Starting phenix.real_space_refine on Sat Dec 9 15:25:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc0_8794/12_2023/5wc0_8794_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc0_8794/12_2023/5wc0_8794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc0_8794/12_2023/5wc0_8794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc0_8794/12_2023/5wc0_8794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc0_8794/12_2023/5wc0_8794_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc0_8794/12_2023/5wc0_8794_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 42 5.16 5 C 7182 2.51 5 N 1990 2.21 5 O 2228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11460 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1865 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 260 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 168 Chain: "B" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1888 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 12, 'TRANS': 264} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 356 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 155 Chain: "C" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1875 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 12, 'TRANS': 264} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 305 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 168 Chain: "D" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1882 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 12, 'TRANS': 264} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 161 Chain: "E" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1882 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 12, 'TRANS': 264} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 161 Chain: "F" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1882 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 12, 'TRANS': 264} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 161 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.19, per 1000 atoms: 0.54 Number of scatterers: 11460 At special positions: 0 Unit cell: (129.69, 138.86, 103.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 18 15.00 O 2228 8.00 N 1990 7.00 C 7182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.87 Conformation dependent library (CDL) restraints added in 2.4 seconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3152 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 9 sheets defined 45.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 211 through 214 No H-bonds generated for 'chain 'A' and resid 211 through 214' Processing helix chain 'A' and resid 239 through 249 removed outlier: 4.179A pdb=" N ALA A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ARG A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 284 removed outlier: 3.561A pdb=" N GLU A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 4.013A pdb=" N LEU A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 364 through 374 Processing helix chain 'A' and resid 386 through 393 removed outlier: 3.821A pdb=" N ARG A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 414 removed outlier: 3.778A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 440 through 449 removed outlier: 3.696A pdb=" N ALA A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.583A pdb=" N GLU A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 239 through 249 removed outlier: 4.251A pdb=" N ALA B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ARG B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 284 removed outlier: 3.617A pdb=" N LEU B 276 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE B 278 " --> pdb=" O ARG B 275 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 279 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 282 " --> pdb=" O GLU B 279 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 283 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 4.097A pdb=" N LEU B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 344 No H-bonds generated for 'chain 'B' and resid 342 through 344' Processing helix chain 'B' and resid 349 through 352 No H-bonds generated for 'chain 'B' and resid 349 through 352' Processing helix chain 'B' and resid 364 through 374 Processing helix chain 'B' and resid 386 through 393 removed outlier: 3.729A pdb=" N THR B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 415 removed outlier: 3.618A pdb=" N ILE B 410 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 431 No H-bonds generated for 'chain 'B' and resid 428 through 431' Processing helix chain 'B' and resid 441 through 448 removed outlier: 4.069A pdb=" N ALA B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ALA B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'C' and resid 174 through 181 removed outlier: 3.777A pdb=" N ALA C 177 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 207 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 272 through 284 removed outlier: 3.767A pdb=" N GLU C 279 " --> pdb=" O ARG C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.581A pdb=" N LEU C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 344 No H-bonds generated for 'chain 'C' and resid 342 through 344' Processing helix chain 'C' and resid 348 through 352 removed outlier: 3.650A pdb=" N ARG C 352 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 374 removed outlier: 3.573A pdb=" N LYS C 368 " --> pdb=" O ILE C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 392 removed outlier: 3.800A pdb=" N ARG C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 414 removed outlier: 4.264A pdb=" N VAL C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU C 413 " --> pdb=" O ALA C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 431 No H-bonds generated for 'chain 'C' and resid 428 through 431' Processing helix chain 'C' and resid 440 through 448 removed outlier: 4.133A pdb=" N ALA C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 465 Processing helix chain 'D' and resid 175 through 181 Processing helix chain 'D' and resid 199 through 207 Processing helix chain 'D' and resid 210 through 214 Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 239 through 249 removed outlier: 4.509A pdb=" N ALA D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA D 245 " --> pdb=" O LEU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 283 removed outlier: 3.658A pdb=" N LEU D 276 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE D 278 " --> pdb=" O ARG D 275 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU D 279 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG D 282 " --> pdb=" O GLU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 4.200A pdb=" N LEU D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL D 319 " --> pdb=" O SER D 315 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 344 No H-bonds generated for 'chain 'D' and resid 342 through 344' Processing helix chain 'D' and resid 349 through 352 No H-bonds generated for 'chain 'D' and resid 349 through 352' Processing helix chain 'D' and resid 364 through 374 Processing helix chain 'D' and resid 386 through 393 removed outlier: 3.936A pdb=" N ARG D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 414 removed outlier: 4.197A pdb=" N LEU D 413 " --> pdb=" O ALA D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 434 removed outlier: 4.843A pdb=" N LYS D 434 " --> pdb=" O MET D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 449 removed outlier: 4.064A pdb=" N ALA D 446 " --> pdb=" O ASP D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 467 removed outlier: 4.083A pdb=" N ASP D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 199 through 208 Processing helix chain 'E' and resid 210 through 214 Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 240 through 249 removed outlier: 3.595A pdb=" N ALA E 243 " --> pdb=" O THR E 240 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG E 244 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA E 247 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 284 removed outlier: 3.673A pdb=" N LEU E 276 " --> pdb=" O ILE E 273 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE E 278 " --> pdb=" O ARG E 275 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU E 279 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG E 282 " --> pdb=" O GLU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 321 removed outlier: 4.610A pdb=" N LEU E 318 " --> pdb=" O LYS E 314 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL E 319 " --> pdb=" O SER E 315 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 344 No H-bonds generated for 'chain 'E' and resid 342 through 344' Processing helix chain 'E' and resid 349 through 352 No H-bonds generated for 'chain 'E' and resid 349 through 352' Processing helix chain 'E' and resid 364 through 374 Processing helix chain 'E' and resid 386 through 390 Processing helix chain 'E' and resid 398 through 415 removed outlier: 3.685A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU E 413 " --> pdb=" O ALA E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 431 No H-bonds generated for 'chain 'E' and resid 428 through 431' Processing helix chain 'E' and resid 440 through 449 removed outlier: 3.940A pdb=" N ALA E 445 " --> pdb=" O ILE E 441 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA E 446 " --> pdb=" O ASP E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 Processing helix chain 'F' and resid 175 through 181 removed outlier: 3.754A pdb=" N GLY F 180 " --> pdb=" O ALA F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 207 Processing helix chain 'F' and resid 211 through 214 No H-bonds generated for 'chain 'F' and resid 211 through 214' Processing helix chain 'F' and resid 221 through 223 No H-bonds generated for 'chain 'F' and resid 221 through 223' Processing helix chain 'F' and resid 242 through 249 Processing helix chain 'F' and resid 271 through 284 removed outlier: 3.583A pdb=" N LEU F 276 " --> pdb=" O ILE F 273 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE F 278 " --> pdb=" O ARG F 275 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG F 282 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.758A pdb=" N LEU F 318 " --> pdb=" O LYS F 314 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL F 319 " --> pdb=" O SER F 315 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN F 320 " --> pdb=" O GLU F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 344 No H-bonds generated for 'chain 'F' and resid 342 through 344' Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 364 through 374 Processing helix chain 'F' and resid 386 through 390 Processing helix chain 'F' and resid 398 through 415 removed outlier: 4.093A pdb=" N LEU F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 431 No H-bonds generated for 'chain 'F' and resid 428 through 431' Processing helix chain 'F' and resid 440 through 449 removed outlier: 4.187A pdb=" N ALA F 445 " --> pdb=" O ILE F 441 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA F 446 " --> pdb=" O ASP F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 465 Processing sheet with id= A, first strand: chain 'A' and resid 253 through 255 removed outlier: 3.748A pdb=" N PHE A 255 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 229 through 233 removed outlier: 6.499A pdb=" N LYS B 355 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ALA B 232 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE B 357 " --> pdb=" O ALA B 232 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 288 through 290 removed outlier: 7.252A pdb=" N PHE B 334 " --> pdb=" O ILE B 289 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'C' and resid 229 through 232 removed outlier: 6.541A pdb=" N LYS C 355 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ALA C 232 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE C 357 " --> pdb=" O ALA C 232 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 287 through 292 removed outlier: 3.647A pdb=" N ALA C 338 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 229 through 232 removed outlier: 6.775A pdb=" N LYS D 355 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ALA D 232 " --> pdb=" O LYS D 355 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE D 357 " --> pdb=" O ALA D 232 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 253 through 257 Processing sheet with id= H, first strand: chain 'E' and resid 288 through 290 removed outlier: 7.212A pdb=" N PHE E 334 " --> pdb=" O ILE E 289 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'F' and resid 253 through 255 removed outlier: 3.787A pdb=" N PHE F 290 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE F 334 " --> pdb=" O SER F 287 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 951 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 5.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3880 1.34 - 1.46: 2354 1.46 - 1.58: 5303 1.58 - 1.69: 30 1.69 - 1.81: 66 Bond restraints: 11633 Sorted by residual: bond pdb=" C4 ATP F 501 " pdb=" C5 ATP F 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.47e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.04e+01 bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.96e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.82e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.81e+01 ... (remaining 11628 not shown) Histogram of bond angle deviations from ideal: 87.77 - 97.52: 3 97.52 - 107.27: 434 107.27 - 117.02: 7877 117.02 - 126.77: 7510 126.77 - 136.53: 121 Bond angle restraints: 15945 Sorted by residual: angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 116.83 23.04 1.00e+00 1.00e+00 5.31e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 115.67 21.16 1.00e+00 1.00e+00 4.48e+02 angle pdb=" PB ATP F 501 " pdb=" O3B ATP F 501 " pdb=" PG ATP F 501 " ideal model delta sigma weight residual 139.87 119.17 20.70 1.00e+00 1.00e+00 4.28e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 119.35 20.52 1.00e+00 1.00e+00 4.21e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.05 19.82 1.00e+00 1.00e+00 3.93e+02 ... (remaining 15940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6744 17.83 - 35.65: 229 35.65 - 53.48: 50 53.48 - 71.30: 14 71.30 - 89.13: 9 Dihedral angle restraints: 7046 sinusoidal: 2242 harmonic: 4804 Sorted by residual: dihedral pdb=" CA ASP E 363 " pdb=" C ASP E 363 " pdb=" N ILE E 364 " pdb=" CA ILE E 364 " ideal model delta harmonic sigma weight residual 180.00 -150.88 -29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA PRO D 360 " pdb=" C PRO D 360 " pdb=" N LEU D 361 " pdb=" CA LEU D 361 " ideal model delta harmonic sigma weight residual 180.00 151.41 28.59 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ASP F 363 " pdb=" C ASP F 363 " pdb=" N ILE F 364 " pdb=" CA ILE F 364 " ideal model delta harmonic sigma weight residual -180.00 -152.07 -27.93 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 7043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1792 0.077 - 0.154: 159 0.154 - 0.230: 6 0.230 - 0.307: 7 0.307 - 0.384: 2 Chirality restraints: 1966 Sorted by residual: chirality pdb=" CA LEU D 345 " pdb=" N LEU D 345 " pdb=" C LEU D 345 " pdb=" CB LEU D 345 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA ARG C 422 " pdb=" N ARG C 422 " pdb=" C ARG C 422 " pdb=" CB ARG C 422 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA LEU B 345 " pdb=" N LEU B 345 " pdb=" C LEU B 345 " pdb=" CB LEU B 345 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 1963 not shown) Planarity restraints: 2061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP D 343 " -0.013 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C TRP D 343 " 0.048 2.00e-02 2.50e+03 pdb=" O TRP D 343 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU D 344 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 359 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO F 360 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO F 360 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 360 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 343 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C TRP B 343 " -0.047 2.00e-02 2.50e+03 pdb=" O TRP B 343 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU B 344 " 0.016 2.00e-02 2.50e+03 ... (remaining 2058 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 183 2.61 - 3.19: 11541 3.19 - 3.76: 17233 3.76 - 4.33: 24018 4.33 - 4.90: 35712 Nonbonded interactions: 88687 Sorted by model distance: nonbonded pdb=" OG SER B 252 " pdb=" O PRO B 286 " model vdw 2.043 2.440 nonbonded pdb=" OG SER A 252 " pdb=" O PRO A 286 " model vdw 2.044 2.440 nonbonded pdb=" OG SER C 451 " pdb=" O ASP D 467 " model vdw 2.068 2.440 nonbonded pdb=" O ASP B 417 " pdb=" OG SER B 420 " model vdw 2.070 2.440 nonbonded pdb=" O ALA A 390 " pdb=" OG1 THR A 393 " model vdw 2.081 2.440 ... (remaining 88682 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 173 through 282 or (resid 283 through 285 and (name N or n \ ame CA or name C or name O or name CB )) or resid 286 through 470 or resid 501)) \ selection = (chain 'C' and (resid 173 through 470 or resid 501)) selection = (chain 'D' and (resid 173 through 283 or (resid 284 through 285 and (name N or n \ ame CA or name C or name O or name CB )) or resid 286 through 470 or resid 501)) \ selection = (chain 'E' and (resid 173 through 283 or (resid 284 through 285 and (name N or n \ ame CA or name C or name O or name CB )) or resid 286 through 470 or resid 501)) \ selection = (chain 'F' and (resid 173 through 283 or (resid 284 through 285 and (name N or n \ ame CA or name C or name O or name CB )) or resid 286 through 470 or resid 501)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.130 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 32.770 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.006 0.080 11633 Z= 0.382 Angle : 1.062 23.038 15945 Z= 0.790 Chirality : 0.047 0.384 1966 Planarity : 0.005 0.069 2061 Dihedral : 11.481 89.128 3894 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.88 % Favored : 91.87 % Rotamer: Outliers : 0.11 % Allowed : 0.96 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.17), residues: 1612 helix: -3.33 (0.12), residues: 823 sheet: -3.02 (0.32), residues: 168 loop : -2.68 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 465 HIS 0.004 0.001 HIS A 206 PHE 0.016 0.002 PHE F 334 TYR 0.012 0.002 TYR E 284 ARG 0.016 0.001 ARG D 351 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.2599 time to fit residues: 84.4131 Evaluate side-chains 130 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.393 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 82 optimal weight: 0.2980 chunk 65 optimal weight: 0.7980 chunk 126 optimal weight: 8.9990 chunk 49 optimal weight: 0.0070 chunk 77 optimal weight: 0.2980 chunk 94 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11633 Z= 0.166 Angle : 0.551 6.383 15945 Z= 0.300 Chirality : 0.042 0.163 1966 Planarity : 0.005 0.053 2061 Dihedral : 12.283 88.583 1928 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.11 % Allowed : 1.17 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.19), residues: 1612 helix: -2.10 (0.15), residues: 844 sheet: -2.05 (0.34), residues: 170 loop : -1.92 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 465 HIS 0.004 0.001 HIS F 206 PHE 0.018 0.001 PHE F 317 TYR 0.011 0.001 TYR F 416 ARG 0.014 0.001 ARG E 392 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.2483 time to fit residues: 65.2070 Evaluate side-chains 119 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.326 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 122 optimal weight: 0.0170 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 159 optimal weight: 0.4980 chunk 131 optimal weight: 7.9990 chunk 146 optimal weight: 0.4980 chunk 50 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11633 Z= 0.162 Angle : 0.509 6.590 15945 Z= 0.274 Chirality : 0.040 0.131 1966 Planarity : 0.004 0.047 2061 Dihedral : 11.491 88.501 1928 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.21 % Allowed : 1.91 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.20), residues: 1612 helix: -1.28 (0.17), residues: 837 sheet: -1.57 (0.35), residues: 178 loop : -1.32 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 226 HIS 0.004 0.002 HIS A 206 PHE 0.023 0.001 PHE E 219 TYR 0.015 0.001 TYR F 284 ARG 0.008 0.000 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.2130 time to fit residues: 57.1430 Evaluate side-chains 117 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.382 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 0.0030 chunk 16 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 147 optimal weight: 0.4980 chunk 156 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11633 Z= 0.220 Angle : 0.552 8.928 15945 Z= 0.291 Chirality : 0.040 0.131 1966 Planarity : 0.004 0.047 2061 Dihedral : 11.215 86.176 1928 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.11 % Allowed : 1.59 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.21), residues: 1612 helix: -0.65 (0.18), residues: 795 sheet: -1.05 (0.37), residues: 178 loop : -0.79 (0.27), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 465 HIS 0.004 0.002 HIS A 206 PHE 0.013 0.001 PHE D 219 TYR 0.025 0.001 TYR F 386 ARG 0.004 0.001 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.2062 time to fit residues: 50.0929 Evaluate side-chains 113 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 1.9990 chunk 88 optimal weight: 0.0050 chunk 2 optimal weight: 0.9980 chunk 116 optimal weight: 0.0170 chunk 64 optimal weight: 2.9990 chunk 133 optimal weight: 0.0870 chunk 108 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 overall best weight: 0.6212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11633 Z= 0.151 Angle : 0.494 9.144 15945 Z= 0.260 Chirality : 0.040 0.139 1966 Planarity : 0.004 0.048 2061 Dihedral : 10.650 84.825 1928 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.22), residues: 1612 helix: -0.15 (0.19), residues: 787 sheet: -0.68 (0.38), residues: 181 loop : -0.28 (0.28), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 465 HIS 0.002 0.001 HIS B 206 PHE 0.008 0.001 PHE D 278 TYR 0.008 0.001 TYR C 386 ARG 0.003 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2121 time to fit residues: 48.4725 Evaluate side-chains 113 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 8.9990 chunk 141 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11633 Z= 0.219 Angle : 0.533 10.140 15945 Z= 0.282 Chirality : 0.040 0.131 1966 Planarity : 0.004 0.044 2061 Dihedral : 10.489 87.501 1928 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1612 helix: -0.27 (0.19), residues: 822 sheet: -0.53 (0.38), residues: 181 loop : -0.44 (0.29), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 465 HIS 0.005 0.002 HIS A 206 PHE 0.011 0.001 PHE D 278 TYR 0.008 0.001 TYR C 386 ARG 0.005 0.000 ARG D 352 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2267 time to fit residues: 49.4786 Evaluate side-chains 110 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.407 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 89 optimal weight: 0.1980 chunk 114 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 131 optimal weight: 0.0570 chunk 87 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11633 Z= 0.158 Angle : 0.488 10.870 15945 Z= 0.255 Chirality : 0.039 0.152 1966 Planarity : 0.003 0.044 2061 Dihedral : 10.189 88.935 1928 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1612 helix: 0.14 (0.19), residues: 798 sheet: -0.14 (0.40), residues: 161 loop : -0.12 (0.29), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 465 HIS 0.003 0.001 HIS A 206 PHE 0.013 0.001 PHE A 219 TYR 0.005 0.001 TYR A 386 ARG 0.002 0.000 ARG E 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2113 time to fit residues: 47.8689 Evaluate side-chains 109 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.614 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.5980 chunk 62 optimal weight: 0.0770 chunk 93 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN F 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11633 Z= 0.156 Angle : 0.490 11.561 15945 Z= 0.255 Chirality : 0.039 0.146 1966 Planarity : 0.004 0.048 2061 Dihedral : 9.767 85.568 1928 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.23), residues: 1612 helix: 0.27 (0.20), residues: 795 sheet: 0.03 (0.41), residues: 165 loop : -0.04 (0.29), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 465 HIS 0.003 0.001 HIS E 206 PHE 0.017 0.001 PHE E 317 TYR 0.013 0.001 TYR E 386 ARG 0.002 0.000 ARG D 352 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2057 time to fit residues: 47.4363 Evaluate side-chains 115 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.7980 chunk 136 optimal weight: 0.4980 chunk 145 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 131 optimal weight: 0.0060 chunk 137 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN F 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11633 Z= 0.148 Angle : 0.481 12.959 15945 Z= 0.250 Chirality : 0.039 0.123 1966 Planarity : 0.003 0.045 2061 Dihedral : 9.533 85.438 1928 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1612 helix: 0.40 (0.20), residues: 787 sheet: 0.22 (0.41), residues: 165 loop : 0.18 (0.29), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 465 HIS 0.003 0.001 HIS E 206 PHE 0.017 0.001 PHE E 317 TYR 0.005 0.001 TYR A 386 ARG 0.002 0.000 ARG E 367 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2017 time to fit residues: 45.4157 Evaluate side-chains 110 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.325 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 20.0000 chunk 93 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 148 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 102 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11633 Z= 0.153 Angle : 0.489 13.424 15945 Z= 0.254 Chirality : 0.039 0.120 1966 Planarity : 0.003 0.045 2061 Dihedral : 9.389 85.488 1928 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.23), residues: 1612 helix: 0.45 (0.20), residues: 786 sheet: 0.35 (0.42), residues: 165 loop : 0.27 (0.29), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 465 HIS 0.004 0.001 HIS E 206 PHE 0.016 0.001 PHE E 317 TYR 0.006 0.001 TYR C 386 ARG 0.002 0.000 ARG B 367 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2071 time to fit residues: 45.6652 Evaluate side-chains 109 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 16 optimal weight: 0.0040 chunk 23 optimal weight: 0.1980 chunk 113 optimal weight: 0.6980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN F 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.057954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.046040 restraints weight = 89538.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.047112 restraints weight = 60292.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.047896 restraints weight = 44620.305| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11633 Z= 0.142 Angle : 0.485 13.535 15945 Z= 0.250 Chirality : 0.039 0.122 1966 Planarity : 0.003 0.042 2061 Dihedral : 9.200 84.138 1928 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.23), residues: 1612 helix: 0.51 (0.20), residues: 784 sheet: 0.40 (0.41), residues: 165 loop : 0.23 (0.29), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 465 HIS 0.003 0.001 HIS E 206 PHE 0.016 0.001 PHE E 317 TYR 0.010 0.001 TYR F 386 ARG 0.002 0.000 ARG C 439 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2285.59 seconds wall clock time: 42 minutes 10.69 seconds (2530.69 seconds total)