Starting phenix.real_space_refine on Sun Nov 17 08:04:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohs_16884/11_2024/8ohs_16884.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohs_16884/11_2024/8ohs_16884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohs_16884/11_2024/8ohs_16884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohs_16884/11_2024/8ohs_16884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohs_16884/11_2024/8ohs_16884.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohs_16884/11_2024/8ohs_16884.cif" } resolution = 4.1 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 8487 2.51 5 N 2286 2.21 5 O 2535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13335 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1756 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "C" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1756 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "D" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1756 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "E" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1756 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "G" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1756 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1756 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Time building chain proxies: 8.38, per 1000 atoms: 0.63 Number of scatterers: 13335 At special positions: 0 Unit cell: (162.5, 167.5, 116.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 2535 8.00 N 2286 7.00 C 8487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.9 seconds 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3288 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 27 sheets defined 43.9% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.681A pdb=" N LYS A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 282 through 298 removed outlier: 3.839A pdb=" N PHE A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 340 through 358 Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.835A pdb=" N GLN A 366 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 452 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'C' and resid 275 through 289 Processing helix chain 'C' and resid 294 through 307 removed outlier: 4.198A pdb=" N PHE C 298 " --> pdb=" O PRO C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 329 Processing helix chain 'C' and resid 399 through 419 removed outlier: 4.562A pdb=" N LYS C 403 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ARG C 404 " --> pdb=" O SER C 400 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 407 " --> pdb=" O LYS C 403 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 408 " --> pdb=" O ARG C 404 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 250 removed outlier: 3.733A pdb=" N LYS B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 272 Processing helix chain 'B' and resid 282 through 298 removed outlier: 3.844A pdb=" N PHE B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 340 through 358 Processing helix chain 'B' and resid 361 through 366 removed outlier: 3.848A pdb=" N GLN B 366 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 452 Processing helix chain 'B' and resid 453 through 457 Processing helix chain 'D' and resid 233 through 250 removed outlier: 3.681A pdb=" N LYS D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 238 " --> pdb=" O GLY D 234 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 272 Processing helix chain 'D' and resid 282 through 298 removed outlier: 3.839A pdb=" N PHE D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 340 through 358 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.834A pdb=" N GLN D 366 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 452 Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'E' and resid 275 through 289 Processing helix chain 'E' and resid 294 through 307 removed outlier: 4.198A pdb=" N PHE E 298 " --> pdb=" O PRO E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 329 Processing helix chain 'E' and resid 399 through 419 removed outlier: 4.562A pdb=" N LYS E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ARG E 404 " --> pdb=" O SER E 400 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 407 " --> pdb=" O LYS E 403 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE E 408 " --> pdb=" O ARG E 404 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU E 417 " --> pdb=" O LYS E 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 250 removed outlier: 3.733A pdb=" N LYS F 237 " --> pdb=" O SER F 233 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR F 238 " --> pdb=" O GLY F 234 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG F 242 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 272 Processing helix chain 'F' and resid 282 through 298 removed outlier: 3.844A pdb=" N PHE F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 340 through 358 Processing helix chain 'F' and resid 361 through 366 removed outlier: 3.848A pdb=" N GLN F 366 " --> pdb=" O GLU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 452 Processing helix chain 'F' and resid 453 through 457 Processing helix chain 'G' and resid 233 through 250 removed outlier: 3.682A pdb=" N LYS G 237 " --> pdb=" O SER G 233 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR G 238 " --> pdb=" O GLY G 234 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG G 242 " --> pdb=" O THR G 238 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 272 Processing helix chain 'G' and resid 282 through 298 removed outlier: 3.839A pdb=" N PHE G 286 " --> pdb=" O SER G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 301 No H-bonds generated for 'chain 'G' and resid 299 through 301' Processing helix chain 'G' and resid 340 through 358 Processing helix chain 'G' and resid 361 through 366 removed outlier: 3.835A pdb=" N GLN G 366 " --> pdb=" O GLU G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 452 Processing helix chain 'G' and resid 453 through 457 Processing helix chain 'H' and resid 275 through 289 Processing helix chain 'H' and resid 294 through 307 removed outlier: 4.199A pdb=" N PHE H 298 " --> pdb=" O PRO H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 329 Processing helix chain 'H' and resid 399 through 419 removed outlier: 4.562A pdb=" N LYS H 403 " --> pdb=" O LYS H 399 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ARG H 404 " --> pdb=" O SER H 400 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA H 407 " --> pdb=" O LYS H 403 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE H 408 " --> pdb=" O ARG H 404 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU H 417 " --> pdb=" O LYS H 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 250 removed outlier: 3.734A pdb=" N LYS I 237 " --> pdb=" O SER I 233 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR I 238 " --> pdb=" O GLY I 234 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE I 239 " --> pdb=" O MET I 235 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG I 242 " --> pdb=" O THR I 238 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 261 through 272 Processing helix chain 'I' and resid 282 through 298 removed outlier: 3.844A pdb=" N PHE I 286 " --> pdb=" O SER I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 301 No H-bonds generated for 'chain 'I' and resid 299 through 301' Processing helix chain 'I' and resid 340 through 358 Processing helix chain 'I' and resid 361 through 366 removed outlier: 3.848A pdb=" N GLN I 366 " --> pdb=" O GLU I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 452 Processing helix chain 'I' and resid 453 through 457 Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 231 Processing sheet with id=AA2, first strand: chain 'A' and resid 332 through 333 removed outlier: 6.474A pdb=" N SER A 319 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN A 374 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER A 371 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL A 398 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER A 373 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 333 removed outlier: 6.474A pdb=" N SER A 319 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN A 374 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER A 371 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL A 398 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER A 373 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 383 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 305 Processing sheet with id=AA5, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA6, first strand: chain 'A' and resid 383 through 384 removed outlier: 3.640A pdb=" N SER A 383 " --> pdb=" O SER G 256 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER G 371 " --> pdb=" O LEU G 396 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL G 398 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER G 373 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER G 319 " --> pdb=" O ILE G 372 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN G 374 " --> pdb=" O SER G 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 383 through 384 removed outlier: 3.640A pdb=" N SER A 383 " --> pdb=" O SER G 256 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR G 414 " --> pdb=" O ASN G 410 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 266 through 271 Processing sheet with id=AA9, first strand: chain 'B' and resid 252 through 260 removed outlier: 6.564A pdb=" N SER B 371 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL B 398 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER B 373 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER B 319 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASN B 374 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 252 through 260 removed outlier: 3.697A pdb=" N THR B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 303 through 305 Processing sheet with id=AB3, first strand: chain 'B' and resid 323 through 324 Processing sheet with id=AB4, first strand: chain 'D' and resid 332 through 333 removed outlier: 6.474A pdb=" N SER D 319 " --> pdb=" O ILE D 372 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN D 374 " --> pdb=" O SER D 319 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER D 371 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL D 398 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER D 373 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 332 through 333 removed outlier: 6.474A pdb=" N SER D 319 " --> pdb=" O ILE D 372 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASN D 374 " --> pdb=" O SER D 319 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER D 371 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL D 398 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER D 373 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER G 383 " --> pdb=" O SER D 256 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 303 through 305 Processing sheet with id=AB7, first strand: chain 'D' and resid 322 through 324 Processing sheet with id=AB8, first strand: chain 'E' and resid 266 through 271 Processing sheet with id=AB9, first strand: chain 'F' and resid 252 through 260 removed outlier: 6.564A pdb=" N SER F 371 " --> pdb=" O LEU F 396 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL F 398 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER F 373 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER F 319 " --> pdb=" O ILE F 372 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASN F 374 " --> pdb=" O SER F 319 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 252 through 260 removed outlier: 3.698A pdb=" N THR F 414 " --> pdb=" O ASN F 410 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 303 through 305 Processing sheet with id=AC3, first strand: chain 'F' and resid 323 through 324 Processing sheet with id=AC4, first strand: chain 'G' and resid 322 through 324 Processing sheet with id=AC5, first strand: chain 'H' and resid 266 through 271 Processing sheet with id=AC6, first strand: chain 'I' and resid 252 through 260 removed outlier: 6.564A pdb=" N SER I 371 " --> pdb=" O LEU I 396 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL I 398 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER I 373 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER I 319 " --> pdb=" O ILE I 372 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASN I 374 " --> pdb=" O SER I 319 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 252 through 260 removed outlier: 3.698A pdb=" N THR I 414 " --> pdb=" O ASN I 410 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 303 through 305 Processing sheet with id=AC9, first strand: chain 'I' and resid 323 through 324 738 hydrogen bonds defined for protein. 2055 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: 3.70 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3773 1.34 - 1.46: 1766 1.46 - 1.58: 7961 1.58 - 1.70: 3 1.70 - 1.82: 54 Bond restraints: 13557 Sorted by residual: bond pdb=" N VAL A 298 " pdb=" CA VAL A 298 " ideal model delta sigma weight residual 1.456 1.486 -0.030 8.60e-03 1.35e+04 1.20e+01 bond pdb=" N VAL G 298 " pdb=" CA VAL G 298 " ideal model delta sigma weight residual 1.456 1.486 -0.030 8.60e-03 1.35e+04 1.19e+01 bond pdb=" N VAL D 298 " pdb=" CA VAL D 298 " ideal model delta sigma weight residual 1.456 1.485 -0.030 8.60e-03 1.35e+04 1.18e+01 bond pdb=" N ILE D 332 " pdb=" CA ILE D 332 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.14e-02 7.69e+03 1.12e+01 bond pdb=" N ILE G 332 " pdb=" CA ILE G 332 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.14e-02 7.69e+03 1.11e+01 ... (remaining 13552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 15276 1.42 - 2.84: 2680 2.84 - 4.26: 329 4.26 - 5.68: 87 5.68 - 7.10: 18 Bond angle restraints: 18390 Sorted by residual: angle pdb=" CA GLY A 327 " pdb=" C GLY A 327 " pdb=" O GLY A 327 " ideal model delta sigma weight residual 122.56 118.22 4.34 1.03e+00 9.43e-01 1.78e+01 angle pdb=" CA GLY G 327 " pdb=" C GLY G 327 " pdb=" O GLY G 327 " ideal model delta sigma weight residual 122.56 118.22 4.34 1.03e+00 9.43e-01 1.78e+01 angle pdb=" CA GLY D 327 " pdb=" C GLY D 327 " pdb=" O GLY D 327 " ideal model delta sigma weight residual 122.56 118.26 4.30 1.03e+00 9.43e-01 1.74e+01 angle pdb=" N GLU E 417 " pdb=" CA GLU E 417 " pdb=" C GLU E 417 " ideal model delta sigma weight residual 113.88 109.03 4.85 1.23e+00 6.61e-01 1.56e+01 angle pdb=" N GLU C 417 " pdb=" CA GLU C 417 " pdb=" C GLU C 417 " ideal model delta sigma weight residual 113.88 109.03 4.85 1.23e+00 6.61e-01 1.56e+01 ... (remaining 18385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7635 17.88 - 35.75: 513 35.75 - 53.63: 132 53.63 - 71.51: 48 71.51 - 89.38: 24 Dihedral angle restraints: 8352 sinusoidal: 3294 harmonic: 5058 Sorted by residual: dihedral pdb=" CB GLU I 445 " pdb=" CG GLU I 445 " pdb=" CD GLU I 445 " pdb=" OE1 GLU I 445 " ideal model delta sinusoidal sigma weight residual 0.00 89.38 -89.38 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU F 445 " pdb=" CG GLU F 445 " pdb=" CD GLU F 445 " pdb=" OE1 GLU F 445 " ideal model delta sinusoidal sigma weight residual 0.00 89.36 -89.36 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU B 445 " pdb=" CG GLU B 445 " pdb=" CD GLU B 445 " pdb=" OE1 GLU B 445 " ideal model delta sinusoidal sigma weight residual 0.00 89.35 -89.35 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 8349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1303 0.059 - 0.117: 615 0.117 - 0.176: 245 0.176 - 0.235: 30 0.235 - 0.293: 6 Chirality restraints: 2199 Sorted by residual: chirality pdb=" CB THR C 345 " pdb=" CA THR C 345 " pdb=" OG1 THR C 345 " pdb=" CG2 THR C 345 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB THR E 345 " pdb=" CA THR E 345 " pdb=" OG1 THR E 345 " pdb=" CG2 THR E 345 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB THR H 345 " pdb=" CA THR H 345 " pdb=" OG1 THR H 345 " pdb=" CG2 THR H 345 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 2196 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL I 348 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C VAL I 348 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL I 348 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS I 349 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 348 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C VAL B 348 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL B 348 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS B 349 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 348 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C VAL F 348 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL F 348 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS F 349 " 0.014 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 0.70 - 1.54: 3 1.54 - 2.38: 6 2.38 - 3.22: 11964 3.22 - 4.06: 30116 4.06 - 4.90: 53895 Warning: very small nonbonded interaction distances. Nonbonded interactions: 95984 Sorted by model distance: nonbonded pdb=" O THR E 288 " pdb=" NZ LYS H 284 " model vdw 0.697 3.120 nonbonded pdb=" NZ LYS C 284 " pdb=" O THR H 288 " model vdw 0.700 3.120 nonbonded pdb=" O THR C 288 " pdb=" NZ LYS E 284 " model vdw 0.702 3.120 nonbonded pdb=" NZ LYS C 284 " pdb=" C THR H 288 " model vdw 1.549 3.350 nonbonded pdb=" C THR E 288 " pdb=" NZ LYS H 284 " model vdw 1.554 3.350 ... (remaining 95979 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'H' } 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.160 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 : 0.009 0.079 13557 Z= 0.597 Angle : 1.089 7.101 18390 Z= 0.722 Chirality : 0.075 0.293 2199 Planarity : 0.004 0.033 2352 Dihedral : 14.895 89.383 5064 Min Nonbonded Distance : 0.697 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.41 % Allowed : 2.44 % Favored : 97.15 % 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: -1.04 (0.19), residues: 1734 helix: 0.64 (0.20), residues: 651 sheet: -0.25 (0.28), residues: 285 loop : -2.05 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP F 442 HIS 0.006 0.002 HIS I 252 PHE 0.017 0.002 PHE E 408 TYR 0.020 0.003 TYR C 316 ARG 0.003 0.001 ARG D 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 422 time to evaluate : 1.441 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: C 415 VAL cc_start: 0.7321 (t) cc_final: 0.7032 (m) REVERT: B 236 ARG cc_start: 0.7409 (ttm-80) cc_final: 0.5155 (tmt170) REVERT: B 382 GLN cc_start: 0.8370 (tt0) cc_final: 0.6662 (pm20) REVERT: B 396 LEU cc_start: 0.9509 (tp) cc_final: 0.9166 (tt) REVERT: D 229 ASP cc_start: 0.7620 (m-30) cc_final: 0.7146 (m-30) REVERT: E 300 THR cc_start: 0.7239 (p) cc_final: 0.6950 (t) REVERT: F 236 ARG cc_start: 0.7262 (ttm-80) cc_final: 0.5409 (tmt170) REVERT: F 382 GLN cc_start: 0.8261 (tt0) cc_final: 0.6533 (pm20) REVERT: G 421 GLU cc_start: 0.7612 (tt0) cc_final: 0.7401 (tt0) REVERT: H 300 THR cc_start: 0.7433 (p) cc_final: 0.7108 (t) REVERT: I 236 ARG cc_start: 0.7175 (ttm-80) cc_final: 0.5162 (tmt170) REVERT: I 382 GLN cc_start: 0.8356 (tt0) cc_final: 0.6380 (pm20) outliers start: 6 outliers final: 0 residues processed: 422 average time/residue: 0.3376 time to fit residues: 189.2781 Evaluate side-chains 181 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 382 GLN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN C 410 GLN D 378 ASN F 250 ASN G 312 GLN G 378 ASN H 317 GLN I 250 ASN I 389 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13557 Z= 0.284 Angle : 0.639 7.093 18390 Z= 0.326 Chirality : 0.045 0.151 2199 Planarity : 0.004 0.038 2352 Dihedral : 4.238 20.832 1836 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: 0.29 (0.20), residues: 1734 helix: 2.03 (0.21), residues: 681 sheet: 0.18 (0.26), residues: 285 loop : -1.57 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 419 HIS 0.003 0.001 HIS B 252 PHE 0.017 0.002 PHE G 253 TYR 0.032 0.003 TYR B 365 ARG 0.007 0.001 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 236 ARG cc_start: 0.7464 (tpp-160) cc_final: 0.5423 (tmt170) REVERT: D 229 ASP cc_start: 0.7906 (m-30) cc_final: 0.7473 (m-30) REVERT: E 322 GLU cc_start: 0.6753 (pt0) cc_final: 0.6475 (pt0) REVERT: E 408 PHE cc_start: 0.4071 (t80) cc_final: 0.3552 (t80) REVERT: F 236 ARG cc_start: 0.7443 (tpp-160) cc_final: 0.5741 (tmt170) REVERT: F 253 PHE cc_start: 0.8847 (p90) cc_final: 0.8467 (p90) REVERT: F 444 ARG cc_start: 0.4666 (mtt-85) cc_final: 0.4302 (mtt90) REVERT: H 300 THR cc_start: 0.7272 (p) cc_final: 0.7049 (p) REVERT: I 236 ARG cc_start: 0.7548 (tpp-160) cc_final: 0.5681 (tmt170) REVERT: I 253 PHE cc_start: 0.8801 (p90) cc_final: 0.8450 (p90) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3547 time to fit residues: 101.6667 Evaluate side-chains 144 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 131 optimal weight: 0.5980 chunk 107 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 158 optimal weight: 0.1980 chunk 171 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 382 GLN A 389 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 GLN C 410 GLN D 284 ASN D 378 ASN F 389 ASN G 378 ASN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13557 Z= 0.232 Angle : 0.553 6.138 18390 Z= 0.281 Chirality : 0.043 0.144 2199 Planarity : 0.004 0.043 2352 Dihedral : 3.995 19.781 1836 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: 0.75 (0.20), residues: 1734 helix: 2.41 (0.21), residues: 681 sheet: 0.15 (0.24), residues: 321 loop : -1.24 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 419 HIS 0.005 0.001 HIS C 286 PHE 0.020 0.002 PHE A 253 TYR 0.019 0.002 TYR G 365 ARG 0.007 0.001 ARG F 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.5823 (tpt) cc_final: 0.4996 (tpp) REVERT: B 236 ARG cc_start: 0.7336 (tpp-160) cc_final: 0.5855 (ttt180) REVERT: D 229 ASP cc_start: 0.7705 (m-30) cc_final: 0.7256 (m-30) REVERT: E 300 THR cc_start: 0.7261 (p) cc_final: 0.6653 (p) REVERT: E 408 PHE cc_start: 0.4179 (t80) cc_final: 0.3939 (t80) REVERT: F 236 ARG cc_start: 0.7402 (tpp-160) cc_final: 0.5975 (tmt170) REVERT: F 375 MET cc_start: 0.8288 (mtp) cc_final: 0.8087 (mtt) REVERT: I 236 ARG cc_start: 0.7420 (tpp-160) cc_final: 0.5995 (tmt170) REVERT: I 382 GLN cc_start: 0.8842 (tt0) cc_final: 0.6835 (pm20) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3890 time to fit residues: 102.8035 Evaluate side-chains 150 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 GLN B 252 HIS B 389 ASN D 378 ASN D 431 HIS E 317 GLN F 250 ASN F 431 HIS G 378 ASN G 389 ASN G 431 HIS H 282 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 13557 Z= 0.537 Angle : 0.744 7.483 18390 Z= 0.382 Chirality : 0.048 0.145 2199 Planarity : 0.005 0.046 2352 Dihedral : 4.859 22.257 1836 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.27 % Allowed : 5.97 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.33 (0.20), residues: 1734 helix: 1.89 (0.20), residues: 675 sheet: 0.15 (0.25), residues: 285 loop : -1.31 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 305 HIS 0.003 0.001 HIS D 252 PHE 0.028 0.003 PHE G 253 TYR 0.017 0.003 TYR G 365 ARG 0.008 0.001 ARG I 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 194 time to evaluate : 1.760 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: B 227 TYR cc_start: 0.6366 (p90) cc_final: 0.5150 (t80) REVERT: B 236 ARG cc_start: 0.7600 (tpp-160) cc_final: 0.6167 (tmt170) REVERT: B 377 MET cc_start: 0.7918 (mpp) cc_final: 0.7549 (mpp) REVERT: D 229 ASP cc_start: 0.7656 (m-30) cc_final: 0.7399 (m-30) REVERT: E 296 SER cc_start: 0.6135 (t) cc_final: 0.5631 (t) REVERT: E 300 THR cc_start: 0.7881 (p) cc_final: 0.7167 (t) REVERT: F 227 TYR cc_start: 0.6178 (p90) cc_final: 0.5435 (t80) REVERT: F 236 ARG cc_start: 0.7577 (tpp-160) cc_final: 0.6406 (ttt180) REVERT: F 375 MET cc_start: 0.8345 (mtp) cc_final: 0.8103 (mtt) REVERT: H 300 THR cc_start: 0.7220 (p) cc_final: 0.6271 (t) REVERT: I 227 TYR cc_start: 0.5801 (p90) cc_final: 0.5248 (t80) REVERT: I 236 ARG cc_start: 0.7684 (tpp-160) cc_final: 0.6322 (tmt170) outliers start: 4 outliers final: 0 residues processed: 196 average time/residue: 0.3841 time to fit residues: 98.5096 Evaluate side-chains 157 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 143 optimal weight: 30.0000 chunk 116 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 GLN ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN G 312 GLN ** G 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 282 GLN H 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13557 Z= 0.346 Angle : 0.629 10.156 18390 Z= 0.320 Chirality : 0.045 0.141 2199 Planarity : 0.004 0.048 2352 Dihedral : 4.428 19.918 1836 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.14 % Allowed : 2.78 % Favored : 97.08 % 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: 0.51 (0.20), residues: 1734 helix: 1.94 (0.20), residues: 681 sheet: 0.25 (0.27), residues: 285 loop : -1.13 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 419 HIS 0.003 0.001 HIS D 431 PHE 0.024 0.002 PHE E 408 TYR 0.016 0.002 TYR E 316 ARG 0.009 0.001 ARG I 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 1.603 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: B 227 TYR cc_start: 0.6577 (p90) cc_final: 0.5065 (t80) REVERT: B 236 ARG cc_start: 0.7466 (tpp-160) cc_final: 0.6117 (tmt170) REVERT: B 377 MET cc_start: 0.7856 (mpp) cc_final: 0.7414 (mpp) REVERT: D 229 ASP cc_start: 0.7762 (m-30) cc_final: 0.7391 (m-30) REVERT: E 300 THR cc_start: 0.8080 (p) cc_final: 0.7100 (t) REVERT: E 402 GLU cc_start: 0.6343 (tp30) cc_final: 0.6062 (tp30) REVERT: F 227 TYR cc_start: 0.6561 (p90) cc_final: 0.5448 (t80) REVERT: F 236 ARG cc_start: 0.7447 (tpp-160) cc_final: 0.6481 (ttt180) REVERT: F 444 ARG cc_start: 0.4872 (mtt-85) cc_final: 0.4411 (mtt90) REVERT: I 227 TYR cc_start: 0.5976 (p90) cc_final: 0.5243 (t80) REVERT: I 236 ARG cc_start: 0.7503 (tpp-160) cc_final: 0.6369 (tmt170) outliers start: 2 outliers final: 0 residues processed: 203 average time/residue: 0.3835 time to fit residues: 101.4301 Evaluate side-chains 164 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 GLN D 312 GLN D 326 ASN E 282 GLN G 269 GLN H 282 GLN H 410 GLN I 252 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.6452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13557 Z= 0.247 Angle : 0.591 11.932 18390 Z= 0.300 Chirality : 0.043 0.174 2199 Planarity : 0.004 0.055 2352 Dihedral : 4.160 18.787 1836 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.20 % Allowed : 1.70 % Favored : 98.10 % 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: 0.73 (0.20), residues: 1734 helix: 2.10 (0.20), residues: 678 sheet: 0.41 (0.27), residues: 285 loop : -1.00 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 419 HIS 0.001 0.000 HIS A 252 PHE 0.020 0.002 PHE C 408 TYR 0.012 0.001 TYR G 365 ARG 0.011 0.001 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 202 time to evaluate : 1.692 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: B 227 TYR cc_start: 0.6699 (p90) cc_final: 0.5043 (t80) REVERT: B 236 ARG cc_start: 0.7527 (tpp-160) cc_final: 0.6207 (tmt170) REVERT: B 377 MET cc_start: 0.7887 (mpp) cc_final: 0.7435 (mpp) REVERT: D 229 ASP cc_start: 0.7760 (m-30) cc_final: 0.7355 (m-30) REVERT: D 312 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7327 (tm-30) REVERT: E 300 THR cc_start: 0.8205 (p) cc_final: 0.7679 (t) REVERT: F 227 TYR cc_start: 0.6472 (p90) cc_final: 0.5381 (t80) REVERT: F 236 ARG cc_start: 0.7347 (tpp-160) cc_final: 0.6431 (ttt180) REVERT: F 434 VAL cc_start: 0.9545 (t) cc_final: 0.9276 (m) REVERT: F 444 ARG cc_start: 0.4806 (mtt-85) cc_final: 0.4307 (mtt90) REVERT: I 227 TYR cc_start: 0.6111 (p90) cc_final: 0.5456 (t80) REVERT: I 236 ARG cc_start: 0.7410 (tpp-160) cc_final: 0.6314 (tmt170) outliers start: 3 outliers final: 0 residues processed: 205 average time/residue: 0.3879 time to fit residues: 104.3298 Evaluate side-chains 173 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 GLN B 366 GLN E 282 GLN F 269 GLN F 366 GLN H 282 GLN H 410 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13557 Z= 0.249 Angle : 0.588 12.957 18390 Z= 0.301 Chirality : 0.043 0.164 2199 Planarity : 0.005 0.058 2352 Dihedral : 4.158 19.994 1836 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.07 % Allowed : 1.70 % Favored : 98.23 % 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: 0.80 (0.20), residues: 1734 helix: 2.15 (0.20), residues: 678 sheet: 0.51 (0.27), residues: 285 loop : -0.98 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 419 HIS 0.002 0.001 HIS A 252 PHE 0.023 0.002 PHE C 408 TYR 0.012 0.002 TYR G 365 ARG 0.012 0.001 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 TYR cc_start: 0.6847 (p90) cc_final: 0.5020 (t80) REVERT: B 236 ARG cc_start: 0.7513 (tpp-160) cc_final: 0.6319 (ttt180) REVERT: B 377 MET cc_start: 0.7860 (mpp) cc_final: 0.7430 (mpp) REVERT: D 229 ASP cc_start: 0.7764 (m-30) cc_final: 0.7362 (m-30) REVERT: E 300 THR cc_start: 0.8276 (p) cc_final: 0.7742 (t) REVERT: E 402 GLU cc_start: 0.5966 (tp30) cc_final: 0.5712 (tp30) REVERT: F 227 TYR cc_start: 0.6611 (p90) cc_final: 0.5290 (t80) REVERT: F 236 ARG cc_start: 0.7330 (tpp-160) cc_final: 0.6458 (ttt180) REVERT: F 434 VAL cc_start: 0.9498 (t) cc_final: 0.9213 (m) REVERT: F 444 ARG cc_start: 0.4664 (mtt-85) cc_final: 0.4246 (mtt90) REVERT: G 375 MET cc_start: 0.8846 (mmm) cc_final: 0.8462 (mmt) REVERT: I 227 TYR cc_start: 0.6318 (p90) cc_final: 0.5215 (t80) REVERT: I 236 ARG cc_start: 0.7416 (tpp-160) cc_final: 0.6320 (tmt170) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.3913 time to fit residues: 105.5864 Evaluate side-chains 167 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 389 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 GLN G 269 GLN G 326 ASN H 282 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.6836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13557 Z= 0.292 Angle : 0.605 11.232 18390 Z= 0.310 Chirality : 0.044 0.166 2199 Planarity : 0.005 0.056 2352 Dihedral : 4.316 25.329 1836 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.07 % Allowed : 0.88 % Favored : 99.05 % 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: 0.79 (0.20), residues: 1734 helix: 2.15 (0.20), residues: 675 sheet: 0.51 (0.27), residues: 285 loop : -0.97 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 419 HIS 0.002 0.001 HIS D 252 PHE 0.019 0.002 PHE E 408 TYR 0.011 0.001 TYR G 365 ARG 0.014 0.001 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 TYR cc_start: 0.6926 (p90) cc_final: 0.5067 (t80) REVERT: B 236 ARG cc_start: 0.7436 (tpp-160) cc_final: 0.6357 (ttt180) REVERT: B 377 MET cc_start: 0.7963 (mpp) cc_final: 0.7471 (mpp) REVERT: D 229 ASP cc_start: 0.7762 (m-30) cc_final: 0.7350 (m-30) REVERT: E 300 THR cc_start: 0.8026 (p) cc_final: 0.7619 (t) REVERT: E 402 GLU cc_start: 0.5976 (tp30) cc_final: 0.5692 (tp30) REVERT: E 411 LYS cc_start: 0.7943 (pttp) cc_final: 0.7452 (pttm) REVERT: F 227 TYR cc_start: 0.6814 (p90) cc_final: 0.5209 (t80) REVERT: F 236 ARG cc_start: 0.7340 (tpp-160) cc_final: 0.6503 (ttt180) REVERT: F 434 VAL cc_start: 0.9502 (t) cc_final: 0.9202 (m) REVERT: F 444 ARG cc_start: 0.4841 (mtt-85) cc_final: 0.4330 (mtt180) REVERT: G 375 MET cc_start: 0.8839 (mmm) cc_final: 0.8452 (mmt) REVERT: I 227 TYR cc_start: 0.6547 (p90) cc_final: 0.5166 (t80) REVERT: I 236 ARG cc_start: 0.7414 (tpp-160) cc_final: 0.6345 (tmt170) outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.3667 time to fit residues: 97.8001 Evaluate side-chains 174 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.7030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13557 Z= 0.280 Angle : 0.627 14.849 18390 Z= 0.320 Chirality : 0.043 0.175 2199 Planarity : 0.005 0.063 2352 Dihedral : 4.245 21.135 1836 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.07 % Allowed : 0.54 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.20), residues: 1734 helix: 2.09 (0.20), residues: 678 sheet: 0.29 (0.26), residues: 321 loop : -0.81 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 419 HIS 0.002 0.001 HIS A 431 PHE 0.023 0.002 PHE H 408 TYR 0.011 0.001 TYR G 365 ARG 0.014 0.001 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.519 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: B 227 TYR cc_start: 0.7053 (p90) cc_final: 0.4998 (t80) REVERT: B 236 ARG cc_start: 0.7385 (tpp-160) cc_final: 0.6358 (ttt180) REVERT: B 377 MET cc_start: 0.7970 (mpp) cc_final: 0.7528 (mpp) REVERT: D 229 ASP cc_start: 0.7811 (m-30) cc_final: 0.7415 (m-30) REVERT: E 402 GLU cc_start: 0.5984 (tp30) cc_final: 0.5678 (tp30) REVERT: E 411 LYS cc_start: 0.7968 (pttp) cc_final: 0.7648 (pttm) REVERT: F 227 TYR cc_start: 0.6946 (p90) cc_final: 0.5006 (t80) REVERT: F 236 ARG cc_start: 0.7339 (tpp-160) cc_final: 0.6480 (ttt180) REVERT: F 434 VAL cc_start: 0.9489 (t) cc_final: 0.9201 (m) REVERT: F 444 ARG cc_start: 0.4986 (mtt-85) cc_final: 0.4515 (mtt180) REVERT: G 375 MET cc_start: 0.8824 (mmm) cc_final: 0.8454 (mmt) REVERT: I 227 TYR cc_start: 0.6805 (p90) cc_final: 0.5060 (t80) REVERT: I 236 ARG cc_start: 0.7403 (tpp-160) cc_final: 0.6337 (tmt170) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.3952 time to fit residues: 104.1705 Evaluate side-chains 169 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 147 optimal weight: 0.1980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 GLN E 282 GLN G 269 GLN G 326 ASN H 282 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.7013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13557 Z= 0.166 Angle : 0.592 12.223 18390 Z= 0.305 Chirality : 0.043 0.174 2199 Planarity : 0.005 0.059 2352 Dihedral : 3.965 22.204 1836 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.14 % Allowed : 0.34 % Favored : 99.52 % 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: 1.08 (0.21), residues: 1734 helix: 2.30 (0.20), residues: 675 sheet: 0.48 (0.27), residues: 321 loop : -0.68 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 419 HIS 0.001 0.000 HIS D 252 PHE 0.030 0.002 PHE E 408 TYR 0.012 0.001 TYR A 227 ARG 0.015 0.001 ARG C 339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ARG cc_start: 0.7363 (ttm-80) cc_final: 0.7131 (ttm170) REVERT: C 341 SER cc_start: 0.7439 (t) cc_final: 0.7230 (t) REVERT: C 408 PHE cc_start: 0.4559 (t80) cc_final: 0.4224 (t80) REVERT: B 227 TYR cc_start: 0.7085 (p90) cc_final: 0.5066 (t80) REVERT: B 236 ARG cc_start: 0.7204 (tpp-160) cc_final: 0.6298 (ttt180) REVERT: B 377 MET cc_start: 0.7877 (mpp) cc_final: 0.7433 (mpp) REVERT: D 229 ASP cc_start: 0.7779 (m-30) cc_final: 0.7350 (m-30) REVERT: D 430 ASP cc_start: 0.8707 (t70) cc_final: 0.8489 (t0) REVERT: E 402 GLU cc_start: 0.5786 (tp30) cc_final: 0.5083 (tp30) REVERT: F 227 TYR cc_start: 0.6803 (p90) cc_final: 0.5122 (t80) REVERT: F 236 ARG cc_start: 0.7301 (tpp-160) cc_final: 0.6320 (tmt170) REVERT: F 434 VAL cc_start: 0.9389 (t) cc_final: 0.9140 (m) REVERT: F 444 ARG cc_start: 0.4843 (mtt-85) cc_final: 0.4452 (mtt90) REVERT: G 375 MET cc_start: 0.8816 (mmm) cc_final: 0.8398 (mmm) REVERT: I 227 TYR cc_start: 0.6710 (p90) cc_final: 0.5167 (t80) REVERT: I 236 ARG cc_start: 0.7328 (tpp-160) cc_final: 0.6306 (tmt170) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.3746 time to fit residues: 101.4502 Evaluate side-chains 170 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 141 optimal weight: 30.0000 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN B 269 GLN E 282 GLN E 286 HIS E 410 GLN G 326 ASN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.085633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.060405 restraints weight = 36062.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.060851 restraints weight = 29041.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.060634 restraints weight = 25471.101| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.7146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13557 Z= 0.223 Angle : 0.607 9.725 18390 Z= 0.315 Chirality : 0.043 0.204 2199 Planarity : 0.005 0.056 2352 Dihedral : 4.005 21.662 1836 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.07 % Allowed : 0.48 % Favored : 99.46 % 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: 1.11 (0.21), residues: 1734 helix: 2.33 (0.20), residues: 675 sheet: 0.45 (0.27), residues: 321 loop : -0.64 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 419 HIS 0.002 0.001 HIS A 252 PHE 0.026 0.002 PHE E 408 TYR 0.011 0.001 TYR G 365 ARG 0.014 0.001 ARG I 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2799.54 seconds wall clock time: 52 minutes 2.59 seconds (3122.59 seconds total)