Starting phenix.real_space_refine on Sat Mar 16 01:42:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohs_16884/03_2024/8ohs_16884.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohs_16884/03_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_16884/03_2024/8ohs_16884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohs_16884/03_2024/8ohs_16884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohs_16884/03_2024/8ohs_16884.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohs_16884/03_2024/8ohs_16884.pdb" } 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 Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D ASP 276": "OD1" <-> "OD2" Residue "D PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 420": "OD1" <-> "OD2" Residue "E GLU 322": "OE1" <-> "OE2" Residue "F GLU 245": "OE1" <-> "OE2" Residue "F ASP 276": "OD1" <-> "OD2" Residue "F PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 420": "OD1" <-> "OD2" Residue "F GLU 445": "OE1" <-> "OE2" Residue "G GLU 245": "OE1" <-> "OE2" Residue "G ASP 276": "OD1" <-> "OD2" Residue "G PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 420": "OD1" <-> "OD2" Residue "H GLU 322": "OE1" <-> "OE2" Residue "I GLU 245": "OE1" <-> "OE2" Residue "I ASP 276": "OD1" <-> "OD2" Residue "I PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 420": "OD1" <-> "OD2" Residue "I GLU 445": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.18, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.31 Conformation dependent library (CDL) restraints added in 2.6 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: 1.60 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: 3.97 Time building geometry restraints manager: 5.79 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: 99.07 - 106.09: 388 106.09 - 113.11: 7462 113.11 - 120.13: 5344 120.13 - 127.16: 5051 127.16 - 134.18: 145 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 2.520 nonbonded pdb=" NZ LYS C 284 " pdb=" O THR H 288 " model vdw 0.700 2.520 nonbonded pdb=" O THR C 288 " pdb=" NZ LYS E 284 " model vdw 0.702 2.520 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 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: 2.060 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: 7.280 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 37.450 Find NCS groups from input model: 0.850 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.710 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 6 poor density : 422 time to evaluate : 1.620 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: 0.3205 time to fit residues: 179.6327 Evaluate side-chains 181 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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: 0.9980 chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 70 optimal weight: 0.6980 chunk 136 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 410 GLN B 389 ASN D 312 GLN D 378 ASN F 389 ASN G 312 GLN G 378 ASN H 317 GLN I 389 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13557 Z= 0.188 Angle : 0.575 7.000 18390 Z= 0.292 Chirality : 0.044 0.150 2199 Planarity : 0.004 0.041 2352 Dihedral : 3.919 17.469 1836 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % 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: 0.29 (0.20), residues: 1734 helix: 2.19 (0.21), residues: 681 sheet: 0.13 (0.26), residues: 285 loop : -1.72 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 419 HIS 0.002 0.001 HIS I 252 PHE 0.015 0.002 PHE G 253 TYR 0.033 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 234 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.647 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 236 ARG cc_start: 0.7318 (tpp-160) cc_final: 0.5249 (tmt170) REVERT: D 229 ASP cc_start: 0.7650 (m-30) cc_final: 0.7146 (m-30) REVERT: E 300 THR cc_start: 0.7194 (p) cc_final: 0.6879 (p) REVERT: E 322 GLU cc_start: 0.6698 (pt0) cc_final: 0.6455 (pt0) REVERT: E 408 PHE cc_start: 0.3909 (t80) cc_final: 0.3405 (t80) REVERT: F 236 ARG cc_start: 0.7202 (tpp-160) cc_final: 0.5374 (tmt170) REVERT: H 300 THR cc_start: 0.7316 (p) cc_final: 0.7089 (p) REVERT: I 236 ARG cc_start: 0.7391 (tpp-160) cc_final: 0.5604 (tmt170) REVERT: I 444 ARG cc_start: 0.5897 (mtt90) cc_final: 0.5240 (mmt180) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3483 time to fit residues: 107.5929 Evaluate side-chains 152 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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: 3.9990 chunk 49 optimal weight: 5.9990 chunk 131 optimal weight: 0.0980 chunk 107 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 378 ASN A 382 GLN A 389 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 GLN C 410 GLN B 402 GLN ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 ASN G 312 GLN G 378 ASN G 389 ASN I 250 ASN I 284 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13557 Z= 0.288 Angle : 0.603 8.279 18390 Z= 0.306 Chirality : 0.044 0.135 2199 Planarity : 0.005 0.049 2352 Dihedral : 4.100 21.680 1836 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % 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: 0.64 (0.20), residues: 1734 helix: 2.27 (0.21), residues: 687 sheet: 0.39 (0.25), residues: 285 loop : -1.38 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 419 HIS 0.007 0.001 HIS C 286 PHE 0.027 0.002 PHE G 253 TYR 0.033 0.003 TYR F 365 ARG 0.008 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 209 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.584 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: B 236 ARG cc_start: 0.7431 (tpp-160) cc_final: 0.5876 (ttt180) REVERT: D 229 ASP cc_start: 0.7718 (m-30) cc_final: 0.7248 (m-30) REVERT: E 322 GLU cc_start: 0.6793 (pt0) cc_final: 0.6376 (pt0) REVERT: F 236 ARG cc_start: 0.7420 (tpp-160) cc_final: 0.5936 (tmt170) REVERT: I 236 ARG cc_start: 0.7476 (tpp-160) cc_final: 0.5871 (tmt170) REVERT: I 382 GLN cc_start: 0.8765 (tt0) cc_final: 0.6832 (pm20) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.3539 time to fit residues: 97.2399 Evaluate side-chains 147 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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: 3.9990 chunk 119 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 75 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN B 252 HIS ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 GLN F 392 GLN G 250 ASN G 378 ASN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5322 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= 0.256 Angle : 0.561 7.016 18390 Z= 0.283 Chirality : 0.043 0.148 2199 Planarity : 0.004 0.041 2352 Dihedral : 4.021 19.489 1836 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.07 % Allowed : 3.39 % Favored : 96.54 % 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: 0.90 (0.20), residues: 1734 helix: 2.39 (0.21), residues: 687 sheet: 0.62 (0.25), residues: 285 loop : -1.17 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 419 HIS 0.003 0.001 HIS D 252 PHE 0.024 0.002 PHE G 253 TYR 0.022 0.002 TYR F 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 188 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 1.452 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 235 MET cc_start: 0.5805 (tpt) cc_final: 0.4944 (tpp) REVERT: B 236 ARG cc_start: 0.7490 (tpp-160) cc_final: 0.6133 (ttt180) REVERT: D 229 ASP cc_start: 0.7653 (m-30) cc_final: 0.7249 (m-30) REVERT: F 236 ARG cc_start: 0.7496 (tpp-160) cc_final: 0.6113 (tmt170) REVERT: I 236 ARG cc_start: 0.7414 (tpp-160) cc_final: 0.6144 (tmt170) REVERT: I 382 GLN cc_start: 0.8797 (tt0) cc_final: 0.7053 (pm20) outliers start: 1 outliers final: 1 residues processed: 188 average time/residue: 0.3979 time to fit residues: 96.1617 Evaluate side-chains 147 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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: 0.8980 chunk 2 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN C 410 GLN D 312 GLN F 392 GLN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 410 GLN I 252 HIS ** I 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.6010 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= 0.318 Angle : 0.590 6.653 18390 Z= 0.301 Chirality : 0.044 0.151 2199 Planarity : 0.004 0.054 2352 Dihedral : 4.235 20.605 1836 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.07 % Allowed : 2.99 % 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: 0.82 (0.20), residues: 1734 helix: 2.26 (0.20), residues: 681 sheet: 0.53 (0.26), residues: 285 loop : -1.07 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 419 HIS 0.007 0.001 HIS F 431 PHE 0.020 0.002 PHE G 253 TYR 0.017 0.002 TYR F 365 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 190 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 236 ARG cc_start: 0.7449 (tpp-160) cc_final: 0.6060 (tmt170) REVERT: B 377 MET cc_start: 0.7952 (mpp) cc_final: 0.7530 (mpp) REVERT: D 229 ASP cc_start: 0.7549 (m-30) cc_final: 0.7156 (m-30) REVERT: E 300 THR cc_start: 0.7815 (p) cc_final: 0.7286 (t) REVERT: F 236 ARG cc_start: 0.7606 (tpp-160) cc_final: 0.6326 (ttt180) REVERT: H 284 LYS cc_start: 0.6098 (pttp) cc_final: 0.5651 (pttm) REVERT: I 227 TYR cc_start: 0.3085 (t80) cc_final: 0.2823 (t80) REVERT: I 236 ARG cc_start: 0.7498 (tpp-160) cc_final: 0.6273 (tmt170) REVERT: I 382 GLN cc_start: 0.8599 (tt0) cc_final: 0.7069 (pm20) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.3959 time to fit residues: 97.0557 Evaluate side-chains 156 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.548 ------------------------------------------------------------------------------- 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: 7.9990 chunk 98 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 77 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 GLN B 392 GLN D 326 ASN F 366 GLN G 269 GLN G 312 GLN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 410 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13557 Z= 0.313 Angle : 0.592 6.829 18390 Z= 0.301 Chirality : 0.044 0.137 2199 Planarity : 0.004 0.049 2352 Dihedral : 4.259 22.832 1836 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.07 % Allowed : 2.51 % Favored : 97.42 % 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: 0.76 (0.20), residues: 1734 helix: 2.10 (0.20), residues: 684 sheet: 0.44 (0.26), residues: 285 loop : -0.99 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 419 HIS 0.003 0.001 HIS I 431 PHE 0.019 0.002 PHE G 253 TYR 0.013 0.002 TYR B 365 ARG 0.009 0.001 ARG B 242 *********************** 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 197 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 236 ARG cc_start: 0.7356 (tpp-160) cc_final: 0.6053 (tmt170) REVERT: B 377 MET cc_start: 0.8116 (mpp) cc_final: 0.7522 (mpp) REVERT: D 229 ASP cc_start: 0.7581 (m-30) cc_final: 0.7185 (m-30) REVERT: E 300 THR cc_start: 0.8219 (p) cc_final: 0.7829 (t) REVERT: F 236 ARG cc_start: 0.7342 (tpp-160) cc_final: 0.6422 (ttt180) REVERT: G 375 MET cc_start: 0.8827 (mmm) cc_final: 0.8422 (mmt) REVERT: I 227 TYR cc_start: 0.3510 (t80) cc_final: 0.3165 (t80) REVERT: I 236 ARG cc_start: 0.7596 (tpp-160) cc_final: 0.6400 (tmt170) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.3792 time to fit residues: 97.5344 Evaluate side-chains 161 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.628 ------------------------------------------------------------------------------- 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: 4.9990 chunk 141 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 GLN B 392 GLN D 326 ASN F 269 GLN ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 GLN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 410 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.6579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13557 Z= 0.233 Angle : 0.553 6.342 18390 Z= 0.281 Chirality : 0.043 0.136 2199 Planarity : 0.004 0.057 2352 Dihedral : 4.096 22.892 1836 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 0.94 (0.20), residues: 1734 helix: 2.35 (0.20), residues: 675 sheet: 0.56 (0.26), residues: 285 loop : -0.96 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 419 HIS 0.002 0.001 HIS I 431 PHE 0.018 0.002 PHE G 253 TYR 0.013 0.002 TYR F 365 ARG 0.011 0.001 ARG B 242 *********************** 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 194 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.5895 (tpt) cc_final: 0.5649 (tpp) REVERT: B 236 ARG cc_start: 0.7408 (tpp-160) cc_final: 0.6164 (tmt170) REVERT: B 377 MET cc_start: 0.8066 (mpp) cc_final: 0.7424 (mpp) REVERT: D 229 ASP cc_start: 0.7533 (m-30) cc_final: 0.7160 (m-30) REVERT: E 300 THR cc_start: 0.8195 (p) cc_final: 0.7779 (t) REVERT: E 402 GLU cc_start: 0.7390 (tp30) cc_final: 0.7146 (tp30) REVERT: F 236 ARG cc_start: 0.7336 (tpp-160) cc_final: 0.6452 (ttt180) REVERT: F 444 ARG cc_start: 0.4749 (mtt180) cc_final: 0.4056 (mtt180) REVERT: G 375 MET cc_start: 0.8857 (mmm) cc_final: 0.8431 (mmt) REVERT: I 227 TYR cc_start: 0.3684 (t80) cc_final: 0.3301 (t80) REVERT: I 236 ARG cc_start: 0.7549 (tpp-160) cc_final: 0.6380 (tmt170) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.3618 time to fit residues: 92.6397 Evaluate side-chains 162 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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: 10.0000 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 GLN B 389 ASN B 392 GLN B 431 HIS ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 GLN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 410 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.6739 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= 0.261 Angle : 0.572 6.445 18390 Z= 0.292 Chirality : 0.043 0.134 2199 Planarity : 0.005 0.053 2352 Dihedral : 4.120 21.046 1836 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: 0.93 (0.20), residues: 1734 helix: 2.28 (0.20), residues: 678 sheet: 0.59 (0.27), residues: 285 loop : -0.94 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 419 HIS 0.009 0.001 HIS B 431 PHE 0.018 0.002 PHE G 253 TYR 0.013 0.002 TYR F 365 ARG 0.013 0.001 ARG B 242 *********************** 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 187 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.5991 (tpt) cc_final: 0.5788 (tpp) REVERT: B 236 ARG cc_start: 0.7523 (tpp-160) cc_final: 0.6340 (ttt180) REVERT: B 377 MET cc_start: 0.8090 (mpp) cc_final: 0.7433 (mpp) REVERT: D 229 ASP cc_start: 0.7569 (m-30) cc_final: 0.7162 (m-30) REVERT: E 300 THR cc_start: 0.8080 (p) cc_final: 0.7676 (t) REVERT: F 236 ARG cc_start: 0.7365 (tpp-160) cc_final: 0.6529 (ttt180) REVERT: F 434 VAL cc_start: 0.9546 (t) cc_final: 0.9312 (m) REVERT: F 444 ARG cc_start: 0.4686 (mtt180) cc_final: 0.4045 (mtt180) REVERT: G 375 MET cc_start: 0.8824 (mmm) cc_final: 0.8454 (mmt) REVERT: H 411 LYS cc_start: 0.7610 (pttp) cc_final: 0.7113 (ptpt) REVERT: I 236 ARG cc_start: 0.7540 (tpp-160) cc_final: 0.6387 (tmt170) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.3559 time to fit residues: 87.7732 Evaluate side-chains 164 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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: 6.9990 chunk 160 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 286 HIS C 308 GLN ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 GLN ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 272 ASN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.6953 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= 0.286 Angle : 0.591 6.841 18390 Z= 0.302 Chirality : 0.043 0.162 2199 Planarity : 0.005 0.070 2352 Dihedral : 4.268 20.489 1836 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.07 % Allowed : 0.95 % Favored : 98.98 % 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: 0.95 (0.20), residues: 1734 helix: 2.23 (0.20), residues: 681 sheet: 0.62 (0.26), residues: 285 loop : -0.87 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 419 HIS 0.001 0.001 HIS A 252 PHE 0.017 0.002 PHE G 253 TYR 0.014 0.002 TYR F 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 196 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 236 ARG cc_start: 0.7527 (tpp-160) cc_final: 0.6429 (ttt180) REVERT: D 229 ASP cc_start: 0.7519 (m-30) cc_final: 0.7116 (m-30) REVERT: D 312 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7944 (tm-30) REVERT: F 236 ARG cc_start: 0.7356 (tpp-160) cc_final: 0.6580 (ttt180) REVERT: F 434 VAL cc_start: 0.9524 (t) cc_final: 0.9289 (m) REVERT: F 444 ARG cc_start: 0.4848 (mtt180) cc_final: 0.4196 (mtt180) REVERT: G 375 MET cc_start: 0.8830 (mmm) cc_final: 0.8462 (mmt) REVERT: H 411 LYS cc_start: 0.7739 (pttp) cc_final: 0.7038 (ptpt) REVERT: I 236 ARG cc_start: 0.7522 (tpp-160) cc_final: 0.6392 (tmt170) outliers start: 1 outliers final: 1 residues processed: 196 average time/residue: 0.3633 time to fit residues: 93.5772 Evaluate side-chains 166 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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: 4.9990 chunk 114 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 84 optimal weight: 0.0870 chunk 109 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 308 GLN B 269 GLN ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 GLN ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 GLN H 410 GLN I 250 ASN I 389 ASN I 392 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.6992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13557 Z= 0.182 Angle : 0.572 7.354 18390 Z= 0.293 Chirality : 0.043 0.137 2199 Planarity : 0.005 0.059 2352 Dihedral : 4.020 20.065 1836 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % 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: 1.17 (0.21), residues: 1734 helix: 2.40 (0.20), residues: 681 sheet: 0.60 (0.27), residues: 321 loop : -0.73 (0.23), residues: 732 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 0.023 0.002 PHE H 393 TYR 0.013 0.001 TYR B 365 ARG 0.014 0.001 ARG B 242 ********************** 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 205 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 236 ARG cc_start: 0.7256 (tpp-160) cc_final: 0.6221 (ttt180) REVERT: D 229 ASP cc_start: 0.7494 (m-30) cc_final: 0.7082 (m-30) REVERT: D 312 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7811 (tm-30) REVERT: D 430 ASP cc_start: 0.8540 (t70) cc_final: 0.8250 (t0) REVERT: F 236 ARG cc_start: 0.7379 (tpp-160) cc_final: 0.6574 (ttt180) REVERT: F 434 VAL cc_start: 0.9466 (t) cc_final: 0.9244 (m) REVERT: F 444 ARG cc_start: 0.4889 (mtt180) cc_final: 0.4101 (mtt180) REVERT: G 375 MET cc_start: 0.8827 (mmm) cc_final: 0.8445 (mmt) REVERT: H 411 LYS cc_start: 0.7771 (pttp) cc_final: 0.6957 (ptpt) REVERT: I 236 ARG cc_start: 0.7506 (tpp-160) cc_final: 0.6335 (tmt170) REVERT: I 287 LEU cc_start: 0.9357 (mt) cc_final: 0.9142 (mm) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.3566 time to fit residues: 96.5981 Evaluate side-chains 171 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.602 ------------------------------------------------------------------------------- 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: 0.0980 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 GLN B 269 GLN ** F 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 GLN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.088223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.065482 restraints weight = 35855.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.064817 restraints weight = 39063.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.065422 restraints weight = 35663.638| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13557 Z= 0.194 Angle : 0.569 11.185 18390 Z= 0.292 Chirality : 0.042 0.137 2199 Planarity : 0.005 0.072 2352 Dihedral : 3.935 20.453 1836 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 1.35 (0.21), residues: 1734 helix: 2.56 (0.20), residues: 681 sheet: 0.68 (0.27), residues: 321 loop : -0.62 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 419 HIS 0.002 0.000 HIS A 252 PHE 0.027 0.002 PHE C 408 TYR 0.013 0.002 TYR A 227 ARG 0.017 0.001 ARG C 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2737.59 seconds wall clock time: 50 minutes 7.70 seconds (3007.70 seconds total)