310 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) Proline residue: E 317 - end of helix removed outlier: 3.525A pdb=" N LYS E 329 " --> pdb=" O ASP E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 354 through 402 Processing helix chain 'E' and resid 405 through 411 Processing helix chain 'E' and resid 413 through 457 Proline residue: E 436 - end of helix removed outlier: 3.523A pdb=" N TRP E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) Proline residue: E 442 - end of helix Processing helix chain 'E' and resid 457 through 505 removed outlier: 4.204A pdb=" N LEU E 461 " --> pdb=" O GLY E 457 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE E 462 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL E 466 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) Proline residue: E 472 - end of helix Processing helix chain 'E' and resid 505 through 512 Processing helix chain 'E' and resid 514 through 564 removed outlier: 3.638A pdb=" N THR E 531 " --> pdb=" O ARG E 527 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER E 532 " --> pdb=" O LYS E 528 " (cutoff:3.500A) Proline residue: E 551 - end of helix Processing helix chain 'E' and resid 572 through 615 removed outlier: 3.591A pdb=" N THR E 588 " --> pdb=" O HIS E 584 " (cutoff:3.500A) Proline residue: E 589 - end of helix removed outlier: 5.254A pdb=" N SER E 594 " --> pdb=" O LEU E 590 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER E 595 " --> pdb=" O PHE E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 719 through 728 Processing helix chain 'E' and resid 783 through 790 Processing helix chain 'E' and resid 795 through 807 removed outlier: 3.515A pdb=" N ILE E 803 " --> pdb=" O TYR E 799 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 815 removed outlier: 3.666A pdb=" N LEU E 815 " --> pdb=" O ASP E 811 " (cutoff:3.500A) Processing helix chain 'E' and resid 831 through 847 removed outlier: 3.557A pdb=" N ALA E 843 " --> pdb=" O SER E 839 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN E 847 " --> pdb=" O ALA E 843 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 881 Processing helix chain 'E' and resid 913 through 921 removed outlier: 4.000A pdb=" N GLN E 918 " --> pdb=" O LEU E 914 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG E 919 " --> pdb=" O LYS E 915 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER E 920 " --> pdb=" O ASP E 916 " (cutoff:3.500A) Processing helix chain 'E' and resid 923 through 928 removed outlier: 4.319A pdb=" N HIS E 927 " --> pdb=" O GLN E 923 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TRP E 928 " --> pdb=" O LEU E 924 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 923 through 928' Processing helix chain 'E' and resid 987 through 993 Processing helix chain 'E' and resid 996 through 1009 Processing helix chain 'E' and resid 1010 through 1040 removed outlier: 3.808A pdb=" N SER E1014 " --> pdb=" O ILE E1010 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU E1016 " --> pdb=" O LEU E1012 " (cutoff:3.500A) Processing helix chain 'E' and resid 1064 through 1106 removed outlier: 3.527A pdb=" N PHE E1068 " --> pdb=" O TYR E1064 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG E1099 " --> pdb=" O LYS E1095 " (cutoff:3.500A) Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.676A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) Processing helix chain 'E' and resid 1117 through 1161 removed outlier: 3.530A pdb=" N ILE E1121 " --> pdb=" O PRO E1117 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE E1136 " --> pdb=" O ILE E1132 " (cutoff:3.500A) Proline residue: E1137 - end of helix Processing helix chain 'E' and resid 1162 through 1210 removed outlier: 4.086A pdb=" N VAL E1166 " --> pdb=" O PRO E1162 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 3.606A pdb=" N TYR E1176 " --> pdb=" O ALA E1172 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP E1188 " --> pdb=" O VAL E1184 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU E1189 " --> pdb=" O ALA E1185 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E1198 " --> pdb=" O ASP E1194 " (cutoff:3.500A) Proline residue: E1199 - end of helix Processing helix chain 'E' and resid 1210 through 1217 Processing helix chain 'E' and resid 1219 through 1274 Processing helix chain 'E' and resid 1277 through 1320 removed outlier: 3.727A pdb=" N MET E1290 " --> pdb=" O THR E1286 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER E1292 " --> pdb=" O ALA E1288 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN E1293 " --> pdb=" O LEU E1289 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY E1310 " --> pdb=" O GLU E1306 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA E1311 " --> pdb=" O ILE E1307 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1386 through 1392 removed outlier: 3.579A pdb=" N LEU E1390 " --> pdb=" O SER E1386 " (cutoff:3.500A) Processing helix chain 'E' and resid 1414 through 1421 removed outlier: 3.973A pdb=" N ARG E1421 " --> pdb=" O THR E1417 " (cutoff:3.500A) Processing helix chain 'E' and resid 1435 through 1441 Processing helix chain 'E' and resid 1448 through 1459 Processing helix chain 'E' and resid 1460 through 1466 Processing helix chain 'E' and resid 1476 through 1480 removed outlier: 3.808A pdb=" N GLU E1480 " --> pdb=" O GLU E1477 " (cutoff:3.500A) Processing helix chain 'E' and resid 1485 through 1499 removed outlier: 3.636A pdb=" N LEU E1489 " --> pdb=" O GLY E1485 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG E1494 " --> pdb=" O PHE E1490 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA E1495 " --> pdb=" O CYS E1491 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE E1496 " --> pdb=" O LEU E1492 " (cutoff:3.500A) Processing helix chain 'E' and resid 1512 through 1530 Processing helix chain 'E' and resid 1539 through 1545 removed outlier: 3.835A pdb=" N SER E1545 " --> pdb=" O HIS E1541 " (cutoff:3.500A) Processing helix chain 'E' and resid 1572 through 1578 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA3, first strand: chain 'A' and resid 259 through 260 removed outlier: 6.516A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.604A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA A 213 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU A 288 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE A 215 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE A 286 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET A 217 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 284 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 219 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A 282 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 249 removed outlier: 4.082A pdb=" N ALA A 213 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA A 213 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU A 288 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE A 215 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE A 286 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET A 217 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 284 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 219 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A 282 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA7, first strand: chain 'A' and resid 319 through 321 removed outlier: 6.385A pdb=" N TYR A 326 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS D 47 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL A 328 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 47 removed outlier: 6.528A pdb=" N ALA B 45 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.588A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 234 through 238 removed outlier: 4.189A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER B 212 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL B 290 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 234 through 238 removed outlier: 4.189A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER B 212 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL B 290 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AB5, first strand: chain 'C' and resid 44 through 47 Processing sheet with id=AB6, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB7, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.811A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 230 through 238 removed outlier: 3.623A pdb=" N THR C 223 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU C 233 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARG C 221 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN C 235 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL C 219 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP C 237 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N MET C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA C 213 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 230 through 238 removed outlier: 3.623A pdb=" N THR C 223 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU C 233 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARG C 221 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN C 235 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL C 219 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP C 237 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N MET C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N SER C 212 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL C 290 " --> pdb=" O SER C 212 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 214 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AC2, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AC3, first strand: chain 'D' and resid 195 through 199 Processing sheet with id=AC4, first strand: chain 'D' and resid 210 through 211 Processing sheet with id=AC5, first strand: chain 'D' and resid 234 through 238 removed outlier: 4.040A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 313 through 315 Processing sheet with id=AC7, first strand: chain 'E' and resid 678 through 681 Processing sheet with id=AC8, first strand: chain 'E' and resid 685 through 687 removed outlier: 7.162A pdb=" N PHE E 685 " --> pdb=" O VAL E 733 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 770 through 771 removed outlier: 5.673A pdb=" N ALA E 771 " --> pdb=" O PHE E 852 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ASP E 854 " --> pdb=" O ALA E 771 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL E 887 " --> pdb=" O LEU E 853 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR E 709 " --> pdb=" O LEU E 886 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP E 899 " --> pdb=" O LEU E 708 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET E 903 " --> pdb=" O VAL E 712 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA E 902 " --> pdb=" O GLN E 909 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 1345 through 1347 Processing sheet with id=AD2, first strand: chain 'E' and resid 1502 through 1507 removed outlier: 3.511A pdb=" N ILE E1536 " --> pdb=" O MET E1505 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU E1507 " --> pdb=" O ILE E1536 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ILE E1375 " --> pdb=" O THR E1535 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ALA E1537 " --> pdb=" O ILE E1375 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE E1377 " --> pdb=" O ALA E1537 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E1548 " --> pdb=" O LYS E1374 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY E1376 " --> pdb=" O LEU E1548 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 1552 through 1553 1188 hydrogen bonds defined for protein. 3438 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: 7.65 Time building geometry restraints manager: 6.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3339 1.32 - 1.44: 5361 1.44 - 1.57: 11884 1.57 - 1.69: 53 1.69 - 1.81: 142 Bond restraints: 20779 Sorted by residual: bond pdb=" N BJX E1602 " pdb=" C6 BJX E1602 " ideal model delta sigma weight residual 1.412 1.532 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" C16 BJX E1602 " pdb=" N1 BJX E1602 " ideal model delta sigma weight residual 1.344 1.455 -0.111 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C21 BJX E1602 " pdb=" O1 BJX E1602 " ideal model delta sigma weight residual 1.347 1.422 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C5 BJX E1602 " pdb=" N1 BJX E1602 " ideal model delta sigma weight residual 1.446 1.516 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C5 BJX E1602 " pdb=" C8 BJX E1602 " ideal model delta sigma weight residual 1.536 1.601 -0.065 2.00e-02 2.50e+03 1.04e+01 ... (remaining 20774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 28112 2.21 - 4.41: 241 4.41 - 6.62: 43 6.62 - 8.82: 4 8.82 - 11.03: 1 Bond angle restraints: 28401 Sorted by residual: angle pdb=" C16 BJX E1602 " pdb=" N1 BJX E1602 " pdb=" C5 BJX E1602 " ideal model delta sigma weight residual 123.13 134.16 -11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C VAL E 33 " pdb=" N VAL E 34 " pdb=" CA VAL E 34 " ideal model delta sigma weight residual 120.33 122.94 -2.61 8.00e-01 1.56e+00 1.07e+01 angle pdb=" CA GLN C 313 " pdb=" CB GLN C 313 " pdb=" CG GLN C 313 " ideal model delta sigma weight residual 114.10 119.29 -5.19 2.00e+00 2.50e-01 6.73e+00 angle pdb=" N ILE E 423 " pdb=" CA ILE E 423 " pdb=" C ILE E 423 " ideal model delta sigma weight residual 110.82 113.25 -2.43 9.70e-01 1.06e+00 6.27e+00 angle pdb=" O2 BJX E1602 " pdb=" C24 BJX E1602 " pdb=" O3 BJX E1602 " ideal model delta sigma weight residual 126.98 119.85 7.13 3.00e+00 1.11e-01 5.65e+00 ... (remaining 28396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.33: 11823 32.33 - 64.66: 494 64.66 - 97.00: 32 97.00 - 129.33: 8 129.33 - 161.66: 8 Dihedral angle restraints: 12365 sinusoidal: 4359 harmonic: 8006 Sorted by residual: dihedral pdb=" CB CYS B 110 " pdb=" SG CYS B 110 " pdb=" SG CYS B 142 " pdb=" CB CYS B 142 " ideal model delta sinusoidal sigma weight residual 93.00 138.49 -45.49 1 1.00e+01 1.00e-02 2.87e+01 dihedral pdb=" O BJX E1602 " pdb=" C16 BJX E1602 " pdb=" C17 BJX E1602 " pdb=" C18 BJX E1602 " ideal model delta sinusoidal sigma weight residual 10.31 -151.35 161.66 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C38 P5S E1607 " pdb=" C39 P5S E1607 " pdb=" C40 P5S E1607 " pdb=" C41 P5S E1607 " ideal model delta sinusoidal sigma weight residual 64.51 -92.08 156.59 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 12362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3089 0.073 - 0.145: 337 0.145 - 0.218: 2 0.218 - 0.290: 1 0.290 - 0.363: 2 Chirality restraints: 3431 Sorted by residual: chirality pdb=" C2 P5S B 403 " pdb=" C1 P5S B 403 " pdb=" C3 P5S B 403 " pdb=" O37 P5S B 403 " both_signs ideal model delta sigma weight residual False 2.59 2.23 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" C2 P5S E1607 " pdb=" C1 P5S E1607 " pdb=" C3 P5S E1607 " pdb=" O37 P5S E1607 " both_signs ideal model delta sigma weight residual False 2.59 2.27 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C5 BJX E1602 " pdb=" C7 BJX E1602 " pdb=" C8 BJX E1602 " pdb=" N1 BJX E1602 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 3428 not shown) Planarity restraints: 3508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 316 " -0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO E 317 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 317 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 317 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 280 " 0.038 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO E 281 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 281 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 281 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 253 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO B 254 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 254 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 254 " -0.027 5.00e-02 4.00e+02 ... (remaining 3505 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.79: 4830 2.79 - 3.38: 22818 3.38 - 3.96: 36732 3.96 - 4.55: 50392 4.55 - 5.14: 73399 Nonbonded interactions: 188171 Sorted by model distance: nonbonded pdb=" OH TYR E 123 " pdb=" O LEU E 135 " model vdw 2.202 3.040 nonbonded pdb=" O ILE A 74 " pdb=" OG SER A 78 " model vdw 2.205 3.040 nonbonded pdb=" O PHE C 168 " pdb=" OG1 THR C 171 " model vdw 2.209 3.040 nonbonded pdb=" ND2 ASN E 781 " pdb=" OE2 GLU E1206 " model vdw 2.216 3.120 nonbonded pdb=" O ILE E 544 " pdb=" OG1 THR E 548 " model vdw 2.233 3.040 ... (remaining 188166 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 31 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 35 or (resid 36 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 42 or (resid 43 and (n \ ame N or name CA or name C or name O or name CB )) or resid 44 through 48 or (re \ sid 49 and (name N or name CA or name C or name O or name CB )) or resid 50 thro \ ugh 51 or (resid 52 and (name N or name CA or name C or name O or name CB )) or \ resid 53 or (resid 54 through 58 and (name N or name CA or name C or name O or n \ ame CB )) or resid 59 through 72 or (resid 73 through 74 and (name N or name CA \ or name C or name O or name CB )) or resid 75 through 81 or (resid 82 and (name \ N or name CA or name C or name O or name CB )) or resid 83 through 91 or (resid \ 92 and (name N or name CA or name C or name O or name CB )) or resid 93 through \ 117 or (resid 118 and (name N or name CA or name C or name O or name CB )) or re \ sid 119 through 139 or (resid 140 through 141 and (name N or name CA or name C o \ r name O or name CB )) or resid 142 through 147 or (resid 148 and (name N or nam \ e CA or name C or name O or name CB )) or resid 149 through 151 or (resid 152 an \ d (name N or name CA or name C or name O or name CB )) or resid 153 through 168 \ or (resid 169 and (name N or name CA or name C or name O or name CB )) or resid \ 170 through 179 or (resid 180 and (name N or name CA or name C or name O or name \ CB )) or resid 181 or (resid 182 and (name N or name CA or name C or name O or \ name CB )) or resid 183 through 187 or (resid 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 through 192 or (resid 193 and (name N or \ name CA or name C or name O or name CB )) or resid 194 or (resid 195 and (name \ N or name CA or name C or name O or name CB )) or resid 196 through 203 or (resi \ d 204 and (name N or name CA or name C or name O or name CB )) or resid 205 thro \ ugh 206 or (resid 207 and (name N or name CA or name C or name O or name CB )) o \ r resid 208 through 209 or (resid 210 through 211 and (name N or name CA or name \ C or name O or name CB )) or resid 212 through 221 or (resid 222 and (name N or \ name CA or name C or name O or name CB )) or resid 223 through 268 or (resid 26 \ 9 through 271 and (name N or name CA or name C or name O or name CB )) or resid \ 272 through 274 or (resid 275 through 276 and (name N or name CA or name C or na \ me O or name CB )) or resid 277 through 278 or (resid 279 through 282 and (name \ N or name CA or name C or name O or name CB )) or resid 283 through 291 or (resi \ d 292 and (name N or name CA or name C or name O or name CB )) or resid 293 thro \ ugh 302 or (resid 303 and (name N or name CA or name C or name O or name CB )) o \ r resid 304 or (resid 305 through 308 and (name N or name CA or name C or name O \ or name CB )) or resid 309 through 317 or (resid 318 and (name N or name CA or \ name C or name O or name CB )) or resid 319 through 328 or (resid 329 and (name \ N or name CA or name C or name O or name CB )) or resid 330 through 343 or (resi \ d 344 and (name N or name CA or name C or name O or name CB )) or resid 345 thro \ ugh 346 or (resid 347 through 348 and (name N or name CA or name C or name O or \ name CB )) or resid 349 through 350 or (resid 351 through 356 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'B' and ((resid 31 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 35 or (resid 36 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 54 or (resid 55 throug \ h 58 and (name N or name CA or name C or name O or name CB )) or resid 59 throug \ h 65 or (resid 66 and (name N or name CA or name C or name O or name CB )) or re \ sid 67 through 70 or (resid 71 and (name N or name CA or name C or name O or nam \ e CB )) or resid 72 through 76 or (resid 77 and (name N or name CA or name C or \ name O or name CB )) or resid 78 through 91 or (resid 92 and (name N or name CA \ or name C or name O or name CB )) or resid 93 through 99 or (resid 100 through 1 \ 01 and (name N or name CA or name C or name O or name CB )) or resid 102 through \ 117 or (resid 118 and (name N or name CA or name C or name O or name CB )) or r \ esid 119 through 147 or (resid 148 and (name N or name CA or name C or name O or \ name CB )) or resid 149 through 153 or (resid 154 and (name N or name CA or nam \ e C or name O or name CB )) or resid 155 through 187 or (resid 188 and (name N o \ r name CA or name C or name O or name CB )) or resid 189 through 191 or (resid 1 \ 92 through 193 and (name N or name CA or name C or name O or name CB )) or resid \ 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) or r \ esid 196 through 206 or (resid 207 and (name N or name CA or name C or name O or \ name CB )) or resid 208 through 209 or (resid 210 through 211 and (name N or na \ me CA or name C or name O or name CB )) or resid 212 through 221 or (resid 222 a \ nd (name N or name CA or name C or name O or name CB )) or resid 223 through 250 \ or (resid 251 and (name N or name CA or name C or name O or name CB )) or resid \ 252 through 259 or (resid 260 through 262 and (name N or name CA or name C or n \ ame O or name CB )) or resid 263 through 264 or (resid 265 and (name N or name C \ A or name C or name O or name CB )) or resid 266 through 269 or (resid 270 throu \ gh 271 and (name N or name CA or name C or name O or name CB )) or resid 272 thr \ ough 280 or (resid 281 through 282 and (name N or name CA or name C or name O or \ name CB )) or resid 283 through 302 or (resid 303 and (name N or name CA or nam \ e C or name O or name CB )) or resid 304 or (resid 305 through 308 and (name N o \ r name CA or name C or name O or name CB )) or resid 309 through 317 or (resid 3 \ 18 and (name N or name CA or name C or name O or name CB )) or resid 319 through \ 328 or (resid 329 and (name N or name CA or name C or name O or name CB )) or r \ esid 330 through 353 or (resid 354 through 356 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'C' and (resid 31 through 35 or (resid 36 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 42 or (resid 43 and (na \ me N or name CA or name C or name O or name CB )) or resid 44 through 48 or (res \ id 49 and (name N or name CA or name C or name O or name CB )) or resid 50 throu \ gh 65 or (resid 66 and (name N or name CA or name C or name O or name CB )) or r \ esid 67 through 70 or (resid 71 and (name N or name CA or name C or name O or na \ me CB )) or resid 72 or (resid 73 through 74 and (name N or name CA or name C or \ name O or name CB )) or resid 75 through 76 or (resid 77 and (name N or name CA \ or name C or name O or name CB )) or resid 78 through 81 or (resid 82 and (name \ N or name CA or name C or name O or name CB )) or resid 83 through 99 or (resid \ 100 through 101 and (name N or name CA or name C or name O or name CB )) or res \ id 102 through 139 or (resid 140 through 141 and (name N or name CA or name C or \ name O or name CB )) or resid 142 through 153 or (resid 154 and (name N or name \ CA or name C or name O or name CB )) or resid 155 through 168 or (resid 169 and \ (name N or name CA or name C or name O or name CB )) or resid 170 through 181 o \ r (resid 182 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 83 through 191 or (resid 192 through 193 and (name N or name CA or name C or nam \ e O or name CB )) or resid 194 through 206 or (resid 207 and (name N or name CA \ or name C or name O or name CB )) or resid 208 through 209 or (resid 210 through \ 211 and (name N or name CA or name C or name O or name CB )) or resid 212 throu \ gh 221 or (resid 222 and (name N or name CA or name C or name O or name CB )) or \ resid 223 through 250 or (resid 251 and (name N or name CA or name C or name O \ or name CB )) or resid 252 through 254 or (resid 255 and (name N or name CA or n \ ame C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 2 \ 64 or (resid 265 and (name N or name CA or name C or name O or name CB )) or res \ id 266 through 268 or (resid 269 through 271 and (name N or name CA or name C or \ name O or name CB )) or resid 272 through 273 or (resid 274 through 276 and (na \ me N or name CA or name C or name O or name CB )) or resid 277 through 278 or (r \ esid 279 through 282 and (name N or name CA or name C or name O or name CB )) or \ resid 283 through 291 or (resid 292 and (name N or name CA or name C or name O \ or name CB )) or resid 293 through 306 or (resid 307 through 308 and (name N or \ name CA or name C or name O or name CB )) or resid 309 through 317 or (resid 318 \ and (name N or name CA or name C or name O or name CB )) or resid 319 through 3 \ 31 or (resid 332 and (name N or name CA or name C or name O or name CB )) or res \ id 333 through 343 or (resid 344 and (name N or name CA or name C or name O or n \ ame CB )) or resid 345 through 346 or (resid 347 through 348 and (name N or name \ CA or name C or name O or name CB )) or resid 349 through 356)) selection = (chain 'D' and (resid 31 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 48 or (resid 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 54 or (resid 55 throu \ gh 58 and (name N or name CA or name C or name O or name CB )) or resid 59 throu \ gh 72 or (resid 73 through 74 and (name N or name CA or name C or name O or name \ CB )) or resid 75 through 76 or (resid 77 and (name N or name CA or name C or n \ ame O or name CB )) or resid 78 through 81 or (resid 82 and (name N or name CA o \ r name C or name O or name CB )) or resid 83 through 91 or (resid 92 and (name N \ or name CA or name C or name O or name CB )) or resid 93 through 99 or (resid 1 \ 00 through 101 and (name N or name CA or name C or name O or name CB )) or resid \ 102 through 114 or (resid 115 and (name N or name CA or name C or name O or nam \ e CB )) or resid 116 through 117 or (resid 118 and (name N or name CA or name C \ or name O or name CB )) or resid 119 through 139 or (resid 140 through 141 and ( \ name N or name CA or name C or name O or name CB )) or resid 142 through 147 or \ (resid 148 and (name N or name CA or name C or name O or name CB )) or resid 149 \ through 151 or (resid 152 and (name N or name CA or name C or name O or name CB \ )) or resid 153 or (resid 154 and (name N or name CA or name C or name O or nam \ e CB )) or resid 155 through 179 or (resid 180 and (name N or name CA or name C \ or name O or name CB )) or resid 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 192 or (resid 193 and (name N o \ r name CA or name C or name O or name CB )) or resid 194 or (resid 195 and (name \ N or name CA or name C or name O or name CB )) or resid 196 through 198 or (res \ id 199 through 200 and (name N or name CA or name C or name O or name CB )) or r \ esid 201 through 210 or (resid 211 and (name N or name CA or name C or name O or \ name CB )) or resid 212 through 250 or (resid 251 and (name N or name CA or nam \ e C or name O or name CB )) or resid 252 through 254 or (resid 255 and (name N o \ r name CA or name C or name O or name CB )) or resid 256 through 259 or (resid 2 \ 60 through 262 and (name N or name CA or name C or name O or name CB )) or resid \ 263 through 264 or (resid 265 and (name N or name CA or name C or name O or nam \ e CB )) or resid 266 through 268 or (resid 269 through 271 and (name N or name C \ A or name C or name O or name CB )) or resid 272 through 273 or (resid 274 throu \ gh 276 and (name N or name CA or name C or name O or name CB )) or resid 277 thr \ ough 278 or (resid 279 through 282 and (name N or name CA or name C or name O or \ name CB )) or resid 283 through 287 or (resid 288 and (name N or name CA or nam \ e C or name O or name CB )) or resid 289 through 291 or (resid 292 and (name N o \ r name CA or name C or name O or name CB )) or resid 293 through 302 or (resid 3 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 304 or (res \ id 305 through 308 and (name N or name CA or name C or name O or name CB )) or r \ esid 309 through 328 or (resid 329 and (name N or name CA or name C or name O or \ name CB )) or resid 330 through 343 or (resid 344 and (name N or name CA or nam \ e C or name O or name CB )) or resid 345 through 346 or (resid 347 through 348 a \ nd (name N or name CA or name C or name O or name CB )) or resid 349 through 351 \ or (resid 352 through 356 and (name N or name CA or name C or name O or name CB \ )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 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: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 48.130 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.004 0.120 20779 Z= 0.275 Angle : 0.565 11.028 28401 Z= 0.301 Chirality : 0.044 0.363 3431 Planarity : 0.004 0.063 3507 Dihedral : 17.875 161.659 7146 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.67 % Allowed : 25.35 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2737 helix: 2.25 (0.14), residues: 1300 sheet: -1.28 (0.29), residues: 315 loop : -0.96 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 65 HIS 0.009 0.001 HIS E1098 PHE 0.021 0.001 PHE B 60 TYR 0.014 0.001 TYR E 123 ARG 0.007 0.000 ARG E1145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 510 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8518 (tt) REVERT: B 186 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.6386 (p-80) REVERT: C 74 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8334 (mp) REVERT: C 84 LEU cc_start: 0.8720 (tt) cc_final: 0.8490 (tt) REVERT: C 191 LEU cc_start: 0.7171 (mp) cc_final: 0.6822 (mp) REVERT: C 230 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8238 (m) REVERT: D 70 HIS cc_start: 0.7919 (OUTLIER) cc_final: 0.7637 (m90) REVERT: E 416 GLN cc_start: 0.8307 (tm-30) cc_final: 0.8026 (tm-30) REVERT: E 427 GLN cc_start: 0.8193 (mt0) cc_final: 0.7973 (mt0) REVERT: E 529 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7519 (tm-30) REVERT: E 1004 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.6315 (m-80) REVERT: E 1036 LYS cc_start: 0.8110 (tppt) cc_final: 0.7837 (mmtp) outliers start: 30 outliers final: 9 residues processed: 523 average time/residue: 0.2914 time to fit residues: 239.9818 Evaluate side-chains 486 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 471 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1316 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 213 optimal weight: 30.0000 chunk 82 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 234 HIS C 299 GLN D 235 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 822 GLN E 836 GLN E1135 HIS E1270 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 20779 Z= 0.367 Angle : 0.619 11.413 28401 Z= 0.321 Chirality : 0.047 0.371 3431 Planarity : 0.005 0.053 3507 Dihedral : 15.175 158.324 3551 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 6.78 % Allowed : 22.35 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.16), residues: 2737 helix: 1.93 (0.14), residues: 1313 sheet: -1.42 (0.30), residues: 289 loop : -1.07 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E1452 HIS 0.009 0.001 HIS E1024 PHE 0.025 0.002 PHE A 86 TYR 0.022 0.002 TYR E 123 ARG 0.006 0.001 ARG E1145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 509 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9461 (OUTLIER) cc_final: 0.9206 (t) REVERT: A 168 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6499 (t80) REVERT: B 186 HIS cc_start: 0.7017 (OUTLIER) cc_final: 0.6444 (p-80) REVERT: C 84 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8481 (tt) REVERT: C 230 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8180 (m) REVERT: C 279 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7588 (tp40) REVERT: D 70 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.7551 (m90) REVERT: D 128 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8236 (tp40) REVERT: D 252 VAL cc_start: 0.8908 (t) cc_final: 0.8416 (p) REVERT: D 308 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7201 (mt-10) REVERT: E 96 ASP cc_start: 0.9016 (p0) cc_final: 0.8807 (p0) REVERT: E 427 GLN cc_start: 0.8161 (mt0) cc_final: 0.7927 (mt0) REVERT: E 1004 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.6695 (m-80) REVERT: E 1092 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8064 (tttp) REVERT: E 1222 ARG cc_start: 0.7766 (tpt90) cc_final: 0.7523 (ttm170) outliers start: 122 outliers final: 72 residues processed: 569 average time/residue: 0.2926 time to fit residues: 261.2828 Evaluate side-chains 564 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 481 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 439 TRP Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 483 GLN Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 784 VAL Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1081 VAL Chi-restraints excluded: chain E residue 1089 THR Chi-restraints excluded: chain E residue 1092 LYS Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1195 THR Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1502 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 248 optimal weight: 50.0000 chunk 268 optimal weight: 50.0000 chunk 221 optimal weight: 2.9990 chunk 246 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 199 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 HIS D 48 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN E 775 GLN E 870 GLN E1270 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20779 Z= 0.212 Angle : 0.555 11.905 28401 Z= 0.283 Chirality : 0.044 0.312 3431 Planarity : 0.004 0.046 3507 Dihedral : 14.867 163.979 3549 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 6.11 % Allowed : 24.68 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 2737 helix: 2.10 (0.14), residues: 1320 sheet: -1.55 (0.28), residues: 323 loop : -1.10 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 430 HIS 0.013 0.001 HIS E 11 PHE 0.023 0.001 PHE E 790 TYR 0.017 0.001 TYR E 123 ARG 0.006 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 496 time to evaluate : 2.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9454 (OUTLIER) cc_final: 0.9185 (t) REVERT: A 168 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.6400 (t80) REVERT: B 186 HIS cc_start: 0.7013 (OUTLIER) cc_final: 0.6507 (p-80) REVERT: C 84 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8421 (tt) REVERT: C 147 LEU cc_start: 0.9120 (tp) cc_final: 0.8766 (tp) REVERT: C 230 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8200 (m) REVERT: C 279 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: D 70 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7606 (m90) REVERT: D 128 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8133 (tp40) REVERT: E 233 MET cc_start: 0.8684 (tpp) cc_final: 0.8387 (tpp) REVERT: E 427 GLN cc_start: 0.8170 (mt0) cc_final: 0.7930 (mt0) REVERT: E 429 MET cc_start: 0.8051 (ttp) cc_final: 0.7768 (ttt) REVERT: E 433 PHE cc_start: 0.8891 (m-10) cc_final: 0.8591 (m-80) REVERT: E 1004 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.6636 (m-80) REVERT: E 1092 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7996 (tttp) REVERT: E 1272 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7328 (mp) outliers start: 110 outliers final: 69 residues processed: 546 average time/residue: 0.2860 time to fit residues: 247.2779 Evaluate side-chains 557 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 477 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 270 PHE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 689 THR Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1092 LYS Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1195 THR Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1306 GLU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1533 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 27 optimal weight: 40.0000 chunk 118 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 249 optimal weight: 0.0060 chunk 263 optimal weight: 8.9990 chunk 130 optimal weight: 0.0060 chunk 236 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 overall best weight: 3.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 48 ASN D 152 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN E 354 ASN E 775 GLN E1270 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20779 Z= 0.234 Angle : 0.545 10.368 28401 Z= 0.281 Chirality : 0.044 0.310 3431 Planarity : 0.004 0.045 3507 Dihedral : 14.588 168.521 3545 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 7.23 % Allowed : 24.62 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 2737 helix: 2.15 (0.14), residues: 1320 sheet: -1.61 (0.28), residues: 323 loop : -1.10 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E1452 HIS 0.012 0.001 HIS E 11 PHE 0.028 0.001 PHE E 790 TYR 0.018 0.001 TYR E 123 ARG 0.005 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 493 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9461 (OUTLIER) cc_final: 0.9195 (t) REVERT: A 168 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6435 (t80) REVERT: A 314 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.5914 (ttm-80) REVERT: B 186 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6560 (p-80) REVERT: C 230 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8154 (m) REVERT: D 70 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7593 (m90) REVERT: D 128 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8158 (tp40) REVERT: E 325 ASP cc_start: 0.8100 (t0) cc_final: 0.7660 (t0) REVERT: E 427 GLN cc_start: 0.8175 (mt0) cc_final: 0.7950 (mt0) REVERT: E 433 PHE cc_start: 0.8886 (m-10) cc_final: 0.8595 (m-80) REVERT: E 1004 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.6564 (m-80) REVERT: E 1092 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8004 (tttp) REVERT: E 1267 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8644 (m) REVERT: E 1272 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7336 (mp) outliers start: 130 outliers final: 89 residues processed: 560 average time/residue: 0.2839 time to fit residues: 251.9674 Evaluate side-chains 573 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 473 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 259 HIS Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 270 PHE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 689 THR Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1092 LYS Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1150 CYS Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1195 THR Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1267 SER Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1306 GLU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1502 ILE Chi-restraints excluded: chain E residue 1533 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 196 optimal weight: 40.0000 chunk 108 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 134 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 GLN D 48 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 ASN E 775 GLN E1270 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20779 Z= 0.246 Angle : 0.557 10.446 28401 Z= 0.286 Chirality : 0.045 0.310 3431 Planarity : 0.004 0.045 3507 Dihedral : 14.455 172.593 3545 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 7.28 % Allowed : 25.63 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.16), residues: 2737 helix: 2.12 (0.14), residues: 1320 sheet: -1.56 (0.28), residues: 324 loop : -1.11 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E1452 HIS 0.011 0.001 HIS E 11 PHE 0.020 0.001 PHE E 577 TYR 0.018 0.001 TYR E 123 ARG 0.005 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 485 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9463 (OUTLIER) cc_final: 0.9188 (t) REVERT: A 168 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6439 (t80) REVERT: A 314 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.5853 (ttm-80) REVERT: B 186 HIS cc_start: 0.7106 (OUTLIER) cc_final: 0.6616 (p-80) REVERT: C 230 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8169 (m) REVERT: D 56 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7078 (mp) REVERT: D 70 HIS cc_start: 0.7866 (OUTLIER) cc_final: 0.7580 (m90) REVERT: D 128 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8087 (tp40) REVERT: E 427 GLN cc_start: 0.8181 (mt0) cc_final: 0.7954 (mt0) REVERT: E 433 PHE cc_start: 0.8912 (m-10) cc_final: 0.8608 (m-80) REVERT: E 1004 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.6706 (m-80) REVERT: E 1092 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7992 (tttp) REVERT: E 1149 LEU cc_start: 0.8884 (mt) cc_final: 0.8593 (mt) REVERT: E 1267 SER cc_start: 0.9075 (OUTLIER) cc_final: 0.8700 (m) REVERT: E 1272 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7357 (mp) outliers start: 131 outliers final: 96 residues processed: 556 average time/residue: 0.2919 time to fit residues: 258.4331 Evaluate side-chains 577 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 469 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 259 HIS Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 270 PHE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 689 THR Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1092 LYS Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1150 CYS Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1195 THR Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1267 SER Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1306 GLU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1502 ILE Chi-restraints excluded: chain E residue 1533 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 0.0970 chunk 237 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 264 optimal weight: 50.0000 chunk 219 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 overall best weight: 4.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 48 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 775 GLN E1270 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20779 Z= 0.269 Angle : 0.569 10.426 28401 Z= 0.292 Chirality : 0.045 0.311 3431 Planarity : 0.004 0.060 3507 Dihedral : 14.403 176.697 3545 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 7.56 % Allowed : 25.90 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 2737 helix: 2.08 (0.14), residues: 1322 sheet: -1.53 (0.30), residues: 292 loop : -1.11 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 899 HIS 0.010 0.001 HIS E 11 PHE 0.021 0.002 PHE E 577 TYR 0.019 0.002 TYR E 123 ARG 0.004 0.000 ARG E1145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 485 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9464 (OUTLIER) cc_final: 0.9195 (t) REVERT: A 168 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6451 (t80) REVERT: A 314 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.5968 (ttm-80) REVERT: B 186 HIS cc_start: 0.7179 (OUTLIER) cc_final: 0.6671 (p-80) REVERT: C 230 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8166 (m) REVERT: D 56 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7127 (mp) REVERT: D 70 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7584 (m90) REVERT: D 128 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8095 (tp40) REVERT: E 427 GLN cc_start: 0.8185 (mt0) cc_final: 0.7961 (mt0) REVERT: E 433 PHE cc_start: 0.8945 (m-10) cc_final: 0.8658 (m-80) REVERT: E 1004 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.6634 (m-80) REVERT: E 1092 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8007 (tttp) REVERT: E 1149 LEU cc_start: 0.8891 (mt) cc_final: 0.8598 (mt) REVERT: E 1267 SER cc_start: 0.9136 (OUTLIER) cc_final: 0.8737 (m) outliers start: 136 outliers final: 104 residues processed: 554 average time/residue: 0.3074 time to fit residues: 272.7795 Evaluate side-chains 588 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 473 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 259 HIS Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 270 PHE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 439 TRP Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 689 THR Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1070 LEU Chi-restraints excluded: chain E residue 1092 LYS Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1150 CYS Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1195 THR Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1267 SER Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1306 GLU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1502 ILE Chi-restraints excluded: chain E residue 1533 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 30.0000 chunk 29 optimal weight: 6.9990 chunk 150 optimal weight: 0.0050 chunk 192 optimal weight: 40.0000 chunk 149 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 263 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 GLN C 247 ASN D 48 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN E 437 ASN E 775 GLN E 787 ASN E1203 HIS E1270 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20779 Z= 0.179 Angle : 0.536 11.474 28401 Z= 0.273 Chirality : 0.044 0.302 3431 Planarity : 0.004 0.060 3507 Dihedral : 14.120 178.388 3545 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.56 % Allowed : 27.90 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.17), residues: 2737 helix: 2.27 (0.14), residues: 1326 sheet: -1.61 (0.28), residues: 331 loop : -1.06 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 90 HIS 0.009 0.001 HIS E 11 PHE 0.027 0.001 PHE E 790 TYR 0.017 0.001 TYR E 123 ARG 0.005 0.000 ARG E 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 492 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9457 (OUTLIER) cc_final: 0.9184 (t) REVERT: A 168 PHE cc_start: 0.7171 (OUTLIER) cc_final: 0.6304 (t80) REVERT: A 314 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.6037 (ttm-80) REVERT: B 186 HIS cc_start: 0.7109 (OUTLIER) cc_final: 0.6653 (p-80) REVERT: C 230 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8227 (m) REVERT: D 34 ARG cc_start: 0.8051 (ttm110) cc_final: 0.7422 (ttt90) REVERT: D 70 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.7445 (m90) REVERT: E 325 ASP cc_start: 0.8034 (t0) cc_final: 0.7594 (t0) REVERT: E 427 GLN cc_start: 0.8116 (mt0) cc_final: 0.7854 (mt0) REVERT: E 433 PHE cc_start: 0.8866 (m-10) cc_final: 0.8537 (m-80) REVERT: E 787 ASN cc_start: 0.7696 (t0) cc_final: 0.7476 (t0) REVERT: E 1004 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.6718 (m-80) REVERT: E 1092 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7931 (tttp) REVERT: E 1149 LEU cc_start: 0.8855 (mt) cc_final: 0.8543 (mt) REVERT: E 1267 SER cc_start: 0.9086 (OUTLIER) cc_final: 0.8721 (m) outliers start: 100 outliers final: 77 residues processed: 545 average time/residue: 0.2888 time to fit residues: 252.0273 Evaluate side-chains 563 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 477 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 270 PHE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 437 ASN Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 689 THR Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1070 LEU Chi-restraints excluded: chain E residue 1092 LYS Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1150 CYS Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1267 SER Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1306 GLU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1533 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 ASN D 48 ASN E 125 HIS ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 775 GLN E 787 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 20779 Z= 0.470 Angle : 0.689 11.474 28401 Z= 0.355 Chirality : 0.049 0.341 3431 Planarity : 0.005 0.062 3507 Dihedral : 14.376 177.474 3545 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 7.00 % Allowed : 27.07 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2737 helix: 1.77 (0.14), residues: 1321 sheet: -1.61 (0.30), residues: 285 loop : -1.29 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 439 HIS 0.010 0.001 HIS E1024 PHE 0.023 0.002 PHE A 86 TYR 0.021 0.002 TYR E 107 ARG 0.005 0.001 ARG E 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 497 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9484 (OUTLIER) cc_final: 0.9232 (t) REVERT: A 314 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.5895 (ttm-80) REVERT: B 186 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6701 (p-80) REVERT: C 230 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8260 (m) REVERT: C 313 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7152 (mm-40) REVERT: D 56 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7175 (mp) REVERT: D 70 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7614 (m90) REVERT: D 252 VAL cc_start: 0.8958 (t) cc_final: 0.8434 (p) REVERT: E 427 GLN cc_start: 0.8194 (mt0) cc_final: 0.7967 (mt0) REVERT: E 433 PHE cc_start: 0.9005 (m-10) cc_final: 0.8689 (m-80) REVERT: E 1004 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.6735 (m-80) REVERT: E 1092 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8120 (tttp) REVERT: E 1149 LEU cc_start: 0.8939 (mt) cc_final: 0.8688 (mt) REVERT: E 1168 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8359 (tp) outliers start: 126 outliers final: 94 residues processed: 559 average time/residue: 0.3059 time to fit residues: 267.5395 Evaluate side-chains 595 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 491 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 259 HIS Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 439 TRP Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 485 GLN Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 689 THR Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 784 VAL Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1070 LEU Chi-restraints excluded: chain E residue 1092 LYS Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1150 CYS Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1195 THR Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1306 GLU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1533 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 229 optimal weight: 7.9990 chunk 245 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 0.3980 chunk 192 optimal weight: 40.0000 chunk 75 optimal weight: 6.9990 chunk 221 optimal weight: 20.0000 chunk 231 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN C 247 ASN D 48 ASN D 152 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 775 GLN E1293 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20779 Z= 0.207 Angle : 0.572 12.287 28401 Z= 0.292 Chirality : 0.044 0.301 3431 Planarity : 0.004 0.064 3507 Dihedral : 14.014 164.742 3545 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.78 % Allowed : 29.85 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2737 helix: 2.09 (0.14), residues: 1325 sheet: -1.63 (0.29), residues: 299 loop : -1.16 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 91 HIS 0.012 0.001 HIS E1098 PHE 0.039 0.001 PHE E 790 TYR 0.018 0.001 TYR E 123 ARG 0.010 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 478 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9468 (OUTLIER) cc_final: 0.9196 (t) REVERT: A 314 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.5939 (ttm-80) REVERT: B 186 HIS cc_start: 0.7177 (OUTLIER) cc_final: 0.6731 (p-80) REVERT: C 77 MET cc_start: 0.7294 (tpt) cc_final: 0.7025 (tpt) REVERT: C 147 LEU cc_start: 0.9085 (tp) cc_final: 0.8710 (tp) REVERT: C 230 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8269 (m) REVERT: C 313 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.7042 (mm-40) REVERT: C 314 ARG cc_start: 0.6067 (ptt180) cc_final: 0.5806 (ptt180) REVERT: D 56 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7142 (mp) REVERT: D 70 HIS cc_start: 0.7811 (OUTLIER) cc_final: 0.7478 (m90) REVERT: E 325 ASP cc_start: 0.8036 (t0) cc_final: 0.7611 (t0) REVERT: E 427 GLN cc_start: 0.8153 (mt0) cc_final: 0.7912 (mt0) REVERT: E 433 PHE cc_start: 0.8928 (m-10) cc_final: 0.8595 (m-80) REVERT: E 1004 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.6676 (m-80) REVERT: E 1092 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8022 (tttp) outliers start: 86 outliers final: 71 residues processed: 527 average time/residue: 0.2903 time to fit residues: 242.8823 Evaluate side-chains 551 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 471 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 485 GLN Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 689 THR Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1070 LEU Chi-restraints excluded: chain E residue 1092 LYS Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1150 CYS Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1306 GLU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1502 ILE Chi-restraints excluded: chain E residue 1520 LEU Chi-restraints excluded: chain E residue 1533 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 4.9990 chunk 259 optimal weight: 40.0000 chunk 158 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 180 optimal weight: 20.0000 chunk 271 optimal weight: 20.0000 chunk 250 optimal weight: 7.9990 chunk 216 optimal weight: 50.0000 chunk 22 optimal weight: 20.0000 chunk 167 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 overall best weight: 8.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN C 247 ASN D 46 HIS D 48 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 775 GLN E 787 ASN E1293 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 20779 Z= 0.421 Angle : 0.672 12.435 28401 Z= 0.345 Chirality : 0.048 0.338 3431 Planarity : 0.005 0.065 3507 Dihedral : 14.146 160.448 3545 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.56 % Allowed : 29.41 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2737 helix: 1.73 (0.14), residues: 1320 sheet: -1.76 (0.29), residues: 298 loop : -1.30 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 439 HIS 0.011 0.001 HIS E1098 PHE 0.036 0.002 PHE E 790 TYR 0.020 0.002 TYR E 123 ARG 0.008 0.001 ARG C 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 490 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9482 (OUTLIER) cc_final: 0.9218 (t) REVERT: A 168 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6579 (t80) REVERT: A 314 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6091 (ttm-80) REVERT: B 186 HIS cc_start: 0.7303 (OUTLIER) cc_final: 0.6796 (p-80) REVERT: B 229 GLU cc_start: 0.7800 (mp0) cc_final: 0.7386 (mp0) REVERT: C 230 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8304 (m) REVERT: C 274 ASP cc_start: 0.7861 (t70) cc_final: 0.7228 (t70) REVERT: C 309 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8859 (mm) REVERT: C 313 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7065 (mm-40) REVERT: D 56 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7156 (mp) REVERT: D 70 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.7599 (m90) REVERT: E 136 LEU cc_start: 0.8560 (mt) cc_final: 0.8344 (mt) REVERT: E 427 GLN cc_start: 0.8188 (mt0) cc_final: 0.7946 (mt0) REVERT: E 433 PHE cc_start: 0.8998 (m-10) cc_final: 0.8680 (m-80) REVERT: E 1004 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.6680 (m-80) REVERT: E 1092 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8107 (tttp) REVERT: E 1149 LEU cc_start: 0.8941 (mt) cc_final: 0.8683 (mt) outliers start: 100 outliers final: 80 residues processed: 545 average time/residue: 0.2923 time to fit residues: 250.2441 Evaluate side-chains 576 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 485 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 259 HIS Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 485 GLN Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 689 THR Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1070 LEU Chi-restraints excluded: chain E residue 1092 LYS Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1150 CYS Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1306 GLU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1502 ILE Chi-restraints excluded: chain E residue 1533 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 216 optimal weight: 40.0000 chunk 90 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 ASN D 48 ASN D 152 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN E 262 ASN ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 775 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.170345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.140207 restraints weight = 26236.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.142011 restraints weight = 16655.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.142671 restraints weight = 11987.737| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20779 Z= 0.310 Angle : 0.630 12.753 28401 Z= 0.322 Chirality : 0.047 0.316 3431 Planarity : 0.005 0.075 3507 Dihedral : 14.038 158.937 3545 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.61 % Allowed : 29.46 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2737 helix: 1.80 (0.14), residues: 1320 sheet: -1.75 (0.29), residues: 298 loop : -1.28 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 439 HIS 0.014 0.001 HIS E1098 PHE 0.039 0.002 PHE E 790 TYR 0.019 0.002 TYR E 123 ARG 0.018 0.001 ARG D 325 =============================================================================== Job complete usr+sys time: 4709.10 seconds wall clock time: 83 minutes 57.07 seconds (5037.07 seconds total)