Starting phenix.real_space_refine on Thu Aug 6 15:28:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28jq_56549/08_2026/28jq_56549.cif Found real_map, /net/cci-nas-00/data/ceres_data/28jq_56549/08_2026/28jq_56549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/28jq_56549/08_2026/28jq_56549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28jq_56549/08_2026/28jq_56549.map" model { file = "/net/cci-nas-00/data/ceres_data/28jq_56549/08_2026/28jq_56549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28jq_56549/08_2026/28jq_56549.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 48 5.16 5 C 9840 2.51 5 N 2745 2.21 5 O 3077 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15711 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6012 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 29, 'TRANS': 740} Chain breaks: 3 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'TYR:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2685 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 347} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1265 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 11, 'TRANS': 170} Chain breaks: 3 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1764 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain: "F" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3260 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 397} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.65, per 1000 atoms: 0.17 Number of scatterers: 15711 At special positions: 0 Unit cell: (122.1, 147.26, 147.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 48 16.00 O 3077 8.00 N 2745 7.00 C 9840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 625.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 601 " pdb="ZN ZN F 601 " - pdb=" ND1 HIS F 246 " pdb="ZN ZN F 601 " - pdb=" NE2 HIS F 136 " pdb="ZN ZN F 601 " - pdb=" NE2 HIS F 140 " 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3752 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 22 sheets defined 36.8% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.516A pdb=" N ALA A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.836A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 118 removed outlier: 3.580A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 142 removed outlier: 4.194A pdb=" N ASP A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.951A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 297 through 315 removed outlier: 4.013A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 368 removed outlier: 4.120A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.994A pdb=" N GLY A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 452 Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 730 removed outlier: 3.727A pdb=" N ALA A 730 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 3.700A pdb=" N LEU B 244 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 33 removed outlier: 4.225A pdb=" N TYR C 31 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 192 through 212 Processing helix chain 'C' and resid 247 through 261 Proline residue: C 256 - end of helix Processing helix chain 'C' and resid 327 through 343 removed outlier: 4.406A pdb=" N ALA C 336 " --> pdb=" O ASP C 332 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 removed outlier: 4.002A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 138 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.850A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.569A pdb=" N GLU D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.780A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 26 removed outlier: 3.822A pdb=" N ARG E 25 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 removed outlier: 3.530A pdb=" N SER E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.682A pdb=" N THR F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 39 through 44' Processing helix chain 'F' and resid 45 through 63 Processing helix chain 'F' and resid 71 through 86 removed outlier: 4.238A pdb=" N HIS F 86 " --> pdb=" O ARG F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 124 removed outlier: 4.269A pdb=" N ARG F 122 " --> pdb=" O SER F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 143 removed outlier: 3.706A pdb=" N VAL F 133 " --> pdb=" O GLN F 129 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 149 removed outlier: 3.722A pdb=" N ALA F 149 " --> pdb=" O HIS F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 216 Processing helix chain 'F' and resid 220 through 236 removed outlier: 3.603A pdb=" N THR F 224 " --> pdb=" O GLN F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 246 removed outlier: 3.898A pdb=" N THR F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 263 Processing helix chain 'F' and resid 271 through 283 removed outlier: 3.704A pdb=" N TYR F 275 " --> pdb=" O SER F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 302 removed outlier: 3.844A pdb=" N LEU F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS F 302 " --> pdb=" O ASP F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 322 removed outlier: 3.675A pdb=" N ALA F 322 " --> pdb=" O GLN F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 339 Proline residue: F 334 - end of helix Processing helix chain 'F' and resid 342 through 356 Processing helix chain 'F' and resid 358 through 367 Processing helix chain 'F' and resid 375 through 389 Processing helix chain 'F' and resid 391 through 406 removed outlier: 3.938A pdb=" N ALA F 395 " --> pdb=" O GLN F 391 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 423 Processing helix chain 'F' and resid 425 through 439 Processing helix chain 'F' and resid 442 through 457 removed outlier: 3.706A pdb=" N SER F 455 " --> pdb=" O SER F 451 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN F 456 " --> pdb=" O SER F 452 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL F 457 " --> pdb=" O ALA F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 486 Proline residue: F 483 - end of helix removed outlier: 3.602A pdb=" N LYS F 486 " --> pdb=" O LYS F 482 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 3.737A pdb=" N LEU A 84 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.511A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE A 169 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 152 " --> pdb=" O VAL A 168 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 181 removed outlier: 6.308A pdb=" N GLU A 176 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL A 256 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLN A 178 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 12.581A pdb=" N VAL A 258 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N ILE A 180 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 11.293A pdb=" N ILE A 260 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER B 193 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 276 removed outlier: 6.531A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A 270 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 276 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 338 " --> pdb=" O MET A 325 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.594A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.594A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 440 through 441 removed outlier: 3.579A pdb=" N THR A 474 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 485 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 486 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 517 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 444 through 447 removed outlier: 3.579A pdb=" N THR A 474 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 485 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 486 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 517 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 524 " --> pdb=" O THR A 577 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 577 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 526 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY A 575 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 580 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN A 594 " --> pdb=" O ASP A 614 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 633 " --> pdb=" O THR A 615 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N MET A 711 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 716 " --> pdb=" O TRP A 739 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TRP A 739 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 738 " --> pdb=" O GLY A 771 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 771 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN A 805 " --> pdb=" O VAL A 784 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 786 " --> pdb=" O GLN A 803 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.254A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.917A pdb=" N THR B 46 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR B 391 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 390 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AB3, first strand: chain 'B' and resid 111 through 118 removed outlier: 5.193A pdb=" N GLY B 114 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY B 125 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B 116 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR B 145 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP B 143 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.696A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 201 through 203 removed outlier: 7.029A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.393A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.739A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.921A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 230 through 234 removed outlier: 6.271A pdb=" N PHE C 318 " --> pdb=" O PRO C 240 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 230 through 234 removed outlier: 6.271A pdb=" N PHE C 318 " --> pdb=" O PRO C 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.603A pdb=" N ILE E 32 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.603A pdb=" N ILE E 32 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN E 103 " --> pdb=" O THR E 94 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.563A pdb=" N HIS F 95 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU F 116 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN F 113 " --> pdb=" O PHE F 109 " (cutoff:3.500A) 804 hydrogen bonds defined for protein. 2271 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5170 1.33 - 1.45: 2305 1.45 - 1.57: 8448 1.57 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 16016 Sorted by residual: bond pdb=" N CYS A 211 " pdb=" CA CYS A 211 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.19e-02 7.06e+03 7.10e+00 bond pdb=" N VAL A 203 " pdb=" CA VAL A 203 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.23e-02 6.61e+03 7.08e+00 bond pdb=" N TYR A 214 " pdb=" CA TYR A 214 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.22e-02 6.72e+03 6.67e+00 bond pdb=" N LYS A 213 " pdb=" CA LYS A 213 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.22e-02 6.72e+03 6.41e+00 bond pdb=" N ARG A 212 " pdb=" CA ARG A 212 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.12e-02 7.97e+03 6.32e+00 ... (remaining 16011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 21647 3.23 - 6.46: 97 6.46 - 9.70: 5 9.70 - 12.93: 1 12.93 - 16.16: 1 Bond angle restraints: 21751 Sorted by residual: angle pdb=" CA LEU C 255 " pdb=" CB LEU C 255 " pdb=" CG LEU C 255 " ideal model delta sigma weight residual 116.30 132.46 -16.16 3.50e+00 8.16e-02 2.13e+01 angle pdb=" N ARG A 212 " pdb=" CA ARG A 212 " pdb=" C ARG A 212 " ideal model delta sigma weight residual 112.97 108.93 4.04 1.06e+00 8.90e-01 1.45e+01 angle pdb=" CA GLU A 134 " pdb=" CB GLU A 134 " pdb=" CG GLU A 134 " ideal model delta sigma weight residual 114.10 121.53 -7.43 2.00e+00 2.50e-01 1.38e+01 angle pdb=" CB MET D 109 " pdb=" CG MET D 109 " pdb=" SD MET D 109 " ideal model delta sigma weight residual 112.70 123.57 -10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" N SER A 702 " pdb=" CA SER A 702 " pdb=" C SER A 702 " ideal model delta sigma weight residual 108.34 113.03 -4.69 1.31e+00 5.83e-01 1.28e+01 ... (remaining 21746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 8131 16.85 - 33.70: 1025 33.70 - 50.55: 313 50.55 - 67.40: 74 67.40 - 84.25: 18 Dihedral angle restraints: 9561 sinusoidal: 3695 harmonic: 5866 Sorted by residual: dihedral pdb=" CA GLN A 542 " pdb=" C GLN A 542 " pdb=" N VAL A 543 " pdb=" CA VAL A 543 " ideal model delta harmonic sigma weight residual -180.00 -159.95 -20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ILE A 260 " pdb=" C ILE A 260 " pdb=" N THR A 261 " pdb=" CA THR A 261 " ideal model delta harmonic sigma weight residual 180.00 161.64 18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA PRO F 70 " pdb=" C PRO F 70 " pdb=" N LEU F 71 " pdb=" CA LEU F 71 " ideal model delta harmonic sigma weight residual 180.00 162.55 17.45 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 9558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1727 0.041 - 0.083: 497 0.083 - 0.124: 158 0.124 - 0.166: 15 0.166 - 0.207: 2 Chirality restraints: 2399 Sorted by residual: chirality pdb=" CB ILE F 471 " pdb=" CA ILE F 471 " pdb=" CG1 ILE F 471 " pdb=" CG2 ILE F 471 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA LEU C 255 " pdb=" N LEU C 255 " pdb=" C LEU C 255 " pdb=" CB LEU C 255 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA ASP A 250 " pdb=" N ASP A 250 " pdb=" C ASP A 250 " pdb=" CB ASP A 250 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 ... (remaining 2396 not shown) Planarity restraints: 2888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 212 " 0.360 9.50e-02 1.11e+02 1.61e-01 1.60e+01 pdb=" NE ARG A 212 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 212 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 212 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 212 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 250 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" CG ASP A 250 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASP A 250 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A 250 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 601 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 602 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 602 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 602 " 0.025 5.00e-02 4.00e+02 ... (remaining 2885 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 473 2.69 - 3.24: 15425 3.24 - 3.79: 24065 3.79 - 4.35: 29597 4.35 - 4.90: 50758 Nonbonded interactions: 120318 Sorted by model distance: nonbonded pdb=" OH TYR B 73 " pdb=" OG1 THR B 136 " model vdw 2.134 3.040 nonbonded pdb=" O SER B 167 " pdb=" OG SER B 167 " model vdw 2.162 3.040 nonbonded pdb=" OD1 ASP D 134 " pdb=" OG SER D 180 " model vdw 2.176 3.040 nonbonded pdb=" O ASP F 35 " pdb=" OG1 THR F 38 " model vdw 2.179 3.040 nonbonded pdb=" OD1 ASP A 622 " pdb=" N ASP A 624 " model vdw 2.182 3.120 ... (remaining 120313 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.280 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16019 Z= 0.239 Angle : 0.643 16.159 21751 Z= 0.343 Chirality : 0.043 0.207 2399 Planarity : 0.005 0.161 2888 Dihedral : 17.055 84.253 5809 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.78 % Favored : 94.17 % Rotamer: Outliers : 6.07 % Allowed : 25.42 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 2008 helix: 1.96 (0.20), residues: 663 sheet: -1.02 (0.24), residues: 462 loop : -1.09 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 254 TYR 0.024 0.002 TYR B 333 PHE 0.019 0.002 PHE A 394 TRP 0.013 0.001 TRP A 576 HIS 0.007 0.001 HIS F 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 (16016) covalent geometry : angle 0.64251 / 0.34 (21751) hydrogen bonds : bond 0.21408 / 13.97 ( 751) hydrogen bonds : angle 8.19003 / 5.80 ( 2271) metal coordination : bond 0.00760 / 0.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 263 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8645 (mpp) cc_final: 0.8352 (mpp) REVERT: A 214 TYR cc_start: 0.8405 (t80) cc_final: 0.8066 (t80) REVERT: A 230 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.8028 (t80) REVERT: A 552 MET cc_start: 0.7776 (mmp) cc_final: 0.7384 (mmp) REVERT: A 580 LYS cc_start: 0.8279 (tttp) cc_final: 0.7857 (tptt) REVERT: A 720 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8745 (m) REVERT: C 83 ARG cc_start: 0.8633 (mtm110) cc_final: 0.8420 (ptp90) REVERT: D 99 ASN cc_start: 0.7945 (m-40) cc_final: 0.6981 (t0) REVERT: D 201 MET cc_start: 0.8900 (mtm) cc_final: 0.8699 (mtp) REVERT: D 209 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7560 (tt0) REVERT: D 241 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8139 (t0) REVERT: E 31 ASP cc_start: 0.7146 (m-30) cc_final: 0.6522 (p0) REVERT: E 33 ASN cc_start: 0.8511 (m-40) cc_final: 0.7500 (p0) REVERT: F 214 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8406 (mtp85) REVERT: F 266 MET cc_start: 0.7573 (ppp) cc_final: 0.6588 (ptt) REVERT: F 336 LEU cc_start: 0.8333 (tt) cc_final: 0.7958 (mm) REVERT: F 467 TYR cc_start: 0.7436 (m-80) cc_final: 0.7136 (m-80) outliers start: 100 outliers final: 67 residues processed: 338 average time/residue: 0.1085 time to fit residues: 55.3543 Evaluate side-chains 288 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 216 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 443 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.2980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 GLN A 371 GLN B 135 ASN B 168 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN B 336 ASN C 331 ASN D 33 ASN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.171188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120389 restraints weight = 21537.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119282 restraints weight = 26782.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119436 restraints weight = 23208.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119101 restraints weight = 18261.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119199 restraints weight = 17801.645| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16019 Z= 0.225 Angle : 0.633 12.199 21751 Z= 0.334 Chirality : 0.044 0.214 2399 Planarity : 0.004 0.050 2888 Dihedral : 8.071 61.472 2341 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 7.77 % Allowed : 23.06 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.19), residues: 2008 helix: 1.97 (0.20), residues: 683 sheet: -0.78 (0.24), residues: 480 loop : -1.10 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 61 TYR 0.026 0.002 TYR A 649 PHE 0.018 0.002 PHE A 395 TRP 0.016 0.002 TRP A 635 HIS 0.006 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (16016) covalent geometry : angle 0.63273 / 0.33 (21751) hydrogen bonds : bond 0.04734 / 3.18 ( 751) hydrogen bonds : angle 5.45034 / 3.88 ( 2271) metal coordination : bond 0.00755 / 0.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 230 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8184 (mpp) REVERT: A 214 TYR cc_start: 0.8303 (t80) cc_final: 0.7985 (t80) REVERT: A 230 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.7729 (t80) REVERT: A 252 LYS cc_start: 0.8639 (mttm) cc_final: 0.8087 (mttm) REVERT: A 305 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: A 539 MET cc_start: 0.7322 (ttm) cc_final: 0.6819 (mtt) REVERT: A 720 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8933 (m) REVERT: A 729 TYR cc_start: 0.7801 (OUTLIER) cc_final: 0.6666 (p90) REVERT: B 189 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.8102 (tpp) REVERT: C 276 MET cc_start: 0.6314 (pmm) cc_final: 0.4728 (pmm) REVERT: C 320 ASP cc_start: 0.4130 (p0) cc_final: 0.3837 (p0) REVERT: C 338 PHE cc_start: 0.7299 (m-80) cc_final: 0.7021 (m-80) REVERT: D 35 ILE cc_start: 0.6707 (mp) cc_final: 0.6494 (mp) REVERT: D 98 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6846 (tp) REVERT: D 99 ASN cc_start: 0.7949 (m-40) cc_final: 0.6960 (t0) REVERT: D 201 MET cc_start: 0.8865 (mtm) cc_final: 0.8644 (mtp) REVERT: E 31 ASP cc_start: 0.7031 (m-30) cc_final: 0.6646 (p0) REVERT: E 33 ASN cc_start: 0.8571 (m-40) cc_final: 0.7711 (p0) REVERT: F 137 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7005 (tm-30) REVERT: F 205 ASP cc_start: 0.8710 (t0) cc_final: 0.8499 (t0) REVERT: F 214 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8368 (mtp85) REVERT: F 222 MET cc_start: 0.8259 (ttm) cc_final: 0.7873 (ttt) REVERT: F 266 MET cc_start: 0.7631 (ppp) cc_final: 0.7132 (ptt) REVERT: F 467 TYR cc_start: 0.7723 (m-80) cc_final: 0.7372 (m-80) outliers start: 128 outliers final: 79 residues processed: 332 average time/residue: 0.0979 time to fit residues: 49.9275 Evaluate side-chains 299 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 212 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 585 TYR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 461 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 18 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 GLN B 336 ASN B 368 GLN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 HIS ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.173629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.122463 restraints weight = 21575.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.120483 restraints weight = 26413.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116167 restraints weight = 19038.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116362 restraints weight = 16301.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116821 restraints weight = 14473.900| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16019 Z= 0.137 Angle : 0.549 11.146 21751 Z= 0.285 Chirality : 0.042 0.207 2399 Planarity : 0.004 0.047 2888 Dihedral : 6.993 59.086 2298 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 7.40 % Allowed : 23.67 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.19), residues: 2008 helix: 2.18 (0.20), residues: 682 sheet: -0.61 (0.24), residues: 476 loop : -1.03 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 196 TYR 0.022 0.001 TYR D 77 PHE 0.015 0.001 PHE F 404 TRP 0.011 0.001 TRP B 48 HIS 0.005 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (16016) covalent geometry : angle 0.54921 / 0.28 (21751) hydrogen bonds : bond 0.03857 / 2.59 ( 751) hydrogen bonds : angle 4.86664 / 3.48 ( 2271) metal coordination : bond 0.01655 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 224 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8052 (mpp) REVERT: A 215 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7734 (mm110) REVERT: A 230 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.7789 (t80) REVERT: A 252 LYS cc_start: 0.8624 (mttm) cc_final: 0.8048 (mttm) REVERT: A 305 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: A 327 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8281 (tm-30) REVERT: A 366 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8721 (mtt90) REVERT: A 720 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8927 (m) REVERT: A 806 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8505 (mm) REVERT: B 188 ASP cc_start: 0.7742 (t0) cc_final: 0.7449 (t0) REVERT: C 316 LEU cc_start: 0.7213 (mp) cc_final: 0.6970 (mt) REVERT: C 320 ASP cc_start: 0.4246 (p0) cc_final: 0.3998 (p0) REVERT: C 338 PHE cc_start: 0.7558 (m-80) cc_final: 0.7079 (m-80) REVERT: D 121 ASP cc_start: 0.8116 (t0) cc_final: 0.7886 (m-30) REVERT: D 162 ASP cc_start: 0.8507 (t70) cc_final: 0.8057 (t0) REVERT: E 31 ASP cc_start: 0.6939 (m-30) cc_final: 0.6712 (p0) REVERT: E 33 ASN cc_start: 0.8494 (m-40) cc_final: 0.7706 (p0) REVERT: F 214 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8169 (mtp85) REVERT: F 220 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7758 (tp40) REVERT: F 222 MET cc_start: 0.8224 (ttm) cc_final: 0.7906 (ttt) REVERT: F 266 MET cc_start: 0.8244 (ppp) cc_final: 0.7867 (ppp) REVERT: F 336 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8135 (mt) REVERT: F 467 TYR cc_start: 0.7744 (m-80) cc_final: 0.7318 (m-80) outliers start: 122 outliers final: 82 residues processed: 325 average time/residue: 0.0955 time to fit residues: 48.3518 Evaluate side-chains 299 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 207 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 220 GLN Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 455 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 46 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 191 optimal weight: 0.0030 chunk 82 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 overall best weight: 1.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 ASN B 368 GLN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN F 145 HIS ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.173829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123111 restraints weight = 21594.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122539 restraints weight = 25820.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118145 restraints weight = 17870.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117539 restraints weight = 18708.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118238 restraints weight = 16031.172| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16019 Z= 0.147 Angle : 0.558 11.844 21751 Z= 0.287 Chirality : 0.042 0.293 2399 Planarity : 0.003 0.046 2888 Dihedral : 6.644 59.139 2288 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 7.83 % Allowed : 23.30 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.19), residues: 2008 helix: 2.24 (0.20), residues: 683 sheet: -0.62 (0.24), residues: 466 loop : -1.02 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 313 TYR 0.019 0.001 TYR D 77 PHE 0.015 0.001 PHE F 404 TRP 0.012 0.001 TRP C 252 HIS 0.004 0.001 HIS A 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (16016) covalent geometry : angle 0.55829 / 0.29 (21751) hydrogen bonds : bond 0.03755 / 2.54 ( 751) hydrogen bonds : angle 4.70269 / 3.37 ( 2271) metal coordination : bond 0.02246 / 1.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 220 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8151 (mpp) REVERT: A 230 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7853 (t80) REVERT: A 252 LYS cc_start: 0.8580 (mttm) cc_final: 0.8014 (mttm) REVERT: A 305 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7547 (tp30) REVERT: A 327 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8289 (tm-30) REVERT: A 366 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8755 (mtt90) REVERT: A 720 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8957 (m) REVERT: A 729 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.6520 (p90) REVERT: A 806 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8484 (mm) REVERT: B 188 ASP cc_start: 0.7780 (t0) cc_final: 0.7386 (t0) REVERT: C 276 MET cc_start: 0.6384 (pmm) cc_final: 0.5839 (pmm) REVERT: C 320 ASP cc_start: 0.4335 (p0) cc_final: 0.4103 (p0) REVERT: D 34 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7107 (tp30) REVERT: D 47 ASN cc_start: 0.7737 (m110) cc_final: 0.7204 (t0) REVERT: D 134 ASP cc_start: 0.9151 (OUTLIER) cc_final: 0.8903 (m-30) REVERT: E 33 ASN cc_start: 0.8523 (m-40) cc_final: 0.7618 (p0) REVERT: F 214 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8074 (mtp85) REVERT: F 220 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7727 (tp40) REVERT: F 266 MET cc_start: 0.8283 (ppp) cc_final: 0.7885 (ppp) REVERT: F 336 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8195 (mt) REVERT: F 467 TYR cc_start: 0.7689 (m-80) cc_final: 0.7368 (m-80) outliers start: 129 outliers final: 98 residues processed: 320 average time/residue: 0.0979 time to fit residues: 48.8673 Evaluate side-chains 314 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 205 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 585 TYR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 220 GLN Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 461 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 38 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 158 optimal weight: 0.1980 chunk 130 optimal weight: 0.4980 chunk 46 optimal weight: 0.0770 chunk 3 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 ASN D 54 GLN F 145 HIS ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.177016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.138524 restraints weight = 21144.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.133061 restraints weight = 27968.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130434 restraints weight = 26160.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131271 restraints weight = 22046.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.130895 restraints weight = 18304.999| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16019 Z= 0.100 Angle : 0.519 12.867 21751 Z= 0.263 Chirality : 0.041 0.199 2399 Planarity : 0.003 0.048 2888 Dihedral : 6.089 58.917 2284 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 6.43 % Allowed : 24.33 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.19), residues: 2008 helix: 2.37 (0.20), residues: 684 sheet: -0.51 (0.24), residues: 476 loop : -0.83 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 47 TYR 0.020 0.001 TYR D 79 PHE 0.015 0.001 PHE F 404 TRP 0.010 0.001 TRP B 279 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (16016) covalent geometry : angle 0.51875 / 0.26 (21751) hydrogen bonds : bond 0.03192 / 2.15 ( 751) hydrogen bonds : angle 4.37910 / 3.15 ( 2271) metal coordination : bond 0.01236 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 229 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8126 (mpp) REVERT: A 230 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7899 (t80) REVERT: A 252 LYS cc_start: 0.8556 (mttm) cc_final: 0.8043 (mttm) REVERT: A 305 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: A 327 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8279 (tm-30) REVERT: A 372 MET cc_start: 0.8756 (mmm) cc_final: 0.8136 (mmt) REVERT: A 645 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6991 (mm-30) REVERT: A 720 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8892 (m) REVERT: A 729 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.6462 (p90) REVERT: A 806 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8393 (mm) REVERT: B 188 ASP cc_start: 0.7711 (t0) cc_final: 0.7110 (t0) REVERT: B 221 MET cc_start: 0.7330 (tpp) cc_final: 0.7119 (tpp) REVERT: C 239 LEU cc_start: 0.7742 (mm) cc_final: 0.7311 (pp) REVERT: C 276 MET cc_start: 0.6108 (pmm) cc_final: 0.5673 (pmm) REVERT: C 320 ASP cc_start: 0.4400 (p0) cc_final: 0.4186 (p0) REVERT: D 79 TYR cc_start: 0.8265 (m-80) cc_final: 0.7905 (m-80) REVERT: D 121 ASP cc_start: 0.8111 (t0) cc_final: 0.7904 (m-30) REVERT: D 201 MET cc_start: 0.8713 (mtp) cc_final: 0.8486 (ttm) REVERT: D 212 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7172 (mtp180) REVERT: E 33 ASN cc_start: 0.8415 (m-40) cc_final: 0.7576 (p0) REVERT: E 66 ASP cc_start: 0.8404 (t0) cc_final: 0.8193 (t70) REVERT: F 214 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7924 (mtp85) REVERT: F 220 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7790 (tp40) REVERT: F 266 MET cc_start: 0.8245 (ppp) cc_final: 0.7866 (ppp) REVERT: F 315 ARG cc_start: 0.8065 (ttm110) cc_final: 0.7577 (ttm-80) REVERT: F 320 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6502 (tpt) REVERT: F 336 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8203 (mt) REVERT: F 352 ILE cc_start: 0.9032 (pt) cc_final: 0.8590 (pt) REVERT: F 467 TYR cc_start: 0.7603 (m-80) cc_final: 0.7261 (m-80) REVERT: F 474 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7247 (mm) outliers start: 106 outliers final: 72 residues processed: 312 average time/residue: 0.1172 time to fit residues: 56.5797 Evaluate side-chains 291 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 207 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 220 GLN Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 474 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 94 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 196 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 ASN F 145 HIS ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.172261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122849 restraints weight = 21556.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122296 restraints weight = 26828.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119840 restraints weight = 19631.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118801 restraints weight = 19815.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119428 restraints weight = 16534.396| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16019 Z= 0.168 Angle : 0.572 12.722 21751 Z= 0.293 Chirality : 0.042 0.313 2399 Planarity : 0.004 0.047 2888 Dihedral : 5.992 59.324 2271 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 7.52 % Allowed : 24.09 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 2008 helix: 2.32 (0.20), residues: 684 sheet: -0.48 (0.24), residues: 464 loop : -0.92 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 313 TYR 0.036 0.002 TYR A 649 PHE 0.021 0.001 PHE A 197 TRP 0.010 0.001 TRP B 48 HIS 0.003 0.001 HIS F 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (16016) covalent geometry : angle 0.57190 / 0.29 (21751) hydrogen bonds : bond 0.03666 / 2.50 ( 751) hydrogen bonds : angle 4.52575 / 3.25 ( 2271) metal coordination : bond 0.00800 / 0.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 212 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8189 (mpp) REVERT: A 230 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7825 (t80) REVERT: A 252 LYS cc_start: 0.8580 (mttm) cc_final: 0.8087 (mttm) REVERT: A 305 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7490 (tp30) REVERT: A 327 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8304 (tm-30) REVERT: A 720 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8929 (m) REVERT: A 729 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.6989 (p90) REVERT: A 806 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8549 (mm) REVERT: B 221 MET cc_start: 0.7523 (tpp) cc_final: 0.7286 (tpp) REVERT: C 43 GLU cc_start: 0.8125 (tp30) cc_final: 0.7803 (tp30) REVERT: C 276 MET cc_start: 0.6280 (pmm) cc_final: 0.5811 (pmm) REVERT: D 79 TYR cc_start: 0.8417 (m-80) cc_final: 0.8001 (m-80) REVERT: D 99 ASN cc_start: 0.8063 (m-40) cc_final: 0.7066 (t0) REVERT: D 121 ASP cc_start: 0.8184 (t0) cc_final: 0.7898 (m-30) REVERT: D 187 GLU cc_start: 0.8082 (tp30) cc_final: 0.7876 (tt0) REVERT: E 33 ASN cc_start: 0.8585 (m-40) cc_final: 0.7590 (p0) REVERT: E 66 ASP cc_start: 0.8567 (t0) cc_final: 0.8243 (t70) REVERT: F 214 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8060 (mtp85) REVERT: F 220 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.6800 (pt0) REVERT: F 222 MET cc_start: 0.8463 (ttm) cc_final: 0.8142 (ttt) REVERT: F 266 MET cc_start: 0.8318 (ppp) cc_final: 0.7872 (ppp) REVERT: F 320 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6645 (tpt) REVERT: F 336 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8196 (mt) REVERT: F 352 ILE cc_start: 0.8994 (pt) cc_final: 0.8559 (pt) REVERT: F 467 TYR cc_start: 0.7669 (m-80) cc_final: 0.7378 (m-80) outliers start: 124 outliers final: 93 residues processed: 308 average time/residue: 0.1144 time to fit residues: 54.7000 Evaluate side-chains 309 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 206 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 220 GLN Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 461 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 136 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 124 optimal weight: 30.0000 chunk 191 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 ASN B 336 ASN D 54 GLN F 145 HIS ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.170157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130935 restraints weight = 21671.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126216 restraints weight = 30915.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.122794 restraints weight = 30396.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.123705 restraints weight = 25964.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.123543 restraints weight = 19866.148| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16019 Z= 0.236 Angle : 0.636 14.013 21751 Z= 0.328 Chirality : 0.044 0.283 2399 Planarity : 0.004 0.045 2888 Dihedral : 6.374 58.731 2271 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 7.83 % Allowed : 24.45 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 2008 helix: 2.10 (0.20), residues: 686 sheet: -0.63 (0.23), residues: 458 loop : -1.09 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 47 TYR 0.032 0.002 TYR A 649 PHE 0.019 0.002 PHE F 404 TRP 0.013 0.002 TRP A 576 HIS 0.003 0.001 HIS F 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 (16016) covalent geometry : angle 0.63550 / 0.33 (21751) hydrogen bonds : bond 0.04181 / 2.85 ( 751) hydrogen bonds : angle 4.76488 / 3.41 ( 2271) metal coordination : bond 0.00594 / 0.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 206 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8364 (mpp) REVERT: A 230 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.7939 (t80) REVERT: A 252 LYS cc_start: 0.8570 (mttm) cc_final: 0.8298 (mttm) REVERT: A 305 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7645 (tp30) REVERT: A 327 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8271 (tm-30) REVERT: A 720 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8887 (m) REVERT: A 729 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7252 (p90) REVERT: A 806 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8704 (mm) REVERT: B 73 TYR cc_start: 0.8397 (m-80) cc_final: 0.8033 (m-80) REVERT: B 377 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7736 (tptm) REVERT: C 43 GLU cc_start: 0.8257 (tp30) cc_final: 0.7850 (tp30) REVERT: D 98 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7109 (tp) REVERT: D 99 ASN cc_start: 0.8230 (m-40) cc_final: 0.7520 (t0) REVERT: D 121 ASP cc_start: 0.8275 (t0) cc_final: 0.7967 (m-30) REVERT: D 134 ASP cc_start: 0.9233 (OUTLIER) cc_final: 0.8820 (t0) REVERT: E 33 ASN cc_start: 0.8543 (m-40) cc_final: 0.7542 (p0) REVERT: E 66 ASP cc_start: 0.8656 (t0) cc_final: 0.8238 (t70) REVERT: F 214 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8179 (mtp85) REVERT: F 220 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7674 (tp40) REVERT: F 266 MET cc_start: 0.8295 (ppp) cc_final: 0.7534 (ppp) REVERT: F 467 TYR cc_start: 0.7642 (m-80) cc_final: 0.7336 (m-80) outliers start: 129 outliers final: 104 residues processed: 307 average time/residue: 0.1122 time to fit residues: 53.5748 Evaluate side-chains 317 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 202 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 37 TYR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 220 GLN Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 474 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 ASN D 54 GLN F 145 HIS ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.173879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.141928 restraints weight = 21133.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140869 restraints weight = 32709.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139141 restraints weight = 25354.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.138782 restraints weight = 22720.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.137713 restraints weight = 20587.766| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16019 Z= 0.106 Angle : 0.549 13.391 21751 Z= 0.275 Chirality : 0.042 0.257 2399 Planarity : 0.003 0.046 2888 Dihedral : 5.704 56.814 2269 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.58 % Allowed : 27.00 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 2008 helix: 2.30 (0.20), residues: 690 sheet: -0.56 (0.23), residues: 475 loop : -0.89 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 47 TYR 0.027 0.001 TYR A 649 PHE 0.018 0.001 PHE F 404 TRP 0.010 0.001 TRP B 48 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (16016) covalent geometry : angle 0.54871 / 0.28 (21751) hydrogen bonds : bond 0.03172 / 2.16 ( 751) hydrogen bonds : angle 4.33503 / 3.10 ( 2271) metal coordination : bond 0.00502 / 0.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 220 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8178 (mpp) REVERT: A 230 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7884 (t80) REVERT: A 305 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: A 327 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8250 (tm-30) REVERT: A 720 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8853 (m) REVERT: A 729 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.7127 (p90) REVERT: A 806 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8551 (mm) REVERT: B 73 TYR cc_start: 0.8281 (m-80) cc_final: 0.7920 (m-80) REVERT: B 221 MET cc_start: 0.7226 (tpp) cc_final: 0.7021 (tpp) REVERT: C 43 GLU cc_start: 0.8178 (tp30) cc_final: 0.7741 (tp30) REVERT: C 276 MET cc_start: 0.6098 (pmm) cc_final: 0.5442 (pmm) REVERT: D 162 ASP cc_start: 0.8343 (t70) cc_final: 0.8084 (t70) REVERT: D 212 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7308 (mtp180) REVERT: E 33 ASN cc_start: 0.8415 (m-40) cc_final: 0.7582 (p0) REVERT: E 66 ASP cc_start: 0.8453 (t0) cc_final: 0.8100 (t70) REVERT: F 214 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8067 (mtp85) REVERT: F 220 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.6811 (pt0) REVERT: F 266 MET cc_start: 0.8193 (ppp) cc_final: 0.7540 (ppp) REVERT: F 315 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7400 (ttm-80) REVERT: F 352 ILE cc_start: 0.9055 (pt) cc_final: 0.8458 (pt) REVERT: F 467 TYR cc_start: 0.7437 (m-80) cc_final: 0.7165 (m-80) REVERT: F 474 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7252 (mm) outliers start: 92 outliers final: 72 residues processed: 293 average time/residue: 0.1107 time to fit residues: 50.9041 Evaluate side-chains 296 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 214 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 220 GLN Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 474 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 87 optimal weight: 20.0000 chunk 163 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 ASN F 145 HIS ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.170022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.142524 restraints weight = 21323.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139214 restraints weight = 29400.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137973 restraints weight = 27592.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137477 restraints weight = 23765.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136759 restraints weight = 22625.327| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16019 Z= 0.177 Angle : 0.606 13.015 21751 Z= 0.307 Chirality : 0.043 0.269 2399 Planarity : 0.004 0.045 2888 Dihedral : 5.875 56.434 2265 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.83 % Allowed : 27.31 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 2008 helix: 2.18 (0.20), residues: 690 sheet: -0.50 (0.23), residues: 468 loop : -1.02 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 47 TYR 0.026 0.002 TYR D 77 PHE 0.017 0.001 PHE F 404 TRP 0.011 0.001 TRP B 48 HIS 0.003 0.001 HIS F 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (16016) covalent geometry : angle 0.60588 / 0.31 (21751) hydrogen bonds : bond 0.03689 / 2.51 ( 751) hydrogen bonds : angle 4.49404 / 3.22 ( 2271) metal coordination : bond 0.00469 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 211 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7995 (t80) REVERT: A 305 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7641 (tp30) REVERT: A 411 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8025 (mt0) REVERT: A 720 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8852 (m) REVERT: A 729 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7289 (p90) REVERT: A 806 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8665 (mm) REVERT: B 73 TYR cc_start: 0.8264 (m-80) cc_final: 0.7906 (m-80) REVERT: C 43 GLU cc_start: 0.8097 (tp30) cc_final: 0.7754 (tp30) REVERT: C 276 MET cc_start: 0.5985 (pmm) cc_final: 0.5376 (pmm) REVERT: D 99 ASN cc_start: 0.7956 (m-40) cc_final: 0.7267 (t0) REVERT: E 66 ASP cc_start: 0.8526 (t0) cc_final: 0.8129 (t70) REVERT: F 214 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8351 (mpp80) REVERT: F 220 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7657 (tp40) REVERT: F 222 MET cc_start: 0.8218 (ttm) cc_final: 0.7910 (ttt) REVERT: F 266 MET cc_start: 0.8192 (ppp) cc_final: 0.7630 (ppp) REVERT: F 315 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7124 (ttm-80) REVERT: F 467 TYR cc_start: 0.7356 (m-80) cc_final: 0.7072 (m-80) outliers start: 96 outliers final: 82 residues processed: 288 average time/residue: 0.1051 time to fit residues: 46.9889 Evaluate side-chains 297 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 207 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 220 GLN Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 474 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 187 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 176 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 ASN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 HIS F 198 GLN ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.170769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.138173 restraints weight = 21130.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.132589 restraints weight = 28328.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128525 restraints weight = 28703.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.127599 restraints weight = 29251.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127179 restraints weight = 24106.204| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16019 Z= 0.169 Angle : 0.608 12.450 21751 Z= 0.307 Chirality : 0.043 0.258 2399 Planarity : 0.004 0.045 2888 Dihedral : 5.883 58.337 2265 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 6.25 % Allowed : 27.06 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.19), residues: 2008 helix: 2.14 (0.20), residues: 690 sheet: -0.52 (0.23), residues: 470 loop : -1.01 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 47 TYR 0.025 0.001 TYR D 77 PHE 0.020 0.001 PHE F 404 TRP 0.011 0.001 TRP B 48 HIS 0.004 0.001 HIS F 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (16016) covalent geometry : angle 0.60822 / 0.31 (21751) hydrogen bonds : bond 0.03630 / 2.48 ( 751) hydrogen bonds : angle 4.49771 / 3.23 ( 2271) metal coordination : bond 0.00493 / 0.24 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 211 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8448 (mpp) cc_final: 0.8153 (mpp) REVERT: A 215 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7585 (mm-40) REVERT: A 230 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7868 (t80) REVERT: A 305 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7570 (tp30) REVERT: A 411 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: A 720 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8890 (m) REVERT: A 729 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7463 (p90) REVERT: A 806 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8640 (mm) REVERT: B 73 TYR cc_start: 0.8371 (m-80) cc_final: 0.8009 (m-80) REVERT: C 43 GLU cc_start: 0.8360 (tp30) cc_final: 0.7977 (tp30) REVERT: C 276 MET cc_start: 0.6215 (pmm) cc_final: 0.5073 (pmm) REVERT: D 99 ASN cc_start: 0.8051 (m-40) cc_final: 0.7180 (t0) REVERT: D 162 ASP cc_start: 0.8574 (t70) cc_final: 0.8311 (t70) REVERT: E 33 ASN cc_start: 0.8504 (m-40) cc_final: 0.7569 (p0) REVERT: E 66 ASP cc_start: 0.8633 (t0) cc_final: 0.8272 (t70) REVERT: F 214 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8126 (mtp85) REVERT: F 220 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7677 (tp40) REVERT: F 222 MET cc_start: 0.8352 (ttm) cc_final: 0.8029 (ttt) REVERT: F 266 MET cc_start: 0.8254 (ppp) cc_final: 0.7610 (ppp) REVERT: F 467 TYR cc_start: 0.7628 (m-80) cc_final: 0.7329 (m-80) outliers start: 103 outliers final: 92 residues processed: 294 average time/residue: 0.0943 time to fit residues: 43.6389 Evaluate side-chains 307 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 206 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 TYR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 220 GLN Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 474 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 167 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 0.1980 chunk 10 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 HIS ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.170370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135598 restraints weight = 21089.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.131330 restraints weight = 31981.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.129647 restraints weight = 31172.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.129550 restraints weight = 25620.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.129257 restraints weight = 21460.775| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 16019 Z= 0.178 Angle : 0.807 59.194 21751 Z= 0.454 Chirality : 0.043 0.469 2399 Planarity : 0.004 0.045 2888 Dihedral : 5.873 58.302 2264 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 6.13 % Allowed : 27.12 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 2008 helix: 2.15 (0.20), residues: 690 sheet: -0.52 (0.23), residues: 470 loop : -1.01 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 47 TYR 0.023 0.001 TYR D 77 PHE 0.020 0.001 PHE F 404 TRP 0.010 0.001 TRP B 48 HIS 0.003 0.001 HIS F 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.18 (16016) covalent geometry : angle 0.80671 / 0.45 (21751) hydrogen bonds : bond 0.03609 / 2.47 ( 751) hydrogen bonds : angle 4.48718 / 3.22 ( 2271) metal coordination : bond 0.00450 / 0.22 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2798.69 seconds wall clock time: 48 minutes 53.46 seconds (2933.46 seconds total)