Starting phenix.real_space_refine on Wed Nov 15 10:33:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc0_8794/11_2023/5wc0_8794_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc0_8794/11_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_8794/11_2023/5wc0_8794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc0_8794/11_2023/5wc0_8794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc0_8794/11_2023/5wc0_8794_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc0_8794/11_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-1.21rc1-5144/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: 6.73, per 1000 atoms: 0.59 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: 4.99 Conformation dependent library (CDL) restraints added in 2.5 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: 2.18 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: 2.76 Time building geometry restraints manager: 5.34 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 - 15.74: 6612 15.74 - 31.47: 225 31.47 - 47.21: 16 47.21 - 62.95: 4 62.95 - 78.68: 3 Dihedral angle restraints: 6860 sinusoidal: 2056 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 6857 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: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 5.920 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 33.720 Find NCS groups from input model: 0.890 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.010 ------------------------------------------------------------------------------- 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 : 8.992 78.683 3708 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 *********************** 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 : 1.323 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: 0.2532 time to fit residues: 82.7017 Evaluate side-chains 130 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.357 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7900 ------------------------------------------------------------------------------- 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 220 GLN ** 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: 0.2353 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= 0.166 Angle : 0.557 6.333 15945 Z= 0.301 Chirality : 0.042 0.197 1966 Planarity : 0.005 0.053 2061 Dihedral : 7.859 83.638 1742 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.96 % Favored : 93.98 % Rotamer: Outliers : 0.11 % Allowed : 1.38 % Favored : 98.51 % 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: -3.29 (0.19), residues: 1612 helix: -2.15 (0.15), residues: 844 sheet: -2.10 (0.33), residues: 170 loop : -1.94 (0.26), residues: 598 *********************** 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 : 1.451 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 outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.2486 time to fit residues: 65.6654 Evaluate side-chains 124 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7245 ------------------------------------------------------------------------------- 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: 5.9990 chunk 122 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 147 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 118 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 D 220 GLN ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11633 Z= 0.163 Angle : 0.511 6.719 15945 Z= 0.273 Chirality : 0.040 0.131 1966 Planarity : 0.004 0.047 2061 Dihedral : 7.080 73.450 1742 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.32 % Allowed : 2.02 % Favored : 97.66 % 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: -2.22 (0.20), residues: 1612 helix: -1.32 (0.17), residues: 841 sheet: -1.63 (0.35), residues: 178 loop : -1.35 (0.27), residues: 593 *********************** 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 179 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 176 time to evaluate : 1.315 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: 3 outliers final: 0 residues processed: 178 average time/residue: 0.2155 time to fit residues: 56.2327 Evaluate side-chains 117 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.323 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6851 ------------------------------------------------------------------------------- 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: 0.7980 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 70 optimal weight: 0.1980 chunk 98 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 77 optimal weight: 0.0060 chunk 140 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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: 0.8047 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11633 Z= 0.202 Angle : 0.526 8.936 15945 Z= 0.277 Chirality : 0.040 0.137 1966 Planarity : 0.004 0.045 2061 Dihedral : 6.828 75.406 1742 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.11 % Allowed : 1.38 % 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: -1.34 (0.22), residues: 1612 helix: -0.69 (0.18), residues: 807 sheet: -1.07 (0.37), residues: 178 loop : -0.87 (0.28), residues: 627 *********************** 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 164 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.351 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: 164 average time/residue: 0.2192 time to fit residues: 52.8909 Evaluate side-chains 117 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6671 ------------------------------------------------------------------------------- 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: 0.0170 chunk 88 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 116 optimal weight: 0.0020 chunk 64 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.6032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11633 Z= 0.252 Angle : 0.557 9.567 15945 Z= 0.294 Chirality : 0.040 0.157 1966 Planarity : 0.004 0.053 2061 Dihedral : 6.818 78.033 1742 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.22), residues: 1612 helix: -0.55 (0.18), residues: 831 sheet: -0.84 (0.37), residues: 179 loop : -0.94 (0.28), residues: 602 *********************** 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 146 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.289 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: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2146 time to fit residues: 46.5212 Evaluate side-chains 110 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.386 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8008 ------------------------------------------------------------------------------- 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: 7.9990 chunk 141 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 156 optimal weight: 0.5980 chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 13 optimal weight: 0.0770 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- 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: 0.8078 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11633 Z= 0.163 Angle : 0.490 9.992 15945 Z= 0.256 Chirality : 0.040 0.152 1966 Planarity : 0.003 0.041 2061 Dihedral : 6.586 81.113 1742 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: -0.60 (0.22), residues: 1612 helix: -0.16 (0.19), residues: 815 sheet: -0.60 (0.38), residues: 183 loop : -0.40 (0.29), residues: 614 *********************** 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 162 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.430 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: 162 average time/residue: 0.2230 time to fit residues: 53.6566 Evaluate side-chains 115 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.410 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7637 ------------------------------------------------------------------------------- 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: 10.0000 chunk 89 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11633 Z= 0.177 Angle : 0.502 11.141 15945 Z= 0.262 Chirality : 0.040 0.183 1966 Planarity : 0.004 0.041 2061 Dihedral : 6.426 80.091 1742 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % 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: -0.01 (0.19), residues: 795 sheet: -0.29 (0.38), residues: 182 loop : -0.19 (0.29), residues: 635 *********************** 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 152 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.436 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: 152 average time/residue: 0.2103 time to fit residues: 48.6244 Evaluate side-chains 113 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.345 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7436 ------------------------------------------------------------------------------- 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: 4.9990 chunk 62 optimal weight: 0.0770 chunk 93 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 99 optimal weight: 0.0270 chunk 106 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 122 optimal weight: 0.0670 chunk 142 optimal weight: 3.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5099 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= 0.139 Angle : 0.473 11.759 15945 Z= 0.244 Chirality : 0.039 0.123 1966 Planarity : 0.003 0.039 2061 Dihedral : 6.178 80.238 1742 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % 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: -0.09 (0.23), residues: 1612 helix: 0.15 (0.19), residues: 795 sheet: 0.02 (0.39), residues: 183 loop : -0.13 (0.29), residues: 634 *********************** 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 158 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.316 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: 158 average time/residue: 0.2049 time to fit residues: 49.0766 Evaluate side-chains 116 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.410 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7208 ------------------------------------------------------------------------------- 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: 3.9990 chunk 136 optimal weight: 0.4980 chunk 145 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 131 optimal weight: 0.0870 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 0.0970 chunk 95 optimal weight: 5.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8069 moved from start: 0.5368 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= 0.141 Angle : 0.478 12.806 15945 Z= 0.245 Chirality : 0.039 0.164 1966 Planarity : 0.003 0.039 2061 Dihedral : 5.967 80.464 1742 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % 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: -0.03 (0.23), residues: 1612 helix: 0.20 (0.19), residues: 813 sheet: 0.10 (0.39), residues: 186 loop : -0.13 (0.30), residues: 613 *********************** 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 153 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.308 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: 0.2091 time to fit residues: 47.5828 Evaluate side-chains 110 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5649 ------------------------------------------------------------------------------- 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: 2.9990 chunk 93 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 161 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 128 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 78 optimal weight: 0.0000 chunk 102 optimal weight: 0.0980 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5564 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= 0.132 Angle : 0.488 13.355 15945 Z= 0.247 Chirality : 0.039 0.154 1966 Planarity : 0.003 0.038 2061 Dihedral : 5.785 80.943 1742 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % 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: 0.22 (0.23), residues: 1612 helix: 0.34 (0.19), residues: 807 sheet: 0.48 (0.40), residues: 183 loop : -0.01 (0.29), residues: 622 ********************** 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 152 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 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 outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2036 time to fit residues: 46.1779 Evaluate side-chains 109 residues out of total 1409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5102 ------------------------------------------------------------------------------- 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: 0.3980 chunk 39 optimal weight: 5.9990 chunk 118 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 53 optimal weight: 0.0000 chunk 132 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 overall best weight: 0.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.058660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046596 restraints weight = 88207.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.047666 restraints weight = 59867.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048427 restraints weight = 44536.846| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5755 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= 0.135 Angle : 0.485 13.408 15945 Z= 0.246 Chirality : 0.039 0.125 1966 Planarity : 0.003 0.036 2061 Dihedral : 5.675 78.862 1742 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: 0.25 (0.23), residues: 1612 helix: 0.39 (0.20), residues: 794 sheet: 0.55 (0.40), residues: 183 loop : -0.04 (0.29), residues: 635 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2227.80 seconds wall clock time: 41 minutes 15.55 seconds (2475.55 seconds total)