Starting phenix.real_space_refine on Wed Feb 4 18:46:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u74_63931/02_2026/9u74_63931.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u74_63931/02_2026/9u74_63931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u74_63931/02_2026/9u74_63931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u74_63931/02_2026/9u74_63931.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u74_63931/02_2026/9u74_63931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u74_63931/02_2026/9u74_63931.map" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.056 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 70 5.16 5 C 7670 2.51 5 N 2024 2.21 5 O 2368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12132 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 491 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 73} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 2771 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 14, 'TRANS': 393} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 482 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 19, 'ASN:plan1': 8, 'ASP:plan': 15, 'GLN:plan1': 9, 'TYR:plan': 3, 'ARG:plan': 4, 'PHE:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 255 Chain: "C" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 585 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3122 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 393} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 566 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3102 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 14, 'TRANS': 393} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 697 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 104, 694 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'ARG:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 86 Conformer: "B" Number of residues, atoms: 104, 694 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'ARG:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 86 bond proxies already assigned to first conformer: 703 Chain: "H" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 798 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ASN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 70 Time building chain proxies: 3.00, per 1000 atoms: 0.25 Number of scatterers: 12132 At special positions: 0 Unit cell: (90.95, 134.82, 156.22, 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 70 16.00 O 2368 8.00 N 2024 7.00 C 7670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS D 439 " distance=2.04 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS D 212 " distance=2.04 Simple disulfide: pdb=" SG CYS D 155 " - pdb=" SG CYS D 290 " distance=2.03 Simple disulfide: pdb=" SG CYS D 313 " - pdb=" SG CYS D 343 " distance=2.03 Simple disulfide: pdb=" SG CYS D 322 " - pdb=" SG CYS D 333 " distance=2.03 Simple disulfide: pdb=" SG CYS D 358 " - pdb=" SG CYS D 367 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 393 " distance=2.03 Simple disulfide: pdb=" SG CYS D 416 " - pdb=" SG CYS D 422 " distance=2.03 Simple disulfide: pdb=" SG CYS E 37 " - pdb=" SG CYS F 439 " distance=2.03 Simple disulfide: pdb=" SG CYS E 69 " - pdb=" SG CYS F 212 " distance=2.03 Simple disulfide: pdb=" SG CYS F 155 " - pdb=" SG CYS F 290 " distance=2.03 Simple disulfide: pdb=" SG CYS F 313 " - pdb=" SG CYS F 343 " distance=2.03 Simple disulfide: pdb=" SG CYS F 322 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 358 " - pdb=" SG CYS F 367 " distance=2.03 Simple disulfide: pdb=" SG CYS F 382 " - pdb=" SG CYS F 393 " distance=2.03 Simple disulfide: pdb=" SG CYS F 416 " - pdb=" SG CYS F 422 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.06 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 675.1 milliseconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3162 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 24 sheets defined 30.0% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 76 through 82 Processing helix chain 'A' and resid 83 through 96 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 195 through 208 removed outlier: 4.231A pdb=" N LEU B 204 " --> pdb=" O ASP B 200 " (cutoff:3.500A) Proline residue: B 205 - end of helix Processing helix chain 'B' and resid 218 through 240 removed outlier: 3.554A pdb=" N GLU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN B 228 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 267 through 270 Processing helix chain 'B' and resid 271 through 276 removed outlier: 3.966A pdb=" N ASN B 276 " --> pdb=" O LYS B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.706A pdb=" N CYS B 358 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.979A pdb=" N VAL B 384 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.621A pdb=" N TYR B 478 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 515 Processing helix chain 'C' and resid 77 through 96 removed outlier: 4.525A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS C 85 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TYR C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 159 Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 195 through 204 removed outlier: 4.105A pdb=" N LYS D 201 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU D 204 " --> pdb=" O ASP D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 220 through 241 removed outlier: 3.733A pdb=" N ASN D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN D 228 " --> pdb=" O GLN D 224 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG D 229 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU D 230 " --> pdb=" O LYS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 263 Processing helix chain 'D' and resid 267 through 275 Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 354 through 358 removed outlier: 3.874A pdb=" N CYS D 358 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'D' and resid 376 through 379 removed outlier: 3.618A pdb=" N VAL D 379 " --> pdb=" O PRO D 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 376 through 379' Processing helix chain 'D' and resid 380 through 385 removed outlier: 3.609A pdb=" N VAL D 384 " --> pdb=" O ASN D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 478 Processing helix chain 'D' and resid 479 through 483 removed outlier: 3.524A pdb=" N PHE D 483 " --> pdb=" O PRO D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 512 removed outlier: 3.693A pdb=" N GLU D 511 " --> pdb=" O ARG D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 516 Processing helix chain 'E' and resid 73 through 96 removed outlier: 4.293A pdb=" N LEU E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 142 removed outlier: 3.842A pdb=" N LEU F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F 142 " --> pdb=" O GLY F 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 138 through 142' Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 163 through 170 Processing helix chain 'F' and resid 195 through 207 Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 218 through 240 removed outlier: 3.756A pdb=" N GLN F 225 " --> pdb=" O ILE F 221 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS F 226 " --> pdb=" O GLU F 222 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG F 229 " --> pdb=" O GLN F 225 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU F 230 " --> pdb=" O LYS F 226 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN F 240 " --> pdb=" O GLU F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 264 Processing helix chain 'F' and resid 267 through 276 removed outlier: 3.501A pdb=" N LYS F 271 " --> pdb=" O THR F 267 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 285 removed outlier: 4.126A pdb=" N ARG F 282 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLN F 283 " --> pdb=" O GLN F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 358 removed outlier: 3.582A pdb=" N CYS F 358 " --> pdb=" O ALA F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 372 No H-bonds generated for 'chain 'F' and resid 370 through 372' Processing helix chain 'F' and resid 378 through 385 removed outlier: 3.925A pdb=" N CYS F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN F 383 " --> pdb=" O VAL F 379 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL F 384 " --> pdb=" O ASN F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 478 Processing helix chain 'F' and resid 492 through 514 Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.018A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.999A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 373 through 375 removed outlier: 4.464A pdb=" N LYS B 315 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 39 " --> pdb=" O HIS B 317 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 29 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 32 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 60 removed outlier: 6.073A pdb=" N LYS B 191 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR A 58 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU B 193 " --> pdb=" O THR A 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 191 through 193 current: chain 'B' and resid 296 through 309 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 296 through 309 current: chain 'B' and resid 364 through 368 Processing sheet with id=AA3, first strand: chain 'B' and resid 178 through 180 Processing sheet with id=AA4, first strand: chain 'B' and resid 321 through 322 removed outlier: 6.144A pdb=" N THR B 397 " --> pdb=" O PHE B 488 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N PHE B 488 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AA6, first strand: chain 'B' and resid 430 through 433 removed outlier: 3.649A pdb=" N GLY B 430 " --> pdb=" O ASN B 426 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 531 through 533 Processing sheet with id=AA8, first strand: chain 'D' and resid 373 through 375 removed outlier: 4.720A pdb=" N THR D 311 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR C 44 " --> pdb=" O CYS D 313 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LYS D 315 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYS C 42 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR C 29 " --> pdb=" O LYS C 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 176 through 180 removed outlier: 4.032A pdb=" N ALA D 177 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 192 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N GLU C 60 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASP D 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER C 55 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 301 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL D 296 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE D 292 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA D 298 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D 287 " --> pdb=" O THR D 244 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 321 through 322 Processing sheet with id=AB2, first strand: chain 'D' and resid 359 through 361 Processing sheet with id=AB3, first strand: chain 'D' and resid 404 through 407 removed outlier: 3.681A pdb=" N VAL D 414 " --> pdb=" O ASP D 440 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS D 416 " --> pdb=" O GLY D 438 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 430 through 434 removed outlier: 6.747A pdb=" N ALA D 424 " --> pdb=" O ILE D 432 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR D 434 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N CYS D 422 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 449 " --> pdb=" O SER D 425 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 531 through 533 Processing sheet with id=AB6, first strand: chain 'E' and resid 29 through 33 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 38 through 60 current: chain 'F' and resid 186 through 191 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 186 through 191 current: chain 'F' and resid 296 through 317 removed outlier: 3.747A pdb=" N ASP F 344 " --> pdb=" O PRO F 312 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 321 through 322 Processing sheet with id=AB8, first strand: chain 'F' and resid 360 through 361 Processing sheet with id=AB9, first strand: chain 'F' and resid 404 through 407 Processing sheet with id=AC1, first strand: chain 'F' and resid 430 through 434 removed outlier: 5.432A pdb=" N ILE F 431 " --> pdb=" O ASN F 426 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASN F 426 " --> pdb=" O ILE F 431 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL F 450 " --> pdb=" O TYR F 457 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 531 through 533 removed outlier: 4.210A pdb=" N VAL F 531 " --> pdb=" O VAL F 538 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL F 538 " --> pdb=" O VAL F 531 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS F 533 " --> pdb=" O GLU F 536 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AC4, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.508A pdb=" N LEU G 11 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR G 85 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA G 34 " --> pdb=" O GLN G 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 60 current: chain 'H' and resid 106 through 109 470 hydrogen bonds defined for protein. 1209 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: 1.77 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2009 1.30 - 1.43: 3038 1.43 - 1.56: 7186 1.56 - 1.69: 0 1.69 - 1.82: 90 Bond restraints: 12323 Sorted by residual: bond pdb=" C ALA H 104 " pdb=" O ALA H 104 " ideal model delta sigma weight residual 1.233 1.173 0.060 1.28e-02 6.10e+03 2.17e+01 bond pdb=" CA ASP H 100 " pdb=" C ASP H 100 " ideal model delta sigma weight residual 1.523 1.472 0.050 1.23e-02 6.61e+03 1.67e+01 bond pdb=" C ASP H 100 " pdb=" O ASP H 100 " ideal model delta sigma weight residual 1.236 1.192 0.043 1.19e-02 7.06e+03 1.33e+01 bond pdb=" N ILE F 217 " pdb=" CA ILE F 217 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.14e-02 7.69e+03 1.14e+01 bond pdb=" N ILE A 64 " pdb=" CA ILE A 64 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.09e+01 ... (remaining 12318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 16358 2.06 - 4.12: 401 4.12 - 6.18: 55 6.18 - 8.24: 2 8.24 - 10.30: 5 Bond angle restraints: 16821 Sorted by residual: angle pdb=" N PRO B 246 " pdb=" CA PRO B 246 " pdb=" CB PRO B 246 " ideal model delta sigma weight residual 103.25 97.66 5.59 1.05e+00 9.07e-01 2.83e+01 angle pdb=" N SER H 103 " pdb=" CA SER H 103 " pdb=" C SER H 103 " ideal model delta sigma weight residual 113.19 121.45 -8.26 1.58e+00 4.01e-01 2.74e+01 angle pdb=" CA GLY G 100 " pdb=" C GLY G 100 " pdb=" O GLY G 100 " ideal model delta sigma weight residual 122.29 118.28 4.01 8.10e-01 1.52e+00 2.45e+01 angle pdb=" CA TRP G 95 " pdb=" C TRP G 95 " pdb=" O TRP G 95 " ideal model delta sigma weight residual 121.33 116.26 5.07 1.08e+00 8.57e-01 2.20e+01 angle pdb=" N TRP H 101 " pdb=" CA TRP H 101 " pdb=" C TRP H 101 " ideal model delta sigma weight residual 112.38 117.59 -5.21 1.22e+00 6.72e-01 1.83e+01 ... (remaining 16816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 6807 17.59 - 35.19: 521 35.19 - 52.78: 81 52.78 - 70.38: 15 70.38 - 87.97: 11 Dihedral angle restraints: 7435 sinusoidal: 2539 harmonic: 4896 Sorted by residual: dihedral pdb=" CB CYS E 37 " pdb=" SG CYS E 37 " pdb=" SG CYS F 439 " pdb=" CB CYS F 439 " ideal model delta sinusoidal sigma weight residual 93.00 145.65 -52.65 1 1.00e+01 1.00e-02 3.78e+01 dihedral pdb=" CB CYS C 69 " pdb=" SG CYS C 69 " pdb=" SG CYS D 212 " pdb=" CB CYS D 212 " ideal model delta sinusoidal sigma weight residual 93.00 43.34 49.66 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CA SER D 211 " pdb=" C SER D 211 " pdb=" N CYS D 212 " pdb=" CA CYS D 212 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 7432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1862 0.079 - 0.158: 208 0.158 - 0.238: 14 0.238 - 0.317: 0 0.317 - 0.396: 3 Chirality restraints: 2087 Sorted by residual: chirality pdb=" CA SER H 103 " pdb=" N SER H 103 " pdb=" C SER H 103 " pdb=" CB SER H 103 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CA ALA H 104 " pdb=" N ALA H 104 " pdb=" C ALA H 104 " pdb=" CB ALA H 104 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA TRP H 101 " pdb=" N TRP H 101 " pdb=" C TRP H 101 " pdb=" CB TRP H 101 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 2084 not shown) Planarity restraints: 2121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP H 100 " -0.021 2.00e-02 2.50e+03 4.17e-02 1.74e+01 pdb=" C ASP H 100 " 0.072 2.00e-02 2.50e+03 pdb=" O ASP H 100 " -0.027 2.00e-02 2.50e+03 pdb=" N TRP H 101 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 99 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C GLU H 99 " 0.060 2.00e-02 2.50e+03 pdb=" O GLU H 99 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP H 100 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP H 101 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.56e+00 pdb=" C TRP H 101 " -0.037 2.00e-02 2.50e+03 pdb=" O TRP H 101 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY H 102 " 0.013 2.00e-02 2.50e+03 ... (remaining 2118 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 6 2.12 - 2.82: 3825 2.82 - 3.51: 16454 3.51 - 4.21: 25599 4.21 - 4.90: 44337 Nonbonded interactions: 90221 Sorted by model distance: nonbonded pdb=" CD2 TYR A 53 " pdb=" CE MET B 264 " model vdw 1.431 3.760 nonbonded pdb=" CE LYS B 176 " pdb=" OD2 ASP B 263 " model vdw 1.640 3.440 nonbonded pdb=" CE2 TYR A 53 " pdb=" CE MET B 264 " model vdw 1.968 3.760 nonbonded pdb=" O ARG D 507 " pdb=" NH1 ARG D 507 " model vdw 2.053 3.120 nonbonded pdb=" O PRO B 265 " pdb=" CG2 ILE B 266 " model vdw 2.058 3.460 ... (remaining 90216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 26 and (name N or name CA or name C or name O or name CB \ )) or resid 27 through 99)) selection = (chain 'C' and ((resid 26 and (name N or name CA or name C or name O or name CB \ )) or resid 27 through 30 or (resid 31 and (name N or name CA or name C or name \ O or name CB )) or resid 32 through 33 or (resid 34 and (name N or name CA or na \ me C or name O or name CB )) or resid 35 or (resid 36 and (name N or name CA or \ name C or name O or name CB )) or resid 37 through 41 or (resid 42 and (name N o \ r name CA or name C or name O or name CB )) or resid 43 through 59 or (resid 60 \ and (name N or name CA or name C or name O or name CB )) or resid 61 through 62 \ or (resid 63 through 70 and (name N or name CA or name C or name O or name CB )) \ or resid 71 through 74 or (resid 75 and (name N or name CA or name C or name O \ or name CB )) or resid 76 or (resid 77 through 78 and (name N or name CA or name \ C or name O or name CB )) or resid 79 or (resid 80 through 85 and (name N or na \ me CA or name C or name O or name CB )) or resid 86 or (resid 87 and (name N or \ name CA or name C or name O or name CB )) or resid 88 through 91 or (resid 92 an \ d (name N or name CA or name C or name O or name CB )) or resid 93 through 96 or \ (resid 97 through 99 and (name N or name CA or name C or name O or name CB )))) \ selection = (chain 'E' and (resid 26 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 33 or (resid 34 and (name N or nam \ e CA or name C or name O or name CB )) or resid 35 or (resid 36 and (name N or n \ ame CA or name C or name O or name CB )) or resid 37 through 41 or (resid 42 and \ (name N or name CA or name C or name O or name CB )) or resid 43 through 59 or \ (resid 60 and (name N or name CA or name C or name O or name CB )) or resid 61 t \ hrough 68 or (resid 69 through 70 and (name N or name CA or name C or name O or \ name CB )) or resid 71 through 80 or (resid 81 through 85 and (name N or name CA \ or name C or name O or name CB )) or resid 86 or (resid 87 and (name N or name \ CA or name C or name O or name CB )) or resid 88 through 91 or (resid 92 and (na \ me N or name CA or name C or name O or name CB )) or resid 93 through 96 or (res \ id 97 through 99 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 137 through 155 or (resid 156 and (name N or name CA or na \ me C or name O or name CB )) or resid 157 through 204 or (resid 205 through 216 \ and (name N or name CA or name C or name O or name CB )) or resid 217 through 22 \ 0 or (resid 221 through 222 and (name N or name CA or name C or name O or name C \ B )) or resid 223 through 234 or (resid 235 through 236 and (name N or name CA o \ r name C or name O or name CB )) or resid 237 through 544)) selection = (chain 'D' and (resid 137 through 160 or (resid 161 and (name N or name CA or na \ me C or name O or name CB )) or resid 162 or (resid 163 and (name N or name CA o \ r name C or name O or name CB )) or resid 164 or (resid 165 through 166 and (nam \ e N or name CA or name C or name O or name CB )) or resid 167 or (resid 168 thro \ ugh 170 and (name N or name CA or name C or name O or name CB )) or resid 171 or \ (resid 172 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 3 through 181 or (resid 182 through 183 and (name N or name CA or name C or name \ O or name CB )) or resid 184 through 185 or (resid 186 and (name N or name CA o \ r name C or name O or name CB )) or resid 187 through 193 or (resid 194 and (nam \ e N or name CA or name C or name O or name CB )) or resid 195 or (resid 196 thro \ ugh 197 and (name N or name CA or name C or name O or name CB )) or resid 198 th \ rough 199 or (resid 200 through 216 and (name N or name CA or name C or name O o \ r name CB )) or resid 217 through 220 or (resid 221 through 222 and (name N or n \ ame CA or name C or name O or name CB )) or resid 223 through 224 or (resid 225 \ through 226 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 7 through 231 or (resid 232 and (name N or name CA or name C or name O or name C \ B )) or resid 233 through 234 or (resid 235 through 236 and (name N or name CA o \ r name C or name O or name CB )) or resid 237 through 250 or (resid 251 and (nam \ e N or name CA or name C or name O or name CB )) or resid 252 through 255 or (re \ sid 256 and (name N or name CA or name C or name O or name CB )) or resid 257 th \ rough 268 or (resid 269 and (name N or name CA or name C or name O or name CB )) \ or resid 270 through 271 or (resid 272 and (name N or name CA or name C or name \ O or name CB )) or resid 273 through 292 or (resid 293 through 295 and (name N \ or name CA or name C or name O or name CB )) or resid 296 through 309 or (resid \ 310 and (name N or name CA or name C or name O or name CB )) or resid 311 throug \ h 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 or (resid 327 through 328 and (name N or name CA or name C or name O o \ r name CB )) or resid 329 through 337 or (resid 338 and (name N or name CA or na \ me C or name O or name CB )) or resid 339 through 343 or (resid 344 and (name N \ or name CA or name C or name O or name CB )) or resid 345 through 353 or (resid \ 354 through 356 and (name N or name CA or name C or name O or name CB )) or resi \ d 357 through 360 or (resid 361 and (name N or name CA or name C or name O or na \ me CB )) or resid 362 through 367 or (resid 368 and (name N or name CA or name C \ or name O or name CB )) or resid 369 through 377 or (resid 378 and (name N or n \ ame CA or name C or name O or name CB )) or resid 379 through 382 or (resid 383 \ and (name N or name CA or name C or name O or name CB )) or resid 384 through 38 \ 9 or (resid 390 through 392 and (name N or name CA or name C or name O or name C \ B )) or resid 393 through 398 or (resid 399 through 401 and (name N or name CA o \ r name C or name O or name CB )) or resid 402 through 408 or (resid 409 and (nam \ e N or name CA or name C or name O or name CB )) or resid 410 through 418 or (re \ sid 419 and (name N or name CA or name C or name O or name CB )) or resid 420 or \ (resid 421 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 2 through 426 or (resid 427 and (name N or name CA or name C or name O or name C \ B )) or resid 428 or (resid 429 and (name N or name CA or name C or name O or na \ me CB )) or resid 430 through 444 or (resid 445 and (name N or name CA or name C \ or name O or name CB )) or resid 446 through 447 or (resid 448 and (name N or n \ ame CA or name C or name O or name CB )) or resid 449 through 453 or (resid 454 \ and (name N or name CA or name C or name O or name CB )) or resid 455 through 46 \ 1 or (resid 462 through 463 and (name N or name CA or name C or name O or name C \ B )) or resid 464 through 469 or (resid 470 and (name N or name CA or name C or \ name O or name CB )) or resid 471 or (resid 472 and (name N or name CA or name C \ or name O or name CB )) or resid 473 through 476 or (resid 477 and (name N or n \ ame CA or name C or name O or name CB )) or resid 478 through 480 or (resid 481 \ and (name N or name CA or name C or name O or name CB )) or resid 482 through 48 \ 4 or (resid 485 through 490 and (name N or name CA or name C or name O or name C \ B )) or resid 491 through 493 or (resid 494 and (name N or name CA or name C or \ name O or name CB )) or resid 495 or (resid 496 through 498 and (name N or name \ CA or name C or name O or name CB )) or resid 499 through 500 or (resid 501 and \ (name N or name CA or name C or name O or name CB )) or resid 502 through 504 or \ (resid 505 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 6 or (resid 507 through 508 and (name N or name CA or name C or name O or name C \ B )) or resid 509 or (resid 510 through 513 and (name N or name CA or name C or \ name O or name CB )) or resid 514 through 518 or (resid 519 and (name N or name \ CA or name C or name O or name CB )) or resid 520 or (resid 521 through 526 and \ (name N or name CA or name C or name O or name CB )) or resid 527 or (resid 528 \ through 530 and (name N or name CA or name C or name O or name CB )) or resid 53 \ 1 or (resid 532 through 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 or (resid 536 through 537 and (name N or name CA or name C or \ name O or name CB )) or resid 538 or (resid 539 through 540 and (name N or name \ CA or name C or name O or name CB )) or resid 541 through 542 or (resid 543 and \ (name N or name CA or name C or name O or name CB )) or resid 544)) selection = (chain 'F' and (resid 137 through 155 or (resid 156 and (name N or name CA or na \ me C or name O or name CB )) or resid 157 through 160 or (resid 161 and (name N \ or name CA or name C or name O or name CB )) or resid 162 or (resid 163 and (nam \ e N or name CA or name C or name O or name CB )) or resid 164 or (resid 165 thro \ ugh 166 and (name N or name CA or name C or name O or name CB )) or resid 167 or \ (resid 168 through 170 and (name N or name CA or name C or name O or name CB )) \ or resid 171 or (resid 172 and (name N or name CA or name C or name O or name C \ B )) or resid 173 through 181 or (resid 182 through 183 and (name N or name CA o \ r name C or name O or name CB )) or resid 184 through 185 or (resid 186 and (nam \ e N or name CA or name C or name O or name CB )) or resid 187 through 193 or (re \ sid 194 and (name N or name CA or name C or name O or name CB )) or resid 195 or \ (resid 196 through 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 199 or (resid 200 through 216 and (name N or name CA or na \ me C or name O or name CB )) or resid 217 through 221 or (resid 222 and (name N \ or name CA or name C or name O or name CB )) or resid 223 through 224 or (resid \ 225 through 226 and (name N or name CA or name C or name O or name CB )) or resi \ d 227 through 231 or (resid 232 and (name N or name CA or name C or name O or na \ me CB )) or resid 233 through 235 or (resid 236 and (name N or name CA or name C \ or name O or name CB )) or resid 237 through 250 or (resid 251 and (name N or n \ ame CA or name C or name O or name CB )) or resid 252 through 255 or (resid 256 \ and (name N or name CA or name C or name O or name CB )) or resid 257 through 26 \ 8 or (resid 269 and (name N or name CA or name C or name O or name CB )) or resi \ d 270 through 271 or (resid 272 and (name N or name CA or name C or name O or na \ me CB )) or resid 273 through 292 or (resid 293 through 295 and (name N or name \ CA or name C or name O or name CB )) or resid 296 through 309 or (resid 310 and \ (name N or name CA or name C or name O or name CB )) or resid 311 through 324 or \ (resid 325 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 6 or (resid 327 through 328 and (name N or name CA or name C or name O or name C \ B )) or resid 329 through 337 or (resid 338 and (name N or name CA or name C or \ name O or name CB )) or resid 339 through 343 or (resid 344 and (name N or name \ CA or name C or name O or name CB )) or resid 345 through 353 or (resid 354 thro \ ugh 356 and (name N or name CA or name C or name O or name CB )) or resid 357 th \ rough 360 or (resid 361 and (name N or name CA or name C or name O or name CB )) \ or resid 362 through 367 or (resid 368 and (name N or name CA or name C or name \ O or name CB )) or resid 369 through 377 or (resid 378 and (name N or name CA o \ r name C or name O or name CB )) or resid 379 through 382 or (resid 383 and (nam \ e N or name CA or name C or name O or name CB )) or resid 384 through 389 or (re \ sid 390 through 392 and (name N or name CA or name C or name O or name CB )) or \ resid 393 through 398 or (resid 399 through 401 and (name N or name CA or name C \ or name O or name CB )) or resid 402 through 408 or (resid 409 and (name N or n \ ame CA or name C or name O or name CB )) or resid 410 through 418 or (resid 419 \ and (name N or name CA or name C or name O or name CB )) or resid 420 or (resid \ 421 and (name N or name CA or name C or name O or name CB )) or resid 422 throug \ h 426 or (resid 427 and (name N or name CA or name C or name O or name CB )) or \ resid 428 or (resid 429 and (name N or name CA or name C or name O or name CB )) \ or resid 430 through 444 or (resid 445 and (name N or name CA or name C or name \ O or name CB )) or resid 446 through 447 or (resid 448 and (name N or name CA o \ r name C or name O or name CB )) or resid 449 through 453 or (resid 454 and (nam \ e N or name CA or name C or name O or name CB )) or resid 455 through 461 or (re \ sid 462 through 463 and (name N or name CA or name C or name O or name CB )) or \ resid 464 through 469 or (resid 470 and (name N or name CA or name C or name O o \ r name CB )) or resid 471 or (resid 472 and (name N or name CA or name C or name \ O or name CB )) or resid 473 through 476 or (resid 477 and (name N or name CA o \ r name C or name O or name CB )) or resid 478 through 480 or (resid 481 and (nam \ e N or name CA or name C or name O or name CB )) or resid 482 through 484 or (re \ sid 485 through 490 and (name N or name CA or name C or name O or name CB )) or \ resid 491 through 493 or (resid 494 and (name N or name CA or name C or name O o \ r name CB )) or resid 495 or (resid 496 through 498 and (name N or name CA or na \ me C or name O or name CB )) or resid 499 through 500 or (resid 501 and (name N \ or name CA or name C or name O or name CB )) or resid 502 through 504 or (resid \ 505 and (name N or name CA or name C or name O or name CB )) or resid 506 or (re \ sid 507 through 508 and (name N or name CA or name C or name O or name CB )) or \ resid 509 or (resid 510 through 513 and (name N or name CA or name C or name O o \ r name CB )) or resid 514 through 518 or (resid 519 and (name N or name CA or na \ me C or name O or name CB )) or resid 520 or (resid 521 through 526 and (name N \ or name CA or name C or name O or name CB )) or resid 527 or (resid 528 through \ 530 and (name N or name CA or name C or name O or name CB )) or resid 531 or (re \ sid 532 through 534 and (name N or name CA or name C or name O or name CB )) or \ resid 535 or (resid 536 through 537 and (name N or name CA or name C or name O o \ r name CB )) or resid 538 or (resid 539 through 540 and (name N or name CA or na \ me C or name O or name CB )) or resid 541 through 542 or (resid 543 and (name N \ or name CA or name C or name O or name CB )) or resid 544)) } 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=0.39 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.400 Find NCS groups from input model: 0.300 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 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 0.085 12348 Z= 0.334 Angle : 0.742 10.299 16871 Z= 0.463 Chirality : 0.050 0.396 2087 Planarity : 0.004 0.044 2121 Dihedral : 13.025 87.974 4198 Min Nonbonded Distance : 1.431 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.10 % Favored : 92.59 % Rotamer: Outliers : 0.55 % Allowed : 0.31 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.47 (0.20), residues: 1662 helix: -0.08 (0.28), residues: 361 sheet: -0.44 (0.28), residues: 324 loop : -1.56 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 507 TYR 0.012 0.001 TYR C 33 PHE 0.009 0.001 PHE B 237 TRP 0.020 0.002 TRP F 537 HIS 0.002 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00505 (12323) covalent geometry : angle 0.74076 (16821) SS BOND : bond 0.00618 ( 25) SS BOND : angle 1.02803 ( 50) hydrogen bonds : bond 0.18992 ( 470) hydrogen bonds : angle 6.42750 ( 1209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 245 THR cc_start: 0.7891 (OUTLIER) cc_final: 0.7584 (t) REVERT: E 82 GLU cc_start: 0.8365 (tt0) cc_final: 0.7738 (tt0) REVERT: G 90 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8174 (tp40) outliers start: 7 outliers final: 2 residues processed: 107 average time/residue: 0.0997 time to fit residues: 16.2495 Evaluate side-chains 80 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.082393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.062207 restraints weight = 68638.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.063851 restraints weight = 39900.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.064266 restraints weight = 26457.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.065033 restraints weight = 23154.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.064975 restraints weight = 20711.338| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12348 Z= 0.125 Angle : 0.550 7.244 16871 Z= 0.297 Chirality : 0.043 0.211 2087 Planarity : 0.004 0.065 2121 Dihedral : 4.537 22.993 1766 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.38 % Favored : 93.50 % Rotamer: Outliers : 0.24 % Allowed : 4.72 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.26 (0.20), residues: 1662 helix: 0.08 (0.28), residues: 376 sheet: -0.28 (0.28), residues: 331 loop : -1.45 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 507 TYR 0.014 0.001 TYR B 468 PHE 0.009 0.001 PHE B 351 TRP 0.013 0.001 TRP D 314 HIS 0.003 0.001 HIS F 159 Details of bonding type rmsd covalent geometry : bond 0.00278 (12323) covalent geometry : angle 0.54784 (16821) SS BOND : bond 0.00266 ( 25) SS BOND : angle 0.95985 ( 50) hydrogen bonds : bond 0.03569 ( 470) hydrogen bonds : angle 4.97773 ( 1209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 537 TRP cc_start: 0.7715 (p90) cc_final: 0.7474 (p90) REVERT: E 88 ASN cc_start: 0.9081 (m110) cc_final: 0.8731 (m110) REVERT: F 251 MET cc_start: 0.8389 (mtt) cc_final: 0.8153 (mtt) REVERT: H 33 ASP cc_start: 0.8076 (t0) cc_final: 0.7649 (m-30) outliers start: 3 outliers final: 1 residues processed: 105 average time/residue: 0.1043 time to fit residues: 16.7671 Evaluate side-chains 85 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 83 optimal weight: 0.0970 chunk 122 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 146 optimal weight: 0.0270 chunk 149 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 82 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 26 optimal weight: 0.0270 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN F 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.085014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.065052 restraints weight = 58138.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.067188 restraints weight = 34887.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.068174 restraints weight = 21633.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.068112 restraints weight = 18046.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.068398 restraints weight = 16889.596| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12348 Z= 0.088 Angle : 0.511 7.525 16871 Z= 0.269 Chirality : 0.042 0.172 2087 Planarity : 0.003 0.043 2121 Dihedral : 4.160 22.977 1766 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.42 % Favored : 94.52 % Rotamer: Outliers : 0.16 % Allowed : 3.31 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.88 (0.21), residues: 1662 helix: 0.57 (0.29), residues: 358 sheet: -0.03 (0.28), residues: 334 loop : -1.27 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 507 TYR 0.011 0.001 TYR B 468 PHE 0.009 0.001 PHE C 32 TRP 0.012 0.001 TRP F 537 HIS 0.003 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00186 (12323) covalent geometry : angle 0.50915 (16821) SS BOND : bond 0.00284 ( 25) SS BOND : angle 0.89052 ( 50) hydrogen bonds : bond 0.02769 ( 470) hydrogen bonds : angle 4.58589 ( 1209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 271 LYS cc_start: 0.8649 (mmtt) cc_final: 0.7855 (mmmt) REVERT: D 519 TYR cc_start: 0.8139 (p90) cc_final: 0.7922 (p90) REVERT: E 81 GLN cc_start: 0.8827 (mp10) cc_final: 0.8364 (mp10) REVERT: E 84 ASP cc_start: 0.8673 (t0) cc_final: 0.8426 (t0) REVERT: E 88 ASN cc_start: 0.9080 (m110) cc_final: 0.8716 (m110) REVERT: H 33 ASP cc_start: 0.7992 (t0) cc_final: 0.7562 (m-30) outliers start: 2 outliers final: 0 residues processed: 114 average time/residue: 0.1071 time to fit residues: 18.3526 Evaluate side-chains 85 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 58 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 88 optimal weight: 0.0270 chunk 11 optimal weight: 0.5980 chunk 142 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 114 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 157 optimal weight: 0.0040 overall best weight: 0.3652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** F 383 ASN ** 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 = 0.3473 r_free = 0.3473 target = 0.085117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.066014 restraints weight = 44352.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.067817 restraints weight = 27381.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.069295 restraints weight = 18861.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.068779 restraints weight = 16043.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.069053 restraints weight = 15223.868| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12348 Z= 0.084 Angle : 0.493 6.893 16871 Z= 0.258 Chirality : 0.041 0.163 2087 Planarity : 0.003 0.040 2121 Dihedral : 3.963 22.358 1766 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.06 % Favored : 94.88 % Rotamer: Outliers : 0.08 % Allowed : 2.05 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.67 (0.21), residues: 1662 helix: 0.70 (0.29), residues: 358 sheet: 0.25 (0.29), residues: 328 loop : -1.17 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 507 TYR 0.009 0.001 TYR B 468 PHE 0.007 0.001 PHE C 32 TRP 0.013 0.001 TRP F 537 HIS 0.002 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00185 (12323) covalent geometry : angle 0.49104 (16821) SS BOND : bond 0.00224 ( 25) SS BOND : angle 0.94471 ( 50) hydrogen bonds : bond 0.02563 ( 470) hydrogen bonds : angle 4.38846 ( 1209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 289 MET cc_start: 0.7318 (tmm) cc_final: 0.6995 (tmm) REVERT: D 519 TYR cc_start: 0.8289 (p90) cc_final: 0.8020 (p90) REVERT: E 81 GLN cc_start: 0.8817 (mp10) cc_final: 0.8364 (mp10) REVERT: E 88 ASN cc_start: 0.9102 (m110) cc_final: 0.8711 (m110) REVERT: H 33 ASP cc_start: 0.8013 (t0) cc_final: 0.7596 (m-30) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1012 time to fit residues: 17.5012 Evaluate side-chains 83 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 42 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 26 optimal weight: 0.1980 chunk 38 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 240 ASN ** F 361 GLN ** 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 = 0.3461 r_free = 0.3461 target = 0.084448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.064471 restraints weight = 72859.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.066023 restraints weight = 42772.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.066763 restraints weight = 27096.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.066947 restraints weight = 22195.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.067110 restraints weight = 20442.051| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12348 Z= 0.089 Angle : 0.504 8.743 16871 Z= 0.261 Chirality : 0.041 0.162 2087 Planarity : 0.003 0.065 2121 Dihedral : 3.888 22.101 1766 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.36 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.58 (0.21), residues: 1662 helix: 1.00 (0.29), residues: 349 sheet: 0.28 (0.28), residues: 358 loop : -1.22 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 507 TYR 0.009 0.001 TYR B 468 PHE 0.007 0.001 PHE C 32 TRP 0.013 0.001 TRP F 537 HIS 0.002 0.000 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00201 (12323) covalent geometry : angle 0.50320 (16821) SS BOND : bond 0.00226 ( 25) SS BOND : angle 0.81827 ( 50) hydrogen bonds : bond 0.02635 ( 470) hydrogen bonds : angle 4.35383 ( 1209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 519 TYR cc_start: 0.8144 (p90) cc_final: 0.7915 (p90) REVERT: E 88 ASN cc_start: 0.9141 (m110) cc_final: 0.8705 (m-40) REVERT: H 33 ASP cc_start: 0.8025 (t0) cc_final: 0.7575 (m-30) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0933 time to fit residues: 14.7752 Evaluate side-chains 77 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 147 optimal weight: 20.0000 chunk 98 optimal weight: 50.0000 chunk 14 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 240 ASN D 270 GLN F 270 GLN ** F 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.081491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.062088 restraints weight = 45429.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.063905 restraints weight = 28490.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.064748 restraints weight = 19825.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.064464 restraints weight = 18031.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.064616 restraints weight = 16673.280| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12348 Z= 0.140 Angle : 0.541 7.126 16871 Z= 0.287 Chirality : 0.042 0.174 2087 Planarity : 0.004 0.051 2121 Dihedral : 4.202 21.242 1766 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.26 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.77 (0.21), residues: 1662 helix: 0.69 (0.29), residues: 370 sheet: 0.14 (0.28), residues: 366 loop : -1.33 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 507 TYR 0.013 0.001 TYR B 468 PHE 0.011 0.001 PHE F 223 TRP 0.016 0.001 TRP F 537 HIS 0.002 0.001 HIS F 159 Details of bonding type rmsd covalent geometry : bond 0.00319 (12323) covalent geometry : angle 0.53869 (16821) SS BOND : bond 0.00327 ( 25) SS BOND : angle 0.97773 ( 50) hydrogen bonds : bond 0.03292 ( 470) hydrogen bonds : angle 4.59154 ( 1209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 289 MET cc_start: 0.7555 (tmm) cc_final: 0.7215 (tmm) REVERT: D 519 TYR cc_start: 0.8146 (p90) cc_final: 0.7890 (p90) REVERT: E 88 ASN cc_start: 0.9110 (m110) cc_final: 0.8713 (m110) REVERT: H 33 ASP cc_start: 0.8229 (t0) cc_final: 0.7659 (m-30) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0862 time to fit residues: 12.5942 Evaluate side-chains 78 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 140 optimal weight: 30.0000 chunk 133 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN D 240 ASN ** F 361 GLN ** 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 = 0.3372 r_free = 0.3372 target = 0.079773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.059662 restraints weight = 53246.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.062279 restraints weight = 31895.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.062522 restraints weight = 19692.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.062642 restraints weight = 19273.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.062825 restraints weight = 17046.347| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12348 Z= 0.181 Angle : 0.581 9.807 16871 Z= 0.310 Chirality : 0.043 0.178 2087 Planarity : 0.004 0.045 2121 Dihedral : 4.556 21.936 1766 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.10 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.92 (0.21), residues: 1662 helix: 0.42 (0.28), residues: 377 sheet: 0.10 (0.29), residues: 334 loop : -1.34 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 507 TYR 0.014 0.001 TYR B 468 PHE 0.013 0.001 PHE B 366 TRP 0.012 0.001 TRP D 314 HIS 0.002 0.001 HIS F 159 Details of bonding type rmsd covalent geometry : bond 0.00413 (12323) covalent geometry : angle 0.57768 (16821) SS BOND : bond 0.00380 ( 25) SS BOND : angle 1.21098 ( 50) hydrogen bonds : bond 0.03602 ( 470) hydrogen bonds : angle 4.80006 ( 1209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 289 MET cc_start: 0.7621 (tmm) cc_final: 0.7229 (tmm) REVERT: D 519 TYR cc_start: 0.8139 (p90) cc_final: 0.7882 (p90) REVERT: E 81 GLN cc_start: 0.8925 (mp10) cc_final: 0.8655 (mp10) REVERT: E 87 LYS cc_start: 0.9410 (mtmm) cc_final: 0.8875 (mtmm) REVERT: E 88 ASN cc_start: 0.9099 (m110) cc_final: 0.8680 (m110) REVERT: G 2 ILE cc_start: 0.8480 (tp) cc_final: 0.8158 (tt) REVERT: H 33 ASP cc_start: 0.8249 (t0) cc_final: 0.7666 (m-30) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.0944 time to fit residues: 12.8272 Evaluate side-chains 72 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 148 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN C 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.079856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.060741 restraints weight = 59812.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.061449 restraints weight = 37014.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.062045 restraints weight = 26631.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.063014 restraints weight = 22299.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.062931 restraints weight = 20015.397| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12348 Z= 0.162 Angle : 0.570 10.377 16871 Z= 0.303 Chirality : 0.043 0.184 2087 Planarity : 0.004 0.042 2121 Dihedral : 4.525 22.350 1766 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.16 % Favored : 92.72 % Rotamer: Outliers : 0.08 % Allowed : 1.81 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.95 (0.21), residues: 1662 helix: 0.47 (0.28), residues: 377 sheet: 0.00 (0.29), residues: 337 loop : -1.36 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 507 TYR 0.013 0.001 TYR B 468 PHE 0.012 0.001 PHE B 366 TRP 0.011 0.001 TRP D 314 HIS 0.003 0.001 HIS F 159 Details of bonding type rmsd covalent geometry : bond 0.00372 (12323) covalent geometry : angle 0.56826 (16821) SS BOND : bond 0.00343 ( 25) SS BOND : angle 0.99162 ( 50) hydrogen bonds : bond 0.03406 ( 470) hydrogen bonds : angle 4.79072 ( 1209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 289 MET cc_start: 0.7554 (tmm) cc_final: 0.7266 (tmm) REVERT: E 88 ASN cc_start: 0.9078 (m110) cc_final: 0.8665 (m110) REVERT: G 2 ILE cc_start: 0.8436 (tp) cc_final: 0.8212 (tt) REVERT: H 33 ASP cc_start: 0.8279 (t0) cc_final: 0.7627 (m-30) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1083 time to fit residues: 15.1311 Evaluate side-chains 75 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 86 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 4 optimal weight: 40.0000 chunk 41 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 143 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN D 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.081293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.061356 restraints weight = 68741.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.062623 restraints weight = 40468.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.063560 restraints weight = 26904.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.063815 restraints weight = 21991.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.063902 restraints weight = 20098.251| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12348 Z= 0.102 Angle : 0.549 11.335 16871 Z= 0.285 Chirality : 0.042 0.186 2087 Planarity : 0.003 0.043 2121 Dihedral : 4.329 28.417 1766 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.78 % Favored : 94.10 % Rotamer: Outliers : 0.08 % Allowed : 0.24 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.77 (0.21), residues: 1662 helix: 0.60 (0.29), residues: 380 sheet: 0.18 (0.29), residues: 331 loop : -1.27 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 507 TYR 0.018 0.001 TYR F 198 PHE 0.010 0.001 PHE B 237 TRP 0.011 0.001 TRP F 537 HIS 0.002 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00231 (12323) covalent geometry : angle 0.54767 (16821) SS BOND : bond 0.00258 ( 25) SS BOND : angle 0.91112 ( 50) hydrogen bonds : bond 0.02795 ( 470) hydrogen bonds : angle 4.59655 ( 1209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 LEU cc_start: 0.9367 (mm) cc_final: 0.8952 (tt) REVERT: D 289 MET cc_start: 0.7329 (tmm) cc_final: 0.7113 (tmm) REVERT: D 519 TYR cc_start: 0.8019 (p90) cc_final: 0.7749 (p90) REVERT: E 88 ASN cc_start: 0.9049 (m110) cc_final: 0.8680 (m110) REVERT: H 33 ASP cc_start: 0.8322 (t0) cc_final: 0.7641 (m-30) outliers start: 1 outliers final: 1 residues processed: 96 average time/residue: 0.0979 time to fit residues: 14.0351 Evaluate side-chains 80 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 4 optimal weight: 40.0000 chunk 57 optimal weight: 0.6980 chunk 128 optimal weight: 0.5980 chunk 82 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 0.2980 chunk 106 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 139 optimal weight: 30.0000 chunk 130 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN D 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.081568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.061667 restraints weight = 68974.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.063181 restraints weight = 40537.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.063821 restraints weight = 26326.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.064349 restraints weight = 22904.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.064451 restraints weight = 20703.540| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12348 Z= 0.104 Angle : 0.546 10.310 16871 Z= 0.283 Chirality : 0.042 0.184 2087 Planarity : 0.003 0.045 2121 Dihedral : 4.187 24.516 1766 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.72 % Favored : 94.16 % Rotamer: Outliers : 0.08 % Allowed : 0.39 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.58 (0.21), residues: 1662 helix: 1.11 (0.29), residues: 353 sheet: 0.24 (0.28), residues: 367 loop : -1.27 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 507 TYR 0.012 0.001 TYR F 198 PHE 0.007 0.001 PHE E 32 TRP 0.012 0.001 TRP F 537 HIS 0.002 0.001 HIS F 159 Details of bonding type rmsd covalent geometry : bond 0.00237 (12323) covalent geometry : angle 0.54489 (16821) SS BOND : bond 0.00243 ( 25) SS BOND : angle 0.85613 ( 50) hydrogen bonds : bond 0.02827 ( 470) hydrogen bonds : angle 4.52490 ( 1209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 289 MET cc_start: 0.7335 (tmm) cc_final: 0.7105 (tmm) REVERT: D 519 TYR cc_start: 0.8105 (p90) cc_final: 0.7834 (p90) REVERT: E 88 ASN cc_start: 0.9062 (m110) cc_final: 0.8657 (m110) REVERT: H 33 ASP cc_start: 0.8358 (t0) cc_final: 0.7668 (m-30) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.0950 time to fit residues: 13.7149 Evaluate side-chains 79 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 0.9990 chunk 152 optimal weight: 0.4980 chunk 126 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 150 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 124 optimal weight: 0.0270 chunk 62 optimal weight: 6.9990 overall best weight: 1.4842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN D 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.080903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.061373 restraints weight = 51497.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.063232 restraints weight = 31153.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.064162 restraints weight = 20664.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.064062 restraints weight = 18236.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.064132 restraints weight = 16638.256| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12348 Z= 0.118 Angle : 0.551 9.876 16871 Z= 0.289 Chirality : 0.042 0.201 2087 Planarity : 0.003 0.045 2121 Dihedral : 4.247 29.720 1766 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.08 % Favored : 93.80 % Rotamer: Outliers : 0.08 % Allowed : 0.39 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.59 (0.21), residues: 1662 helix: 1.11 (0.29), residues: 353 sheet: 0.21 (0.28), residues: 367 loop : -1.28 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 507 TYR 0.015 0.001 TYR F 198 PHE 0.008 0.001 PHE B 366 TRP 0.012 0.001 TRP F 537 HIS 0.002 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00272 (12323) covalent geometry : angle 0.55000 (16821) SS BOND : bond 0.00268 ( 25) SS BOND : angle 0.87828 ( 50) hydrogen bonds : bond 0.02901 ( 470) hydrogen bonds : angle 4.54545 ( 1209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1796.64 seconds wall clock time: 31 minutes 55.98 seconds (1915.98 seconds total)