Starting phenix.real_space_refine on Sun Dec 29 18:40:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r5m_14331/12_2024/7r5m_14331.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r5m_14331/12_2024/7r5m_14331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r5m_14331/12_2024/7r5m_14331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r5m_14331/12_2024/7r5m_14331.map" model { file = "/net/cci-nas-00/data/ceres_data/7r5m_14331/12_2024/7r5m_14331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r5m_14331/12_2024/7r5m_14331.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 24 5.16 5 C 7203 2.51 5 N 1920 2.21 5 O 2148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11295 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: "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: "F" 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: "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: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1076 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 5 Chain: "J" 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: "K" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1076 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 5 Chain: "L" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1076 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 5 Chain: "M" 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 Time building chain proxies: 7.07, per 1000 atoms: 0.63 Number of scatterers: 11295 At special positions: 0 Unit cell: (116.96, 126.42, 115.24, 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 24 16.00 O 2148 8.00 N 1920 7.00 C 7203 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: 2.97 Conformation dependent library (CDL) restraints added in 1.6 seconds 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2796 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 24 sheets defined 44.9% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.733A pdb=" N LYS A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 239 " --> pdb=" O MET A 235 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.754A 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: 3.844A 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: 3.848A 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 'B' and resid 233 through 250 removed outlier: 3.734A pdb=" N LYS B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.721A 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 'F' and resid 275 through 289 Processing helix chain 'F' and resid 294 through 307 removed outlier: 4.199A pdb=" N PHE F 298 " --> pdb=" O PRO F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 329 Processing helix chain 'F' and resid 399 through 419 removed outlier: 4.561A pdb=" N LYS F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ARG F 404 " --> pdb=" O SER F 400 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 407 " --> pdb=" O LYS F 403 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE F 408 " --> pdb=" O ARG F 404 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU F 417 " --> pdb=" O LYS F 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 250 removed outlier: 3.733A pdb=" N LYS G 237 " --> pdb=" O SER G 233 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR G 238 " --> pdb=" O GLY G 234 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE G 239 " --> pdb=" O MET G 235 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG G 242 " --> pdb=" O THR G 238 " (cutoff:3.500A) removed outlier: 3.753A 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: 3.844A 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: 3.848A 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 261 through 272 Processing helix chain 'H' and resid 282 through 298 removed outlier: 3.738A pdb=" N PHE H 286 " --> pdb=" O SER H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 355 removed outlier: 3.502A pdb=" N ALA H 352 " --> pdb=" O VAL H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 439 through 452 Processing helix chain 'H' and resid 453 through 457 Processing helix chain 'J' and resid 275 through 289 Processing helix chain 'J' and resid 294 through 307 removed outlier: 4.199A pdb=" N PHE J 298 " --> pdb=" O PRO J 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 329 Processing helix chain 'J' and resid 399 through 419 removed outlier: 4.561A pdb=" N LYS J 403 " --> pdb=" O LYS J 399 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ARG J 404 " --> pdb=" O SER J 400 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA J 407 " --> pdb=" O LYS J 403 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE J 408 " --> pdb=" O ARG J 404 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU J 417 " --> pdb=" O LYS J 413 " (cutoff:3.500A) Processing helix chain 'K' and resid 261 through 272 Processing helix chain 'K' and resid 282 through 298 removed outlier: 3.738A pdb=" N PHE K 286 " --> pdb=" O SER K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 355 removed outlier: 3.502A pdb=" N ALA K 352 " --> pdb=" O VAL K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 439 through 452 Processing helix chain 'K' and resid 453 through 457 Processing helix chain 'L' and resid 261 through 272 Processing helix chain 'L' and resid 282 through 298 removed outlier: 3.738A pdb=" N PHE L 286 " --> pdb=" O SER L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 355 removed outlier: 3.502A pdb=" N ALA L 352 " --> pdb=" O VAL L 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 439 through 452 Processing helix chain 'L' and resid 453 through 457 Processing helix chain 'M' and resid 275 through 289 Processing helix chain 'M' and resid 294 through 307 removed outlier: 4.199A pdb=" N PHE M 298 " --> pdb=" O PRO M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 329 Processing helix chain 'M' and resid 399 through 419 removed outlier: 4.561A pdb=" N LYS M 403 " --> pdb=" O LYS M 399 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ARG M 404 " --> pdb=" O SER M 400 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA M 407 " --> pdb=" O LYS M 403 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE M 408 " --> pdb=" O ARG M 404 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU M 417 " --> pdb=" O LYS M 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 231 removed outlier: 3.512A pdb=" N VAL A 230 " --> pdb=" O ILE B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 332 through 333 removed outlier: 6.509A pdb=" N SER A 319 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASN A 374 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER A 371 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL A 398 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER A 373 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.698A 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: 6.509A pdb=" N SER A 319 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASN A 374 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER A 371 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL A 398 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER A 373 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER G 383 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 305 removed outlier: 3.546A pdb=" N ILE A 310 " --> pdb=" O VAL G 230 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL G 230 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 323 through 324 Processing sheet with id=AA6, first strand: chain 'A' and resid 383 through 384 removed outlier: 3.777A pdb=" N SER A 383 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 6.563A 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: 8.220A pdb=" N ASN B 374 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 383 through 384 removed outlier: 3.777A pdb=" N SER A 383 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 228 through 231 Processing sheet with id=AA9, first strand: chain 'B' and resid 322 through 324 removed outlier: 3.882A pdb=" N VAL B 322 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 383 through 384 removed outlier: 3.845A pdb=" N SER B 383 " --> pdb=" O SER G 256 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER G 371 " --> pdb=" O LEU G 396 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL G 398 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER G 373 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER G 319 " --> pdb=" O ILE G 372 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ASN G 374 " --> pdb=" O SER G 319 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 383 through 384 removed outlier: 3.845A pdb=" N SER B 383 " --> pdb=" O SER G 256 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR G 414 " --> pdb=" O ASN G 410 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 266 through 271 Processing sheet with id=AB4, first strand: chain 'G' and resid 322 through 324 removed outlier: 3.891A pdb=" N VAL G 322 " --> pdb=" O ILE G 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 257 through 260 removed outlier: 7.015A pdb=" N SER H 373 " --> pdb=" O VAL H 398 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 257 through 260 removed outlier: 3.850A pdb=" N THR H 414 " --> pdb=" O ASN H 410 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 317 through 319 Processing sheet with id=AB8, first strand: chain 'J' and resid 266 through 271 Processing sheet with id=AB9, first strand: chain 'K' and resid 257 through 260 removed outlier: 7.015A pdb=" N SER K 373 " --> pdb=" O VAL K 398 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 257 through 260 removed outlier: 3.850A pdb=" N THR K 414 " --> pdb=" O ASN K 410 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 317 through 319 Processing sheet with id=AC3, first strand: chain 'L' and resid 257 through 260 removed outlier: 7.014A pdb=" N SER L 373 " --> pdb=" O VAL L 398 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 257 through 260 removed outlier: 3.850A pdb=" N THR L 414 " --> pdb=" O ASN L 410 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 317 through 319 Processing sheet with id=AC6, first strand: chain 'M' and resid 266 through 271 632 hydrogen bonds defined for protein. 1758 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: 3.41 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2388 1.33 - 1.45: 2130 1.45 - 1.57: 6885 1.57 - 1.69: 3 1.69 - 1.81: 48 Bond restraints: 11454 Sorted by residual: bond pdb=" N VAL F 327 " pdb=" CA VAL F 327 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.35e+00 bond pdb=" N VAL M 327 " pdb=" CA VAL M 327 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.12e+00 bond pdb=" N VAL J 327 " pdb=" CA VAL J 327 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.24e-02 6.50e+03 7.10e+00 bond pdb=" CB GLN G 366 " pdb=" CG GLN G 366 " ideal model delta sigma weight residual 1.520 1.600 -0.080 3.00e-02 1.11e+03 7.05e+00 bond pdb=" CB GLN A 366 " pdb=" CG GLN A 366 " ideal model delta sigma weight residual 1.520 1.600 -0.080 3.00e-02 1.11e+03 7.04e+00 ... (remaining 11449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 13937 1.42 - 2.83: 1229 2.83 - 4.25: 241 4.25 - 5.67: 85 5.67 - 7.08: 15 Bond angle restraints: 15507 Sorted by residual: angle pdb=" CA MET A 291 " pdb=" C MET A 291 " pdb=" O MET A 291 " ideal model delta sigma weight residual 120.55 116.55 4.00 1.06e+00 8.90e-01 1.42e+01 angle pdb=" CA MET B 291 " pdb=" C MET B 291 " pdb=" O MET B 291 " ideal model delta sigma weight residual 120.55 116.58 3.97 1.06e+00 8.90e-01 1.41e+01 angle pdb=" CA MET G 291 " pdb=" C MET G 291 " pdb=" O MET G 291 " ideal model delta sigma weight residual 120.55 116.61 3.94 1.06e+00 8.90e-01 1.38e+01 angle pdb=" CB GLN B 366 " pdb=" CG GLN B 366 " pdb=" CD GLN B 366 " ideal model delta sigma weight residual 112.60 118.70 -6.10 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CB GLN G 366 " pdb=" CG GLN G 366 " pdb=" CD GLN G 366 " ideal model delta sigma weight residual 112.60 118.68 -6.08 1.70e+00 3.46e-01 1.28e+01 ... (remaining 15502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6479 17.88 - 35.75: 426 35.75 - 53.63: 116 53.63 - 71.50: 41 71.50 - 89.38: 15 Dihedral angle restraints: 7077 sinusoidal: 2799 harmonic: 4278 Sorted by residual: 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 89.38 -89.38 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 445 " pdb=" CG GLU A 445 " pdb=" CD GLU A 445 " pdb=" OE1 GLU A 445 " ideal model delta sinusoidal sigma weight residual 0.00 89.37 -89.37 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU G 445 " pdb=" CG GLU G 445 " pdb=" CD GLU G 445 " pdb=" OE1 GLU G 445 " ideal model delta sinusoidal sigma weight residual 0.00 89.37 -89.37 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 7074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1414 0.058 - 0.117: 344 0.117 - 0.175: 120 0.175 - 0.233: 3 0.233 - 0.292: 6 Chirality restraints: 1887 Sorted by residual: chirality pdb=" CB THR J 345 " pdb=" CA THR J 345 " pdb=" OG1 THR J 345 " pdb=" CG2 THR J 345 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB THR F 345 " pdb=" CA THR F 345 " pdb=" OG1 THR F 345 " pdb=" CG2 THR F 345 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB THR M 345 " pdb=" CA THR M 345 " pdb=" OG1 THR M 345 " pdb=" CG2 THR M 345 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 1884 not shown) Planarity restraints: 1959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 348 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+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 A 348 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.54e+00 pdb=" C VAL A 348 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL A 348 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS A 349 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 348 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C VAL G 348 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL G 348 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS G 349 " 0.014 2.00e-02 2.50e+03 ... (remaining 1956 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 4064 2.91 - 3.41: 10428 3.41 - 3.90: 16167 3.90 - 4.40: 17071 4.40 - 4.90: 30845 Nonbonded interactions: 78575 Sorted by model distance: nonbonded pdb=" OD1 ASP L 420 " pdb=" N GLU L 421 " model vdw 2.411 3.120 nonbonded pdb=" OD1 ASP K 420 " pdb=" N GLU K 421 " model vdw 2.412 3.120 nonbonded pdb=" OD1 ASP H 420 " pdb=" N GLU H 421 " model vdw 2.412 3.120 nonbonded pdb=" CE LYS M 413 " pdb=" OE2 GLU M 417 " model vdw 2.423 3.440 nonbonded pdb=" O GLU J 337 " pdb=" OG SER J 338 " model vdw 2.481 3.040 ... (remaining 78570 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 'G' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'L' } 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 individual isotropic 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: 0.690 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.110 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 11454 Z= 0.412 Angle : 0.945 7.085 15507 Z= 0.534 Chirality : 0.057 0.292 1887 Planarity : 0.004 0.033 1959 Dihedral : 14.644 89.377 4281 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.80 % Allowed : 2.15 % Favored : 97.06 % 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 (0.22), residues: 1437 helix: 0.79 (0.22), residues: 588 sheet: -0.38 (0.35), residues: 192 loop : -1.83 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 442 HIS 0.006 0.001 HIS B 252 PHE 0.017 0.002 PHE F 408 TYR 0.021 0.003 TYR F 316 ARG 0.005 0.001 ARG H 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 256 time to evaluate : 1.273 Fit side-chains REVERT: M 322 GLU cc_start: 0.5810 (tt0) cc_final: 0.5587 (tt0) outliers start: 10 outliers final: 1 residues processed: 261 average time/residue: 0.2513 time to fit residues: 90.3585 Evaluate side-chains 197 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 332 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 2.9990 chunk 111 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 85 optimal weight: 0.0670 chunk 133 optimal weight: 2.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11454 Z= 0.159 Angle : 0.529 6.117 15507 Z= 0.274 Chirality : 0.044 0.161 1887 Planarity : 0.004 0.040 1959 Dihedral : 3.840 38.931 1537 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.67 % Allowed : 7.56 % Favored : 90.77 % 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: 0.59 (0.23), residues: 1437 helix: 2.27 (0.22), residues: 594 sheet: 0.02 (0.33), residues: 192 loop : -1.35 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 305 HIS 0.001 0.000 HIS B 252 PHE 0.011 0.001 PHE G 384 TYR 0.012 0.001 TYR B 365 ARG 0.004 0.000 ARG M 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 1.409 Fit side-chains REVERT: A 329 ILE cc_start: 0.7566 (mm) cc_final: 0.7294 (mm) REVERT: B 329 ILE cc_start: 0.7521 (mm) cc_final: 0.7236 (mm) REVERT: B 451 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7182 (mm-30) REVERT: G 329 ILE cc_start: 0.7481 (mm) cc_final: 0.7255 (mm) REVERT: J 293 LEU cc_start: 0.7724 (pp) cc_final: 0.7342 (pp) outliers start: 21 outliers final: 18 residues processed: 223 average time/residue: 0.2804 time to fit residues: 85.1987 Evaluate side-chains 203 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain J residue 274 SER Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain J residue 415 VAL Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain L residue 348 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain M residue 291 VAL Chi-restraints excluded: chain M residue 414 LEU Chi-restraints excluded: chain M residue 415 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 144 optimal weight: 0.3980 chunk 119 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 269 GLN F 307 ASN F 325 ASN J 307 ASN M 283 ASN M 307 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11454 Z= 0.187 Angle : 0.520 5.922 15507 Z= 0.266 Chirality : 0.044 0.146 1887 Planarity : 0.004 0.041 1959 Dihedral : 3.960 38.018 1537 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.55 % Allowed : 9.23 % Favored : 88.23 % 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: 1.07 (0.22), residues: 1437 helix: 2.47 (0.21), residues: 618 sheet: 0.52 (0.32), residues: 207 loop : -1.14 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 442 HIS 0.002 0.001 HIS G 252 PHE 0.011 0.002 PHE A 384 TYR 0.011 0.001 TYR G 365 ARG 0.005 0.000 ARG M 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 1.516 Fit side-chains REVERT: B 329 ILE cc_start: 0.7512 (mm) cc_final: 0.7237 (tp) REVERT: H 451 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.5584 (mp0) REVERT: J 293 LEU cc_start: 0.7795 (pp) cc_final: 0.7344 (pp) REVERT: J 339 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7655 (mtp180) REVERT: K 451 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.5366 (mp0) REVERT: L 451 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.5216 (mp0) outliers start: 32 outliers final: 21 residues processed: 236 average time/residue: 0.2767 time to fit residues: 89.3132 Evaluate side-chains 209 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain G residue 235 MET Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 424 ILE Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 345 THR Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 348 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 451 GLU Chi-restraints excluded: chain M residue 283 ASN Chi-restraints excluded: chain M residue 291 VAL Chi-restraints excluded: chain M residue 414 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 38 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 269 GLN G 269 GLN J 283 ASN J 307 ASN M 283 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11454 Z= 0.133 Angle : 0.467 5.862 15507 Z= 0.238 Chirality : 0.042 0.167 1887 Planarity : 0.004 0.042 1959 Dihedral : 3.692 36.994 1537 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.07 % Allowed : 10.66 % Favored : 87.27 % 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: 1.49 (0.23), residues: 1437 helix: 2.96 (0.21), residues: 609 sheet: 0.47 (0.29), residues: 234 loop : -0.98 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 442 HIS 0.002 0.000 HIS B 252 PHE 0.030 0.001 PHE J 393 TYR 0.010 0.001 TYR B 365 ARG 0.006 0.000 ARG K 297 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 1.486 Fit side-chains REVERT: B 329 ILE cc_start: 0.7517 (mm) cc_final: 0.7241 (tp) REVERT: B 359 LYS cc_start: 0.7574 (ptpp) cc_final: 0.7216 (ptpt) REVERT: F 337 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6051 (mm-30) REVERT: G 359 LYS cc_start: 0.7377 (ptpp) cc_final: 0.7101 (ptpt) REVERT: H 451 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.5578 (mp0) REVERT: J 293 LEU cc_start: 0.7826 (pp) cc_final: 0.7436 (pp) REVERT: J 339 ARG cc_start: 0.7960 (mtp180) cc_final: 0.7666 (mtp180) REVERT: K 349 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7202 (mtpp) REVERT: K 451 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.5293 (mp0) REVERT: L 451 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.5194 (mp0) outliers start: 26 outliers final: 17 residues processed: 224 average time/residue: 0.2747 time to fit residues: 83.4526 Evaluate side-chains 204 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain J residue 274 SER Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 349 LYS Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 348 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 451 GLU Chi-restraints excluded: chain M residue 283 ASN Chi-restraints excluded: chain M residue 414 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 98 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 269 GLN J 307 ASN M 283 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11454 Z= 0.139 Angle : 0.456 5.801 15507 Z= 0.235 Chirality : 0.042 0.131 1887 Planarity : 0.004 0.044 1959 Dihedral : 3.610 36.682 1537 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.07 % Allowed : 12.65 % Favored : 85.28 % 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: 1.68 (0.23), residues: 1437 helix: 3.12 (0.21), residues: 609 sheet: 0.74 (0.30), residues: 219 loop : -0.92 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 442 HIS 0.001 0.000 HIS F 286 PHE 0.013 0.001 PHE B 253 TYR 0.009 0.001 TYR B 365 ARG 0.006 0.000 ARG H 297 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 1.238 Fit side-chains REVERT: B 359 LYS cc_start: 0.7571 (ptpp) cc_final: 0.7185 (ptpt) REVERT: F 337 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6059 (mm-30) REVERT: G 359 LYS cc_start: 0.7343 (ptpp) cc_final: 0.7035 (ptpt) REVERT: H 451 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.5497 (mp0) REVERT: J 339 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7650 (mtp180) REVERT: K 349 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7213 (mtpp) REVERT: K 451 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.5292 (mp0) REVERT: L 451 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.5182 (mp0) REVERT: M 284 LYS cc_start: 0.8091 (tttm) cc_final: 0.7814 (tmtt) REVERT: M 288 THR cc_start: 0.7603 (m) cc_final: 0.7345 (m) outliers start: 26 outliers final: 18 residues processed: 220 average time/residue: 0.2881 time to fit residues: 85.9485 Evaluate side-chains 207 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 307 ASN Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 349 LYS Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 348 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 451 GLU Chi-restraints excluded: chain M residue 283 ASN Chi-restraints excluded: chain M residue 291 VAL Chi-restraints excluded: chain M residue 414 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 137 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN G 269 GLN J 283 ASN J 307 ASN M 283 ASN ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11454 Z= 0.154 Angle : 0.461 5.777 15507 Z= 0.237 Chirality : 0.042 0.125 1887 Planarity : 0.004 0.037 1959 Dihedral : 3.629 36.389 1537 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.55 % Allowed : 12.81 % Favored : 84.65 % 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: 1.77 (0.23), residues: 1437 helix: 3.17 (0.21), residues: 609 sheet: 0.83 (0.30), residues: 219 loop : -0.86 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 305 HIS 0.001 0.000 HIS B 252 PHE 0.017 0.001 PHE J 393 TYR 0.008 0.001 TYR B 365 ARG 0.005 0.000 ARG H 297 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 1.403 Fit side-chains REVERT: B 359 LYS cc_start: 0.7600 (ptpp) cc_final: 0.7171 (ptpt) REVERT: B 445 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7372 (mm-30) REVERT: F 337 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6113 (mm-30) REVERT: G 359 LYS cc_start: 0.7385 (ptpp) cc_final: 0.7096 (ptpt) REVERT: H 451 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.5420 (mp0) REVERT: J 339 ARG cc_start: 0.7968 (mtp180) cc_final: 0.7619 (mtp180) REVERT: K 349 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7250 (mtpp) REVERT: K 451 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.5326 (mp0) REVERT: L 451 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.5210 (mp0) outliers start: 32 outliers final: 23 residues processed: 217 average time/residue: 0.2816 time to fit residues: 82.4710 Evaluate side-chains 208 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 349 LYS Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 348 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 451 GLU Chi-restraints excluded: chain M residue 283 ASN Chi-restraints excluded: chain M residue 291 VAL Chi-restraints excluded: chain M residue 333 VAL Chi-restraints excluded: chain M residue 414 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 119 optimal weight: 0.0170 chunk 79 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 269 GLN J 307 ASN M 283 ASN ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11454 Z= 0.157 Angle : 0.464 5.764 15507 Z= 0.238 Chirality : 0.042 0.124 1887 Planarity : 0.004 0.037 1959 Dihedral : 3.640 36.115 1537 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.63 % Allowed : 13.29 % Favored : 84.09 % 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: 1.79 (0.22), residues: 1437 helix: 3.16 (0.21), residues: 609 sheet: 0.85 (0.29), residues: 219 loop : -0.82 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 305 HIS 0.001 0.000 HIS B 252 PHE 0.016 0.001 PHE F 393 TYR 0.008 0.001 TYR B 365 ARG 0.005 0.000 ARG H 297 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.445 Fit side-chains REVERT: B 359 LYS cc_start: 0.7612 (ptpp) cc_final: 0.7167 (ptpt) REVERT: B 445 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7372 (mm-30) REVERT: F 337 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6096 (mm-30) REVERT: G 359 LYS cc_start: 0.7424 (ptpp) cc_final: 0.7126 (ptpt) REVERT: H 451 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.5419 (mp0) REVERT: J 293 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7557 (pp) REVERT: J 339 ARG cc_start: 0.7962 (mtp180) cc_final: 0.7603 (mtp180) REVERT: K 349 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7194 (mtpp) REVERT: K 451 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.5289 (mp0) REVERT: L 278 ARG cc_start: 0.7114 (mtp180) cc_final: 0.6884 (ttp-170) REVERT: L 336 VAL cc_start: 0.8165 (m) cc_final: 0.7869 (t) REVERT: L 451 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5193 (mp0) outliers start: 33 outliers final: 25 residues processed: 213 average time/residue: 0.2790 time to fit residues: 80.5618 Evaluate side-chains 209 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 307 ASN Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 349 LYS Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 348 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 451 GLU Chi-restraints excluded: chain M residue 283 ASN Chi-restraints excluded: chain M residue 291 VAL Chi-restraints excluded: chain M residue 333 VAL Chi-restraints excluded: chain M residue 414 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 111 optimal weight: 0.0470 chunk 128 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 overall best weight: 1.2880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 ASN ** J 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 283 ASN ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11454 Z= 0.192 Angle : 0.482 5.780 15507 Z= 0.248 Chirality : 0.042 0.125 1887 Planarity : 0.004 0.036 1959 Dihedral : 3.757 35.915 1537 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.47 % Allowed : 13.68 % Favored : 83.85 % 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: 1.69 (0.22), residues: 1437 helix: 3.08 (0.20), residues: 609 sheet: 0.86 (0.29), residues: 219 loop : -0.91 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 305 HIS 0.002 0.001 HIS B 252 PHE 0.016 0.001 PHE J 393 TYR 0.008 0.001 TYR B 365 ARG 0.005 0.000 ARG L 297 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 1.216 Fit side-chains REVERT: B 359 LYS cc_start: 0.7690 (ptpp) cc_final: 0.7209 (ptpt) REVERT: B 445 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7399 (mm-30) REVERT: G 359 LYS cc_start: 0.7500 (ptpp) cc_final: 0.7185 (ptpt) REVERT: H 451 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.5338 (mp0) REVERT: J 293 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7550 (pp) REVERT: J 339 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7617 (mtp180) REVERT: K 336 VAL cc_start: 0.8233 (m) cc_final: 0.8026 (t) REVERT: K 349 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7142 (mtpp) REVERT: K 451 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.5252 (mp0) REVERT: L 278 ARG cc_start: 0.7177 (mtp180) cc_final: 0.6829 (ttp-170) REVERT: L 336 VAL cc_start: 0.8226 (m) cc_final: 0.7988 (t) REVERT: L 451 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.5191 (mp0) outliers start: 31 outliers final: 24 residues processed: 220 average time/residue: 0.2864 time to fit residues: 85.9711 Evaluate side-chains 213 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 349 LYS Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 348 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 451 GLU Chi-restraints excluded: chain M residue 283 ASN Chi-restraints excluded: chain M residue 291 VAL Chi-restraints excluded: chain M residue 333 VAL Chi-restraints excluded: chain M residue 414 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 0.0970 chunk 86 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN ** F 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN G 392 GLN J 307 ASN M 283 ASN ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11454 Z= 0.206 Angle : 0.500 5.799 15507 Z= 0.257 Chirality : 0.042 0.126 1887 Planarity : 0.004 0.036 1959 Dihedral : 3.847 35.351 1537 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.55 % Allowed : 14.16 % Favored : 83.29 % 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: 1.60 (0.22), residues: 1437 helix: 2.98 (0.20), residues: 609 sheet: 0.88 (0.29), residues: 219 loop : -0.95 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 305 HIS 0.003 0.001 HIS M 286 PHE 0.016 0.001 PHE J 393 TYR 0.008 0.001 TYR B 365 ARG 0.005 0.000 ARG L 297 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 1.306 Fit side-chains REVERT: B 359 LYS cc_start: 0.7754 (ptpp) cc_final: 0.7399 (ptpt) REVERT: B 445 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7411 (mm-30) REVERT: F 284 LYS cc_start: 0.8519 (tppt) cc_final: 0.8309 (tttm) REVERT: F 337 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6055 (mm-30) REVERT: H 451 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.5312 (mp0) REVERT: J 283 ASN cc_start: 0.7115 (p0) cc_final: 0.6866 (m-40) REVERT: K 349 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7173 (mtpp) REVERT: K 451 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.5264 (mp0) REVERT: L 278 ARG cc_start: 0.7213 (mtp180) cc_final: 0.6879 (ttp-170) REVERT: L 336 VAL cc_start: 0.8281 (m) cc_final: 0.8034 (t) REVERT: L 451 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.5143 (mp0) outliers start: 32 outliers final: 24 residues processed: 217 average time/residue: 0.2804 time to fit residues: 82.6703 Evaluate side-chains 211 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 307 ASN Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 349 LYS Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 348 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 451 GLU Chi-restraints excluded: chain M residue 283 ASN Chi-restraints excluded: chain M residue 291 VAL Chi-restraints excluded: chain M residue 333 VAL Chi-restraints excluded: chain M residue 414 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 146 optimal weight: 0.0370 chunk 134 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 307 ASN M 283 ASN ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11454 Z= 0.227 Angle : 0.515 5.820 15507 Z= 0.266 Chirality : 0.043 0.131 1887 Planarity : 0.004 0.036 1959 Dihedral : 3.935 34.983 1537 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.31 % Allowed : 14.40 % Favored : 83.29 % 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: 1.49 (0.22), residues: 1437 helix: 2.87 (0.20), residues: 609 sheet: 0.87 (0.28), residues: 219 loop : -1.01 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 305 HIS 0.003 0.001 HIS B 252 PHE 0.015 0.002 PHE J 393 TYR 0.007 0.001 TYR B 365 ARG 0.005 0.000 ARG H 297 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 1.424 Fit side-chains REVERT: B 445 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7424 (mm-30) REVERT: F 337 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.6051 (mm-30) REVERT: H 336 VAL cc_start: 0.8367 (m) cc_final: 0.8121 (t) REVERT: H 451 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.5097 (mp0) REVERT: J 283 ASN cc_start: 0.7152 (p0) cc_final: 0.6879 (m-40) REVERT: J 284 LYS cc_start: 0.8430 (tppt) cc_final: 0.8178 (tppt) REVERT: K 451 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.5251 (mp0) REVERT: L 278 ARG cc_start: 0.7198 (mtp180) cc_final: 0.6894 (ttp-170) REVERT: L 336 VAL cc_start: 0.8322 (m) cc_final: 0.8096 (t) REVERT: L 451 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.5128 (mp0) outliers start: 29 outliers final: 23 residues processed: 218 average time/residue: 0.2743 time to fit residues: 81.8525 Evaluate side-chains 217 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 307 ASN Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 348 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 451 GLU Chi-restraints excluded: chain M residue 283 ASN Chi-restraints excluded: chain M residue 291 VAL Chi-restraints excluded: chain M residue 333 VAL Chi-restraints excluded: chain M residue 414 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 392 GLN ** F 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 307 ASN M 283 ASN ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.168757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.119740 restraints weight = 14390.826| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.44 r_work: 0.3032 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11454 Z= 0.189 Angle : 0.494 5.791 15507 Z= 0.255 Chirality : 0.042 0.133 1887 Planarity : 0.004 0.037 1959 Dihedral : 3.883 34.299 1537 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.15 % Allowed : 15.04 % Favored : 82.82 % 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: 1.57 (0.22), residues: 1437 helix: 2.94 (0.20), residues: 609 sheet: 0.89 (0.29), residues: 219 loop : -0.97 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 305 HIS 0.002 0.001 HIS B 252 PHE 0.015 0.001 PHE B 253 TYR 0.008 0.001 TYR B 365 ARG 0.005 0.000 ARG H 297 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2627.97 seconds wall clock time: 48 minutes 39.98 seconds (2919.98 seconds total)