Starting phenix.real_space_refine on Sat Mar 16 23:52:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khp_37247/03_2024/8khp_37247.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khp_37247/03_2024/8khp_37247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khp_37247/03_2024/8khp_37247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khp_37247/03_2024/8khp_37247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khp_37247/03_2024/8khp_37247.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khp_37247/03_2024/8khp_37247.pdb" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.003 sd= 0.029 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: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 9890 2.51 5 N 3008 2.21 5 O 3076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 62": "OE1" <-> "OE2" Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 35": "OD1" <-> "OD2" Residue "D ASP 204": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16023 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 3343 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 333} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 547} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1259 Unresolved non-hydrogen angles: 1632 Unresolved non-hydrogen dihedrals: 1058 Unresolved non-hydrogen chiralities: 98 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 16, 'TYR:plan': 20, 'ASN:plan1': 19, 'TRP:plan': 8, 'ASP:plan': 23, 'PHE:plan': 6, 'GLU:plan': 29, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 792 Chain: "B" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 3289 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 351} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 547} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1316 Unresolved non-hydrogen angles: 1708 Unresolved non-hydrogen dihedrals: 1103 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 24, 'TYR:plan': 22, 'ASN:plan1': 20, 'TRP:plan': 8, 'HIS:plan': 16, 'PHE:plan': 6, 'GLU:plan': 30, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 817 Chain: "C" Number of atoms: 4592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 4592 Classifications: {'peptide': 730} Incomplete info: {'truncation_to_alanine': 385} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 711} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1431 Unresolved non-hydrogen angles: 1782 Unresolved non-hydrogen dihedrals: 1186 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'GLN:plan1': 24, 'HIS:plan': 11, 'TYR:plan': 10, 'ASN:plan1': 13, 'TRP:plan': 1, 'ASP:plan': 20, 'PHE:plan': 18, 'GLU:plan': 52, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 805 Chain: "D" Number of atoms: 4241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 4241 Classifications: {'peptide': 722} Incomplete info: {'truncation_to_alanine': 468} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 702} Chain breaks: 4 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1742 Unresolved non-hydrogen angles: 2172 Unresolved non-hydrogen dihedrals: 1451 Unresolved non-hydrogen chiralities: 123 Planarities with less than four sites: {'GLN:plan1': 28, 'HIS:plan': 14, 'TYR:plan': 15, 'ASN:plan1': 23, 'TRP:plan': 1, 'ASP:plan': 25, 'PHE:plan': 24, 'GLU:plan': 54, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 1000 Chain: "E" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 259 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 131 Chain: "F" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 299 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 5, 'HIS:plan': 4, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 150 Time building chain proxies: 9.64, per 1000 atoms: 0.60 Number of scatterers: 16023 At special positions: 0 Unit cell: (131.75, 249.9, 133.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 3076 8.00 N 3008 7.00 C 9890 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 - 3.50 Amino acid : False - 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: 6.57 Conformation dependent library (CDL) restraints added in 4.0 seconds 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 25 sheets defined 55.5% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 64 through 72 removed outlier: 3.701A pdb=" N LEU A 68 " --> pdb=" O HIS A 64 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 81 Processing helix chain 'A' and resid 83 through 88 removed outlier: 3.854A pdb=" N GLN A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.607A pdb=" N VAL A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 145 Processing helix chain 'A' and resid 151 through 162 Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 178 through 184 removed outlier: 3.869A pdb=" N ARG A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 211 through 222 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 238 through 244 removed outlier: 3.536A pdb=" N LEU A 241 " --> pdb=" O PRO A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 253 through 261 removed outlier: 3.583A pdb=" N LYS A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.548A pdb=" N THR A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 292 removed outlier: 3.784A pdb=" N GLU A 292 " --> pdb=" O PRO A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.712A pdb=" N ALA A 505 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 600 removed outlier: 3.826A pdb=" N LEU A 598 " --> pdb=" O PRO A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.651A pdb=" N ALA B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 70 Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 83 through 88 removed outlier: 3.591A pdb=" N GLN B 88 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 111 Processing helix chain 'B' and resid 119 through 131 Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 151 through 162 Processing helix chain 'B' and resid 164 through 178 removed outlier: 3.712A pdb=" N THR B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLN B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 185 removed outlier: 3.773A pdb=" N ARG B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 209 through 222 removed outlier: 3.984A pdb=" N VAL B 213 " --> pdb=" O CYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 288 through 292 removed outlier: 4.019A pdb=" N GLU B 292 " --> pdb=" O PRO B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 594 through 599 Processing helix chain 'C' and resid 28 through 46 Processing helix chain 'C' and resid 53 through 67 removed outlier: 3.665A pdb=" N LEU C 57 " --> pdb=" O SER C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 88 Processing helix chain 'C' and resid 88 through 94 Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 100 through 123 Processing helix chain 'C' and resid 123 through 135 removed outlier: 3.870A pdb=" N VAL C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLN C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 151 Processing helix chain 'C' and resid 154 through 174 Processing helix chain 'C' and resid 180 through 194 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 205 through 228 removed outlier: 3.614A pdb=" N GLU C 227 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 251 Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 270 removed outlier: 3.530A pdb=" N ILE C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 removed outlier: 3.856A pdb=" N MET C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 291 Processing helix chain 'C' and resid 292 through 303 Processing helix chain 'C' and resid 308 through 329 removed outlier: 3.756A pdb=" N THR C 312 " --> pdb=" O ASN C 308 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N MET C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N CYS C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU C 315 " --> pdb=" O LYS C 311 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS C 316 " --> pdb=" O THR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 360 Processing helix chain 'C' and resid 363 through 379 removed outlier: 4.156A pdb=" N ASN C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 397 removed outlier: 3.807A pdb=" N LEU C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 422 removed outlier: 3.510A pdb=" N PHE C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 443 removed outlier: 3.885A pdb=" N PHE C 428 " --> pdb=" O GLU C 424 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 463 Processing helix chain 'C' and resid 463 through 494 removed outlier: 5.346A pdb=" N LYS C 469 " --> pdb=" O GLN C 465 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU C 470 " --> pdb=" O PHE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 543 Processing helix chain 'C' and resid 595 through 608 removed outlier: 3.919A pdb=" N THR C 600 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE C 601 " --> pdb=" O PHE C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 621 Processing helix chain 'C' and resid 623 through 635 Processing helix chain 'C' and resid 684 through 715 removed outlier: 3.820A pdb=" N VAL C 708 " --> pdb=" O GLU C 704 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG C 709 " --> pdb=" O ALA C 705 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 710 " --> pdb=" O ALA C 706 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET C 711 " --> pdb=" O ILE C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 730 removed outlier: 3.593A pdb=" N VAL C 723 " --> pdb=" O HIS C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 751 removed outlier: 3.510A pdb=" N ILE C 749 " --> pdb=" O ILE C 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 46 Processing helix chain 'D' and resid 54 through 67 Processing helix chain 'D' and resid 69 through 96 removed outlier: 5.214A pdb=" N GLU D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASP D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 123 removed outlier: 3.910A pdb=" N THR D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 135 removed outlier: 4.467A pdb=" N VAL D 131 " --> pdb=" O ASP D 127 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN D 132 " --> pdb=" O ARG D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 175 Processing helix chain 'D' and resid 179 through 193 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 205 through 228 Processing helix chain 'D' and resid 229 through 251 Processing helix chain 'D' and resid 257 through 269 Processing helix chain 'D' and resid 272 through 278 Processing helix chain 'D' and resid 283 through 291 Processing helix chain 'D' and resid 293 through 306 removed outlier: 3.948A pdb=" N ARG D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 329 Processing helix chain 'D' and resid 337 through 361 removed outlier: 3.846A pdb=" N TYR D 341 " --> pdb=" O ASN D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 380 Processing helix chain 'D' and resid 383 through 396 Processing helix chain 'D' and resid 406 through 421 Processing helix chain 'D' and resid 424 through 442 removed outlier: 3.910A pdb=" N PHE D 428 " --> pdb=" O GLU D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 463 removed outlier: 3.721A pdb=" N GLY D 463 " --> pdb=" O LYS D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 494 Processing helix chain 'D' and resid 509 through 513 removed outlier: 3.652A pdb=" N TYR D 512 " --> pdb=" O THR D 509 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP D 513 " --> pdb=" O THR D 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 509 through 513' Processing helix chain 'D' and resid 529 through 543 Processing helix chain 'D' and resid 598 through 608 removed outlier: 3.816A pdb=" N LEU D 602 " --> pdb=" O GLN D 598 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG D 608 " --> pdb=" O LEU D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 621 removed outlier: 3.609A pdb=" N ILE D 616 " --> pdb=" O THR D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 636 removed outlier: 3.517A pdb=" N ALA D 635 " --> pdb=" O LEU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 715 removed outlier: 3.934A pdb=" N HIS D 701 " --> pdb=" O ASP D 697 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE D 707 " --> pdb=" O ILE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 732 removed outlier: 4.019A pdb=" N VAL D 723 " --> pdb=" O HIS D 719 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA D 732 " --> pdb=" O GLN D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 747 Processing helix chain 'D' and resid 748 through 752 removed outlier: 3.519A pdb=" N GLU D 752 " --> pdb=" O ILE D 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 89 Processing helix chain 'F' and resid 80 through 90 removed outlier: 3.868A pdb=" N LYS F 89 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 63 removed outlier: 6.323A pdb=" N VAL A 53 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 346 removed outlier: 4.160A pdb=" N CYS A 369 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.910A pdb=" N SER A 393 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 403 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLU A 417 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 440 through 444 removed outlier: 4.323A pdb=" N ALA A 440 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 453 through 455 removed outlier: 3.865A pdb=" N ASP A 458 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 464 through 467 removed outlier: 3.596A pdb=" N THR A 472 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 487 through 491 removed outlier: 3.730A pdb=" N GLY A 487 " --> pdb=" O ILE A 498 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 517 through 518 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.885A pdb=" N GLY A 538 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 549 " --> pdb=" O GLY A 538 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 540 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 546 " --> pdb=" O TYR A 566 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A 572 " --> pdb=" O ASP A 567 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 552 through 553 removed outlier: 3.701A pdb=" N SER A 553 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 558 " --> pdb=" O SER A 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 59 through 63 Processing sheet with id=AB6, first strand: chain 'B' and resid 327 through 332 removed outlier: 4.546A pdb=" N VAL B 300 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE B 297 " --> pdb=" O LEU B 593 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 587 " --> pdb=" O PHE B 303 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 306 through 307 removed outlier: 3.758A pdb=" N ILE B 306 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL B 563 " --> pdb=" O GLY B 576 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLN B 578 " --> pdb=" O GLY B 561 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N GLY B 561 " --> pdb=" O GLN B 578 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N ASP B 580 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 11.786A pdb=" N ARG B 559 " --> pdb=" O ASP B 580 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 343 through 347 Processing sheet with id=AB9, first strand: chain 'B' and resid 394 through 397 removed outlier: 3.635A pdb=" N TYR B 400 " --> pdb=" O VAL B 397 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 417 through 420 Processing sheet with id=AC2, first strand: chain 'B' and resid 440 through 443 Processing sheet with id=AC3, first strand: chain 'B' and resid 454 through 455 Processing sheet with id=AC4, first strand: chain 'B' and resid 488 through 491 removed outlier: 3.782A pdb=" N LEU B 495 " --> pdb=" O TYR B 517 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 497 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 515 " --> pdb=" O VAL B 497 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 538 through 541 Processing sheet with id=AC6, first strand: chain 'C' and resid 557 through 559 removed outlier: 4.959A pdb=" N ALA C 557 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL C 594 " --> pdb=" O ALA C 557 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 559 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 557 through 559 removed outlier: 4.369A pdb=" N ALA D 557 " --> pdb=" O VAL D 594 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL D 594 " --> pdb=" O ALA D 557 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU D 559 " --> pdb=" O LEU D 592 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D 592 " --> pdb=" O LEU D 559 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 1128 hydrogen bonds defined for protein. 3219 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: 6.04 Time building geometry restraints manager: 7.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5873 1.34 - 1.46: 1681 1.46 - 1.58: 8528 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 16162 Sorted by residual: bond pdb=" N PRO B 310 " pdb=" CD PRO B 310 " ideal model delta sigma weight residual 1.474 1.529 -0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" N PRO D 648 " pdb=" CD PRO D 648 " ideal model delta sigma weight residual 1.474 1.528 -0.054 1.40e-02 5.10e+03 1.51e+01 bond pdb=" N PRO A 310 " pdb=" CD PRO A 310 " ideal model delta sigma weight residual 1.474 1.528 -0.054 1.40e-02 5.10e+03 1.51e+01 bond pdb=" N PRO C 648 " pdb=" CD PRO C 648 " ideal model delta sigma weight residual 1.474 1.528 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" CA CYS D 522 " pdb=" C CYS D 522 " ideal model delta sigma weight residual 1.523 1.562 -0.039 1.34e-02 5.57e+03 8.50e+00 ... (remaining 16157 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.96: 206 105.96 - 113.83: 9280 113.83 - 121.71: 8745 121.71 - 129.58: 3968 129.58 - 137.46: 48 Bond angle restraints: 22247 Sorted by residual: angle pdb=" C ILE D 524 " pdb=" N PRO D 525 " pdb=" CA PRO D 525 " ideal model delta sigma weight residual 120.38 133.46 -13.08 1.03e+00 9.43e-01 1.61e+02 angle pdb=" CA PRO D 648 " pdb=" N PRO D 648 " pdb=" CD PRO D 648 " ideal model delta sigma weight residual 111.50 98.86 12.64 1.40e+00 5.10e-01 8.15e+01 angle pdb=" CA PRO A 310 " pdb=" N PRO A 310 " pdb=" CD PRO A 310 " ideal model delta sigma weight residual 111.50 98.89 12.61 1.40e+00 5.10e-01 8.11e+01 angle pdb=" CA PRO B 310 " pdb=" N PRO B 310 " pdb=" CD PRO B 310 " ideal model delta sigma weight residual 111.50 98.89 12.61 1.40e+00 5.10e-01 8.11e+01 angle pdb=" CA PRO C 648 " pdb=" N PRO C 648 " pdb=" CD PRO C 648 " ideal model delta sigma weight residual 111.50 98.90 12.60 1.40e+00 5.10e-01 8.10e+01 ... (remaining 22242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 9048 17.13 - 34.27: 374 34.27 - 51.40: 95 51.40 - 68.54: 11 68.54 - 85.67: 9 Dihedral angle restraints: 9537 sinusoidal: 1689 harmonic: 7848 Sorted by residual: dihedral pdb=" CA THR A 168 " pdb=" C THR A 168 " pdb=" N GLU A 169 " pdb=" CA GLU A 169 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" C ILE D 524 " pdb=" N ILE D 524 " pdb=" CA ILE D 524 " pdb=" CB ILE D 524 " ideal model delta harmonic sigma weight residual -122.00 -130.35 8.35 0 2.50e+00 1.60e-01 1.12e+01 dihedral pdb=" CG ARG C 322 " pdb=" CD ARG C 322 " pdb=" NE ARG C 322 " pdb=" CZ ARG C 322 " ideal model delta sinusoidal sigma weight residual -180.00 -136.54 -43.46 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 9534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2643 0.078 - 0.156: 198 0.156 - 0.235: 1 0.235 - 0.313: 1 0.313 - 0.391: 1 Chirality restraints: 2844 Sorted by residual: chirality pdb=" CA ILE D 524 " pdb=" N ILE D 524 " pdb=" C ILE D 524 " pdb=" CB ILE D 524 " both_signs ideal model delta sigma weight residual False 2.43 2.04 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CA LEU C 498 " pdb=" N LEU C 498 " pdb=" C LEU C 498 " pdb=" CB LEU C 498 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA ASN D 523 " pdb=" N ASN D 523 " pdb=" C ASN D 523 " pdb=" CB ASN D 523 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.83e-01 ... (remaining 2841 not shown) Planarity restraints: 3049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 524 " -0.092 5.00e-02 4.00e+02 1.36e-01 2.98e+01 pdb=" N PRO D 525 " 0.235 5.00e-02 4.00e+02 pdb=" CA PRO D 525 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO D 525 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 527 " 0.087 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO D 528 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO D 528 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO D 528 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 647 " 0.060 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO D 648 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO D 648 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 648 " 0.041 5.00e-02 4.00e+02 ... (remaining 3046 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2052 2.75 - 3.29: 15502 3.29 - 3.83: 26179 3.83 - 4.36: 23599 4.36 - 4.90: 44577 Nonbonded interactions: 111909 Sorted by model distance: nonbonded pdb=" OH TYR C 74 " pdb=" O GLU C 137 " model vdw 2.213 2.440 nonbonded pdb=" OG SER C 96 " pdb=" O ASN C 99 " model vdw 2.225 2.440 nonbonded pdb=" O HIS A 106 " pdb=" OG1 THR A 110 " model vdw 2.233 2.440 nonbonded pdb=" O LEU A 191 " pdb=" OH TYR A 220 " model vdw 2.243 2.440 nonbonded pdb=" O ASP B 420 " pdb=" N ASN B 424 " model vdw 2.253 2.520 ... (remaining 111904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 44 or (resid 45 and (name N or nam \ e CA or name C or name O or name CB )) or resid 46 through 96 or (resid 97 and ( \ name N or name CA or name C or name O or name CB )) or resid 98 through 146 or ( \ resid 147 through 151 and (name N or name CA or name C or name O or name CB )) o \ r resid 152 through 153 or (resid 154 and (name N or name CA or name C or name O \ or name CB )) or resid 155 through 164 or (resid 165 through 166 and (name N or \ name CA or name C or name O or name CB )) or resid 167 through 168 or (resid 16 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 170 through \ 179 or (resid 180 through 181 and (name N or name CA or name C or name O or name \ CB )) or resid 182 through 190 or (resid 191 and (name N or name CA or name C o \ r name O or name CB )) or resid 192 or (resid 193 through 196 and (name N or nam \ e CA or name C or name O or name CB )) or resid 197 or (resid 198 through 215 an \ d (name N or name CA or name C or name O or name CB )) or (resid 216 through 228 \ and (name N or name CA or name C or name O or name CB )) or resid 238 through 2 \ 62 or (resid 263 through 264 and (name N or name CA or name C or name O or name \ CB )) or resid 265 through 275 or (resid 276 through 283 and (name N or name CA \ or name C or name O or name CB )) or resid 284 through 600)) selection = (chain 'B' and (resid 23 or (resid 24 and (name N or name CA or name C or name O \ or name CB )) or resid 25 through 148 or (resid 149 through 151 and (name N or \ name CA or name C or name O or name CB )) or resid 152 through 156 or (resid 157 \ and (name N or name CA or name C or name O or name CB )) or resid 158 through 1 \ 62 or (resid 163 and (name N or name CA or name C or name O or name CB )) or res \ id 164 through 176 or (resid 177 and (name N or name CA or name C or name O or n \ ame CB )) or resid 178 through 184 or (resid 185 through 186 and (name N or name \ CA or name C or name O or name CB )) or resid 187 through 189 or (resid 190 thr \ ough 191 and (name N or name CA or name C or name O or name CB )) or resid 192 t \ hrough 263 or (resid 264 and (name N or name CA or name C or name O or name CB ) \ ) or resid 265 through 280 or (resid 281 through 283 and (name N or name CA or n \ ame C or name O or name CB )) or resid 284 through 600)) } ncs_group { reference = (chain 'C' and (resid 17 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 87 or (resid 88 and (name N or nam \ e CA or name C or name O or name CB )) or resid 89 through 90 or (resid 91 and ( \ name N or name CA or name C or name O or name CB )) or resid 92 through 95 or (r \ esid 96 and (name N or name CA or name C or name O or name CB )) or resid 97 or \ (resid 98 through 100 and (name N or name CA or name C or name O or name CB )) o \ r resid 101 through 102 or (resid 103 and (name N or name CA or name C or name O \ or name CB )) or resid 104 through 110 or (resid 111 and (name N or name CA or \ name C or name O or name CB )) or resid 112 through 136 or (resid 137 and (name \ N or name CA or name C or name O or name CB )) or resid 138 through 148 or (resi \ d 149 and (name N or name CA or name C or name O or name CB )) or resid 150 thro \ ugh 158 or (resid 159 and (name N or name CA or name C or name O or name CB )) o \ r resid 160 through 170 or (resid 171 through 174 and (name N or name CA or name \ C or name O or name CB )) or (resid 175 through 179 and (name N or name CA or n \ ame C or name O or name CB )) or resid 180 through 186 or (resid 187 and (name N \ or name CA or name C or name O or name CB )) or resid 188 through 217 or (resid \ 218 through 230 and (name N or name CA or name C or name O or name CB )) or res \ id 231 or (resid 232 through 233 and (name N or name CA or name C or name O or n \ ame CB )) or resid 234 through 237 or (resid 238 through 240 and (name N or name \ CA or name C or name O or name CB )) or resid 241 or (resid 242 through 244 and \ (name N or name CA or name C or name O or name CB )) or resid 245 or (resid 246 \ through 247 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 48 through 249 or (resid 250 through 251 and (name N or name CA or name C or nam \ e O or name CB )) or resid 252 through 256 or (resid 257 through 258 and (name N \ or name CA or name C or name O or name CB )) or resid 259 through 265 or (resid \ 266 and (name N or name CA or name C or name O or name CB )) or resid 267 or (r \ esid 268 through 282 and (name N or name CA or name C or name O or name CB )) or \ resid 283 or (resid 284 through 290 and (name N or name CA or name C or name O \ or name CB )) or (resid 291 through 296 and (name N or name CA or name C or name \ O or name CB )) or resid 297 or (resid 298 through 306 and (name N or name CA o \ r name C or name O or name CB )) or resid 307 or (resid 308 and (name N or name \ CA or name C or name O or name CB )) or resid 309 or (resid 310 through 324 and \ (name N or name CA or name C or name O or name CB )) or (resid 325 through 332 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 333 through 34 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 344 or (resi \ d 345 through 368 and (name N or name CA or name C or name O or name CB )) or re \ sid 369 or (resid 370 through 371 and (name N or name CA or name C or name O or \ name CB )) or (resid 372 through 377 and (name N or name CA or name C or name O \ or name CB )) or resid 378 or (resid 379 through 384 and (name N or name CA or n \ ame C or name O or name CB )) or resid 385 through 386 or (resid 387 through 398 \ and (name N or name CA or name C or name O or name CB )) or resid 399 through 4 \ 00 or resid 405 through 419 or (resid 420 through 462 and (name N or name CA or \ name C or name O or name CB )) or resid 463 through 495 or resid 499 through 564 \ or resid 588 through 675 or resid 681 through 768)) selection = (chain 'D' and (resid 17 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 23 or (resid 24 through 29 and (na \ me N or name CA or name C or name O or name CB )) or resid 30 through 31 or (res \ id 32 and (name N or name CA or name C or name O or name CB )) or resid 33 throu \ gh 46 or (resid 47 and (name N or name CA or name C or name O or name CB )) or r \ esid 48 through 201 or (resid 202 through 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 243 or (resid 244 and (name N or nam \ e CA or name C or name O or name CB )) or resid 245 through 372 or (resid 373 th \ rough 377 and (name N or name CA or name C or name O or name CB )) or resid 378 \ through 388 or (resid 389 through 398 and (name N or name CA or name C or name O \ or name CB )) or (resid 399 through 409 and (name N or name CA or name C or nam \ e O or name CB )) or resid 410 or (resid 411 through 416 and (name N or name CA \ or name C or name O or name CB )) or resid 417 through 418 or (resid 419 through \ 462 and (name N or name CA or name C or name O or name CB )) or (resid 463 thro \ ugh 544 and (name N or name CA or name C or name O or name CB )) or resid 545 th \ rough 564 or resid 588 through 768)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 34 through 49 or resid 70 through 105)) } 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: 5.860 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: 22.960 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 47.710 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 : 0.002 0.055 16162 Z= 0.170 Angle : 0.617 21.684 22247 Z= 0.371 Chirality : 0.040 0.391 2844 Planarity : 0.004 0.136 3049 Dihedral : 11.295 85.671 4417 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.45 % Allowed : 3.22 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.17), residues: 2672 helix: 2.97 (0.15), residues: 1329 sheet: -1.10 (0.48), residues: 134 loop : -1.22 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 34 HIS 0.003 0.001 HIS D 112 PHE 0.009 0.001 PHE C 377 TYR 0.013 0.001 TYR C 201 ARG 0.002 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 2.062 Fit side-chains REVERT: C 317 MET cc_start: 0.8855 (ppp) cc_final: 0.8569 (ppp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1844 time to fit residues: 29.7304 Evaluate side-chains 84 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 50.0000 chunk 203 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 108 optimal weight: 40.0000 chunk 210 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 243 optimal weight: 50.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS C 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16162 Z= 0.345 Angle : 0.564 11.587 22247 Z= 0.305 Chirality : 0.040 0.132 2844 Planarity : 0.004 0.123 3049 Dihedral : 3.331 21.048 2775 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.12 % Favored : 95.62 % Rotamer: Outliers : 0.13 % Allowed : 6.91 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.17), residues: 2672 helix: 2.77 (0.15), residues: 1351 sheet: -1.17 (0.45), residues: 143 loop : -1.18 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 34 HIS 0.008 0.001 HIS C 272 PHE 0.013 0.001 PHE C 377 TYR 0.025 0.002 TYR C 201 ARG 0.003 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 1.841 Fit side-chains REVERT: C 317 MET cc_start: 0.8925 (ppp) cc_final: 0.8676 (ppp) REVERT: D 422 MET cc_start: 0.6910 (pmm) cc_final: 0.6682 (pmm) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.1829 time to fit residues: 28.6322 Evaluate side-chains 84 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 202 optimal weight: 3.9990 chunk 165 optimal weight: 50.0000 chunk 67 optimal weight: 0.7980 chunk 243 optimal weight: 30.0000 chunk 263 optimal weight: 30.0000 chunk 217 optimal weight: 30.0000 chunk 241 optimal weight: 50.0000 chunk 83 optimal weight: 6.9990 chunk 195 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 16162 Z= 0.242 Angle : 0.468 7.611 22247 Z= 0.257 Chirality : 0.040 0.143 2844 Planarity : 0.003 0.112 3049 Dihedral : 3.234 20.625 2775 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.37 % Favored : 96.41 % Rotamer: Outliers : 0.78 % Allowed : 9.52 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.17), residues: 2672 helix: 2.92 (0.15), residues: 1353 sheet: -1.19 (0.42), residues: 162 loop : -1.16 (0.18), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 34 HIS 0.007 0.001 HIS C 112 PHE 0.015 0.001 PHE A 107 TYR 0.017 0.001 TYR C 201 ARG 0.002 0.000 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 2.057 Fit side-chains REVERT: C 317 MET cc_start: 0.8931 (ppp) cc_final: 0.8671 (ppp) REVERT: D 422 MET cc_start: 0.6866 (pmm) cc_final: 0.6631 (pmm) outliers start: 6 outliers final: 0 residues processed: 89 average time/residue: 0.1889 time to fit residues: 30.6559 Evaluate side-chains 84 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 50.0000 chunk 183 optimal weight: 50.0000 chunk 126 optimal weight: 2.9990 chunk 26 optimal weight: 50.0000 chunk 116 optimal weight: 0.6980 chunk 163 optimal weight: 50.0000 chunk 244 optimal weight: 50.0000 chunk 259 optimal weight: 50.0000 chunk 127 optimal weight: 0.5980 chunk 231 optimal weight: 50.0000 chunk 69 optimal weight: 3.9990 overall best weight: 11.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 103 GLN B 31 GLN ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS D 42 GLN D 106 ASN D 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.089 16162 Z= 0.896 Angle : 1.067 17.540 22247 Z= 0.553 Chirality : 0.050 0.233 2844 Planarity : 0.006 0.113 3049 Dihedral : 5.095 27.391 2775 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.08 % Favored : 91.69 % Rotamer: Outliers : 2.48 % Allowed : 14.99 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2672 helix: 1.06 (0.14), residues: 1351 sheet: -1.70 (0.47), residues: 124 loop : -1.74 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 146 HIS 0.015 0.003 HIS C 272 PHE 0.031 0.003 PHE D 217 TYR 0.036 0.004 TYR B 156 ARG 0.008 0.001 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 2.240 Fit side-chains REVERT: B 85 GLU cc_start: 0.9503 (OUTLIER) cc_final: 0.9186 (mp0) REVERT: C 224 PHE cc_start: 0.9420 (OUTLIER) cc_final: 0.8939 (m-80) REVERT: C 317 MET cc_start: 0.9140 (ppp) cc_final: 0.8832 (ppp) REVERT: D 191 MET cc_start: 0.9276 (ttm) cc_final: 0.8937 (ttm) outliers start: 19 outliers final: 8 residues processed: 98 average time/residue: 0.2253 time to fit residues: 39.5244 Evaluate side-chains 92 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 224 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 106 optimal weight: 50.0000 chunk 221 optimal weight: 9.9990 chunk 179 optimal weight: 50.0000 chunk 0 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 232 optimal weight: 50.0000 chunk 65 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 HIS D 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 16162 Z= 0.165 Angle : 0.473 7.348 22247 Z= 0.265 Chirality : 0.040 0.141 2844 Planarity : 0.003 0.109 3049 Dihedral : 3.875 25.677 2775 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.78 % Favored : 96.03 % Rotamer: Outliers : 1.04 % Allowed : 15.65 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2672 helix: 2.50 (0.14), residues: 1352 sheet: -1.79 (0.41), residues: 148 loop : -1.47 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 109 HIS 0.004 0.001 HIS A 106 PHE 0.019 0.001 PHE A 107 TYR 0.016 0.001 TYR C 341 ARG 0.004 0.001 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.755 Fit side-chains REVERT: C 317 MET cc_start: 0.9038 (ppp) cc_final: 0.8698 (ppp) REVERT: D 191 MET cc_start: 0.9207 (ttm) cc_final: 0.8930 (ttm) outliers start: 8 outliers final: 1 residues processed: 88 average time/residue: 0.1760 time to fit residues: 28.7468 Evaluate side-chains 83 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 273 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 50.0000 chunk 233 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 152 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 chunk 215 optimal weight: 40.0000 chunk 120 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 40.0000 chunk 136 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16162 Z= 0.274 Angle : 0.506 6.137 22247 Z= 0.275 Chirality : 0.040 0.132 2844 Planarity : 0.003 0.108 3049 Dihedral : 3.705 25.672 2775 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.61 % Favored : 94.20 % Rotamer: Outliers : 1.30 % Allowed : 16.95 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2672 helix: 2.67 (0.14), residues: 1353 sheet: -1.75 (0.42), residues: 148 loop : -1.45 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 34 HIS 0.007 0.001 HIS C 272 PHE 0.012 0.001 PHE D 217 TYR 0.018 0.001 TYR A 74 ARG 0.002 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 1.943 Fit side-chains revert: symmetry clash REVERT: B 85 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.9161 (mp0) REVERT: C 317 MET cc_start: 0.9037 (ppp) cc_final: 0.8750 (ppp) REVERT: D 191 MET cc_start: 0.9241 (ttm) cc_final: 0.8934 (ttm) outliers start: 10 outliers final: 4 residues processed: 91 average time/residue: 0.1860 time to fit residues: 31.3367 Evaluate side-chains 87 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 163 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 8.9990 chunk 29 optimal weight: 30.0000 chunk 147 optimal weight: 0.7980 chunk 189 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 258 optimal weight: 50.0000 chunk 161 optimal weight: 50.0000 chunk 157 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16162 Z= 0.209 Angle : 0.455 6.385 22247 Z= 0.252 Chirality : 0.039 0.128 2844 Planarity : 0.003 0.106 3049 Dihedral : 3.544 24.888 2775 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.19 % Favored : 95.62 % Rotamer: Outliers : 0.91 % Allowed : 17.99 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.17), residues: 2672 helix: 2.92 (0.14), residues: 1344 sheet: -1.65 (0.43), residues: 141 loop : -1.32 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 109 HIS 0.008 0.001 HIS C 272 PHE 0.013 0.001 PHE A 107 TYR 0.017 0.001 TYR A 74 ARG 0.001 0.000 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 1.911 Fit side-chains revert: symmetry clash REVERT: C 168 MET cc_start: 0.9012 (ttm) cc_final: 0.8797 (ttm) REVERT: C 317 MET cc_start: 0.9005 (ppp) cc_final: 0.8701 (ppp) REVERT: D 191 MET cc_start: 0.9232 (ttm) cc_final: 0.8920 (ttm) outliers start: 7 outliers final: 4 residues processed: 87 average time/residue: 0.1827 time to fit residues: 29.7370 Evaluate side-chains 86 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain D residue 163 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 30.0000 chunk 103 optimal weight: 40.0000 chunk 154 optimal weight: 4.9990 chunk 77 optimal weight: 0.0060 chunk 50 optimal weight: 30.0000 chunk 164 optimal weight: 30.0000 chunk 175 optimal weight: 50.0000 chunk 127 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 203 optimal weight: 0.0770 chunk 234 optimal weight: 2.9990 overall best weight: 2.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16162 Z= 0.220 Angle : 0.462 6.072 22247 Z= 0.253 Chirality : 0.039 0.129 2844 Planarity : 0.003 0.105 3049 Dihedral : 3.461 24.653 2775 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.90 % Favored : 94.95 % Rotamer: Outliers : 1.30 % Allowed : 17.60 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.17), residues: 2672 helix: 3.00 (0.14), residues: 1345 sheet: -1.65 (0.43), residues: 141 loop : -1.29 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 34 HIS 0.008 0.001 HIS D 112 PHE 0.012 0.001 PHE A 107 TYR 0.017 0.001 TYR A 74 ARG 0.002 0.000 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 1.664 Fit side-chains revert: symmetry clash REVERT: C 168 MET cc_start: 0.9039 (ttm) cc_final: 0.8826 (ttm) REVERT: C 317 MET cc_start: 0.9019 (ppp) cc_final: 0.8712 (ppp) REVERT: D 191 MET cc_start: 0.9235 (ttm) cc_final: 0.8947 (ttm) outliers start: 10 outliers final: 5 residues processed: 92 average time/residue: 0.2058 time to fit residues: 34.4329 Evaluate side-chains 87 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 163 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 40.0000 chunk 225 optimal weight: 30.0000 chunk 240 optimal weight: 50.0000 chunk 144 optimal weight: 0.4980 chunk 104 optimal weight: 50.0000 chunk 189 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 217 optimal weight: 20.0000 chunk 227 optimal weight: 50.0000 chunk 239 optimal weight: 0.0050 chunk 158 optimal weight: 40.0000 overall best weight: 4.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN C 84 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 16162 Z= 0.369 Angle : 0.584 8.093 22247 Z= 0.313 Chirality : 0.041 0.145 2844 Planarity : 0.003 0.104 3049 Dihedral : 3.805 24.521 2775 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.99 % Favored : 93.86 % Rotamer: Outliers : 1.17 % Allowed : 18.25 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.17), residues: 2672 helix: 2.68 (0.14), residues: 1355 sheet: -1.60 (0.46), residues: 120 loop : -1.42 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 146 HIS 0.010 0.002 HIS C 272 PHE 0.014 0.001 PHE D 217 TYR 0.018 0.002 TYR C 201 ARG 0.002 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 1.928 Fit side-chains revert: symmetry clash REVERT: C 317 MET cc_start: 0.9072 (ppp) cc_final: 0.8715 (ppp) REVERT: D 191 MET cc_start: 0.9262 (ttm) cc_final: 0.8912 (ttm) outliers start: 9 outliers final: 7 residues processed: 91 average time/residue: 0.1894 time to fit residues: 31.5231 Evaluate side-chains 89 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 163 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 50.0000 chunk 155 optimal weight: 0.0870 chunk 120 optimal weight: 0.9980 chunk 176 optimal weight: 20.0000 chunk 266 optimal weight: 50.0000 chunk 245 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 16162 Z= 0.164 Angle : 0.442 6.661 22247 Z= 0.245 Chirality : 0.039 0.140 2844 Planarity : 0.003 0.103 3049 Dihedral : 3.479 24.204 2775 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.30 % Favored : 95.55 % Rotamer: Outliers : 0.65 % Allowed : 18.77 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.17), residues: 2672 helix: 3.07 (0.14), residues: 1347 sheet: -1.67 (0.44), residues: 130 loop : -1.24 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 109 HIS 0.010 0.001 HIS D 112 PHE 0.023 0.001 PHE A 107 TYR 0.016 0.001 TYR A 74 ARG 0.003 0.000 ARG A 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 1.932 Fit side-chains REVERT: C 317 MET cc_start: 0.9021 (ppp) cc_final: 0.8721 (ppp) REVERT: D 191 MET cc_start: 0.9242 (ttm) cc_final: 0.8935 (ttm) outliers start: 5 outliers final: 4 residues processed: 86 average time/residue: 0.1999 time to fit residues: 31.5997 Evaluate side-chains 86 residues out of total 2406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 156 TYR Chi-restraints excluded: chain C residue 167 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 50.0000 chunk 65 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 31 optimal weight: 50.0000 chunk 59 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 26 optimal weight: 40.0000 chunk 39 optimal weight: 9.9990 chunk 186 optimal weight: 0.6980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.061262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.028795 restraints weight = 145611.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.029354 restraints weight = 92760.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.029055 restraints weight = 60012.505| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16162 Z= 0.255 Angle : 0.497 7.754 22247 Z= 0.270 Chirality : 0.040 0.154 2844 Planarity : 0.003 0.102 3049 Dihedral : 3.492 24.179 2775 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.09 % Favored : 94.76 % Rotamer: Outliers : 0.78 % Allowed : 19.04 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.17), residues: 2672 helix: 3.04 (0.14), residues: 1348 sheet: -1.36 (0.46), residues: 124 loop : -1.30 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 34 HIS 0.011 0.002 HIS D 112 PHE 0.016 0.001 PHE A 107 TYR 0.017 0.001 TYR A 74 ARG 0.002 0.000 ARG D 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2984.80 seconds wall clock time: 54 minutes 19.00 seconds (3259.00 seconds total)