Starting phenix.real_space_refine on Tue Jun 10 00:51:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r5m_14331/06_2025/7r5m_14331.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r5m_14331/06_2025/7r5m_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_14331/06_2025/7r5m_14331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r5m_14331/06_2025/7r5m_14331.map" model { file = "/net/cci-nas-00/data/ceres_data/7r5m_14331/06_2025/7r5m_14331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r5m_14331/06_2025/7r5m_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 2.51 Conformation dependent library (CDL) restraints added in 1.4 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: 1.37 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: 3.31 Time building geometry restraints manager: 3.02 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: 0.02 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.800 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.100 ------------------------------------------------------------------------------- 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= 0.321 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 Details of bonding type rmsd hydrogen bonds : bond 0.18894 ( 596) hydrogen bonds : angle 6.05898 ( 1758) covalent geometry : bond 0.00642 (11454) covalent geometry : angle 0.94465 (15507) *********************** 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 : 1.214 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: 0.2471 time to fit residues: 89.1736 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 : 1.380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.178613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.129326 restraints weight = 14157.330| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.36 r_work: 0.3167 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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= 0.109 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 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 596) hydrogen bonds : angle 3.78511 ( 1758) covalent geometry : bond 0.00240 (11454) covalent geometry : angle 0.52868 (15507) *********************** 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 : 1.375 Fit side-chains REVERT: A 329 ILE cc_start: 0.7579 (mm) cc_final: 0.7342 (mm) REVERT: A 366 GLN cc_start: 0.7250 (mm110) cc_final: 0.6902 (mm-40) REVERT: B 329 ILE cc_start: 0.7520 (mm) cc_final: 0.7259 (mm) REVERT: B 444 ARG cc_start: 0.8112 (ttp-170) cc_final: 0.7828 (ttp-170) REVERT: B 451 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7584 (mm-30) REVERT: G 329 ILE cc_start: 0.7524 (mm) cc_final: 0.7309 (mm) REVERT: G 445 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8187 (mm-30) REVERT: H 334 LYS cc_start: 0.7140 (mttm) cc_final: 0.6939 (mtpt) REVERT: J 283 ASN cc_start: 0.7844 (m110) cc_final: 0.7581 (p0) REVERT: J 293 LEU cc_start: 0.7367 (pp) cc_final: 0.6855 (pp) REVERT: K 334 LYS cc_start: 0.7307 (mttm) cc_final: 0.7052 (mtpt) REVERT: L 334 LYS cc_start: 0.7498 (mttm) cc_final: 0.7136 (mptt) REVERT: M 322 GLU cc_start: 0.7279 (tt0) cc_final: 0.6833 (tt0) REVERT: M 406 GLN cc_start: 0.7824 (tt0) cc_final: 0.7558 (tp40) outliers start: 21 outliers final: 18 residues processed: 223 average time/residue: 0.2676 time to fit residues: 81.4714 Evaluate side-chains 208 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 1 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 54 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 M 283 ASN M 307 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.173671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.124508 restraints weight = 14418.682| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.27 r_work: 0.3161 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11454 Z= 0.103 Angle : 0.492 5.932 15507 Z= 0.249 Chirality : 0.043 0.140 1887 Planarity : 0.004 0.038 1959 Dihedral : 3.756 38.113 1537 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.47 % Allowed : 8.91 % Favored : 88.62 % 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: 1.19 (0.23), residues: 1437 helix: 2.64 (0.21), residues: 615 sheet: 0.53 (0.32), residues: 207 loop : -1.12 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 442 HIS 0.002 0.001 HIS A 252 PHE 0.010 0.001 PHE A 253 TYR 0.012 0.001 TYR B 365 ARG 0.005 0.000 ARG H 297 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 596) hydrogen bonds : angle 3.38808 ( 1758) covalent geometry : bond 0.00235 (11454) covalent geometry : angle 0.49187 (15507) *********************** 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 245 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 1.285 Fit side-chains revert: symmetry clash REVERT: A 329 ILE cc_start: 0.7519 (mm) cc_final: 0.7176 (tp) REVERT: B 329 ILE cc_start: 0.7438 (mm) cc_final: 0.7053 (tp) REVERT: F 283 ASN cc_start: 0.7209 (p0) cc_final: 0.6794 (m-40) REVERT: F 284 LYS cc_start: 0.8533 (tttm) cc_final: 0.8229 (tttm) REVERT: G 329 ILE cc_start: 0.7538 (mm) cc_final: 0.7189 (tp) REVERT: G 445 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7997 (mm-30) REVERT: H 451 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.5725 (mp0) REVERT: J 293 LEU cc_start: 0.7491 (pp) cc_final: 0.6937 (pp) REVERT: K 451 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.5496 (mp0) REVERT: L 334 LYS cc_start: 0.7550 (mttm) cc_final: 0.7273 (mtpt) REVERT: L 451 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.5324 (mp0) REVERT: M 322 GLU cc_start: 0.7054 (tt0) cc_final: 0.6614 (tt0) REVERT: M 406 GLN cc_start: 0.7814 (tt0) cc_final: 0.7602 (tp40) outliers start: 31 outliers final: 19 residues processed: 234 average time/residue: 0.2833 time to fit residues: 90.6291 Evaluate side-chains 213 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 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 274 SER 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 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 122 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 137 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS A 269 GLN B 269 GLN ** F 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN J 283 ASN J 307 ASN M 283 ASN M 307 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.168745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.118914 restraints weight = 14310.744| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.37 r_work: 0.3012 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11454 Z= 0.149 Angle : 0.545 5.902 15507 Z= 0.279 Chirality : 0.044 0.176 1887 Planarity : 0.004 0.043 1959 Dihedral : 4.063 37.105 1537 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.78 % Allowed : 10.98 % Favored : 86.24 % 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: 1.19 (0.22), residues: 1437 helix: 2.63 (0.20), residues: 609 sheet: 0.43 (0.29), residues: 222 loop : -1.07 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 305 HIS 0.002 0.001 HIS M 286 PHE 0.014 0.002 PHE B 253 TYR 0.009 0.001 TYR B 365 ARG 0.007 0.000 ARG K 297 Details of bonding type rmsd hydrogen bonds : bond 0.04703 ( 596) hydrogen bonds : angle 3.54179 ( 1758) covalent geometry : bond 0.00373 (11454) covalent geometry : angle 0.54514 (15507) *********************** 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 248 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 1.449 Fit side-chains revert: symmetry clash REVERT: A 329 ILE cc_start: 0.7536 (mm) cc_final: 0.7273 (tp) REVERT: A 349 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7781 (tttt) REVERT: B 329 ILE cc_start: 0.7562 (mm) cc_final: 0.7192 (tp) REVERT: F 322 GLU cc_start: 0.7254 (tt0) cc_final: 0.6740 (tt0) REVERT: G 445 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8113 (mm-30) REVERT: H 451 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.5366 (mp0) REVERT: H 455 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8323 (mm-30) REVERT: J 293 LEU cc_start: 0.7409 (pp) cc_final: 0.6854 (pp) REVERT: J 339 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7840 (mtp180) REVERT: K 451 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.5451 (mp0) REVERT: L 334 LYS cc_start: 0.7716 (mttm) cc_final: 0.7447 (mtpt) REVERT: L 451 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.5287 (mp0) REVERT: M 283 ASN cc_start: 0.7618 (OUTLIER) cc_final: 0.7282 (p0) outliers start: 35 outliers final: 27 residues processed: 234 average time/residue: 0.2905 time to fit residues: 92.2666 Evaluate side-chains 223 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 337 GLU 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 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 414 THR Chi-restraints excluded: chain H residue 424 ILE 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 288 THR Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 307 ASN 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 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 307 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 126 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 chunk 23 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN 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 = 0.3865 r_free = 0.3865 target = 0.170690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.121097 restraints weight = 14294.213| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.26 r_work: 0.3075 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11454 Z= 0.100 Angle : 0.480 5.822 15507 Z= 0.248 Chirality : 0.042 0.137 1887 Planarity : 0.004 0.040 1959 Dihedral : 3.817 36.057 1537 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.39 % Allowed : 12.57 % Favored : 85.04 % 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: 2.93 (0.20), residues: 609 sheet: 0.77 (0.29), residues: 219 loop : -1.04 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 442 HIS 0.002 0.000 HIS B 252 PHE 0.013 0.001 PHE B 253 TYR 0.009 0.001 TYR B 365 ARG 0.006 0.000 ARG H 297 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 596) hydrogen bonds : angle 3.31011 ( 1758) covalent geometry : bond 0.00236 (11454) covalent geometry : angle 0.48001 (15507) *********************** 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 232 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: A 349 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7783 (tttt) REVERT: F 283 ASN cc_start: 0.7339 (p0) cc_final: 0.6859 (m-40) REVERT: H 451 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.5293 (mp0) REVERT: H 455 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8350 (mm-30) REVERT: J 287 LYS cc_start: 0.8289 (tppt) cc_final: 0.8081 (mmmt) REVERT: J 339 ARG cc_start: 0.8127 (mtp180) cc_final: 0.7799 (mtp180) REVERT: J 393 PHE cc_start: 0.6514 (m-80) cc_final: 0.6235 (m-80) REVERT: K 349 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7144 (mtpp) REVERT: K 451 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.5399 (mp0) REVERT: L 334 LYS cc_start: 0.7639 (mttm) cc_final: 0.7376 (mtpt) REVERT: M 293 LEU cc_start: 0.7744 (pt) cc_final: 0.7411 (pp) REVERT: M 339 ARG cc_start: 0.7836 (mtp-110) cc_final: 0.7617 (mtp180) outliers start: 30 outliers final: 20 residues processed: 222 average time/residue: 0.2613 time to fit residues: 78.8320 Evaluate side-chains 209 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 332 LYS 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 375 MET 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 291 VAL 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 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 136 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 81 optimal weight: 0.0370 chunk 137 optimal weight: 6.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.170486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.121005 restraints weight = 14311.745| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.51 r_work: 0.3040 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3554 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= 0.111 Angle : 0.484 5.807 15507 Z= 0.249 Chirality : 0.042 0.128 1887 Planarity : 0.004 0.037 1959 Dihedral : 3.812 35.590 1537 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.55 % Allowed : 13.29 % Favored : 84.17 % 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: 1.53 (0.22), residues: 1437 helix: 2.98 (0.20), residues: 609 sheet: 0.76 (0.29), residues: 219 loop : -1.02 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 305 HIS 0.002 0.001 HIS B 252 PHE 0.014 0.002 PHE B 253 TYR 0.008 0.001 TYR B 365 ARG 0.006 0.000 ARG H 297 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 596) hydrogen bonds : angle 3.29024 ( 1758) covalent geometry : bond 0.00272 (11454) covalent geometry : angle 0.48406 (15507) *********************** 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 233 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 1.585 Fit side-chains revert: symmetry clash REVERT: A 349 LYS cc_start: 0.8104 (mtmt) cc_final: 0.7802 (tttt) REVERT: B 359 LYS cc_start: 0.7608 (ptpp) cc_final: 0.6821 (ptpt) REVERT: H 451 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.5334 (mp0) REVERT: H 455 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8401 (mm-30) REVERT: J 287 LYS cc_start: 0.8302 (tppt) cc_final: 0.8075 (mmmt) REVERT: J 339 ARG cc_start: 0.8138 (mtp180) cc_final: 0.7800 (mtp180) REVERT: K 349 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7060 (mtpp) REVERT: K 451 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.5413 (mp0) REVERT: L 278 ARG cc_start: 0.7447 (mtp180) cc_final: 0.6796 (ttp-170) REVERT: L 334 LYS cc_start: 0.7609 (mttm) cc_final: 0.7322 (mtpt) REVERT: L 455 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8666 (mm-30) REVERT: M 339 ARG cc_start: 0.7821 (mtp-110) cc_final: 0.7613 (mtp180) outliers start: 32 outliers final: 25 residues processed: 224 average time/residue: 0.2897 time to fit residues: 87.7807 Evaluate side-chains 212 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 375 MET 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 291 VAL 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 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 17 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN ** F 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.168960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.118819 restraints weight = 14585.958| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.47 r_work: 0.3058 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11454 Z= 0.120 Angle : 0.496 5.812 15507 Z= 0.256 Chirality : 0.043 0.129 1887 Planarity : 0.004 0.036 1959 Dihedral : 3.874 35.196 1537 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.47 % Allowed : 14.40 % Favored : 83.13 % 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: 1.51 (0.22), residues: 1437 helix: 2.95 (0.20), residues: 609 sheet: 0.74 (0.28), residues: 219 loop : -1.03 (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 A 431 PHE 0.014 0.001 PHE B 253 TYR 0.008 0.001 TYR B 365 ARG 0.005 0.000 ARG H 297 Details of bonding type rmsd hydrogen bonds : bond 0.03916 ( 596) hydrogen bonds : angle 3.31643 ( 1758) covalent geometry : bond 0.00296 (11454) covalent geometry : angle 0.49551 (15507) *********************** 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 230 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 1.411 Fit side-chains revert: symmetry clash REVERT: A 349 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7820 (tttt) REVERT: F 322 GLU cc_start: 0.7257 (tt0) cc_final: 0.6843 (tt0) REVERT: G 445 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8077 (mm-30) REVERT: H 451 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.5311 (mp0) REVERT: H 455 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8417 (mm-30) REVERT: J 287 LYS cc_start: 0.8324 (tppt) cc_final: 0.8110 (mmmt) REVERT: J 293 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7205 (pp) REVERT: J 339 ARG cc_start: 0.8131 (mtp180) cc_final: 0.7767 (mtp180) REVERT: K 451 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.5424 (mp0) REVERT: L 278 ARG cc_start: 0.7484 (mtp180) cc_final: 0.6890 (ttp-170) REVERT: L 334 LYS cc_start: 0.7655 (mttm) cc_final: 0.7406 (mtpt) REVERT: L 455 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8700 (mm-30) REVERT: M 339 ARG cc_start: 0.7832 (mtp-110) cc_final: 0.7625 (mtp180) outliers start: 31 outliers final: 24 residues processed: 221 average time/residue: 0.2692 time to fit residues: 80.9204 Evaluate side-chains 214 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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 293 LEU Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 392 VAL 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 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 45 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** 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 = 0.3868 r_free = 0.3868 target = 0.171099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.121880 restraints weight = 14402.834| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.39 r_work: 0.3067 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11454 Z= 0.097 Angle : 0.468 5.780 15507 Z= 0.241 Chirality : 0.042 0.127 1887 Planarity : 0.004 0.038 1959 Dihedral : 3.731 34.465 1537 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.07 % Allowed : 15.19 % Favored : 82.74 % 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: 1.64 (0.22), residues: 1437 helix: 3.07 (0.21), residues: 609 sheet: 0.77 (0.28), residues: 219 loop : -0.95 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 442 HIS 0.002 0.001 HIS M 286 PHE 0.018 0.001 PHE F 393 TYR 0.008 0.001 TYR B 365 ARG 0.004 0.000 ARG H 297 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 596) hydrogen bonds : angle 3.19711 ( 1758) covalent geometry : bond 0.00233 (11454) covalent geometry : angle 0.46806 (15507) *********************** 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 226 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: A 349 LYS cc_start: 0.8058 (mtmt) cc_final: 0.7806 (tttt) REVERT: B 359 LYS cc_start: 0.7592 (ptpp) cc_final: 0.6852 (ptpt) REVERT: F 337 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6057 (mm-30) REVERT: G 445 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8089 (mm-30) REVERT: H 451 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.5246 (mp0) REVERT: H 455 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8420 (mm-30) REVERT: J 339 ARG cc_start: 0.8112 (mtp180) cc_final: 0.7757 (mtp180) REVERT: K 349 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7088 (mtpp) REVERT: K 451 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.5385 (mp0) REVERT: L 278 ARG cc_start: 0.7453 (mtp180) cc_final: 0.6890 (ttp-170) REVERT: L 336 VAL cc_start: 0.8321 (m) cc_final: 0.8033 (t) REVERT: L 455 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8715 (mm-30) REVERT: M 339 ARG cc_start: 0.7834 (mtp-110) cc_final: 0.7632 (mtp180) outliers start: 26 outliers final: 21 residues processed: 220 average time/residue: 0.2755 time to fit residues: 82.0750 Evaluate side-chains 212 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 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 307 ASN Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 333 VAL 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 M residue 283 ASN Chi-restraints excluded: chain M residue 291 VAL Chi-restraints excluded: chain M residue 333 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 39 optimal weight: 0.0060 chunk 53 optimal weight: 7.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN ** F 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.171001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.121462 restraints weight = 14336.807| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.38 r_work: 0.3064 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11454 Z= 0.094 Angle : 0.462 5.782 15507 Z= 0.238 Chirality : 0.041 0.125 1887 Planarity : 0.004 0.037 1959 Dihedral : 3.658 34.239 1537 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.99 % Allowed : 15.67 % Favored : 82.34 % 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: 1.73 (0.22), residues: 1437 helix: 3.10 (0.21), residues: 609 sheet: 0.83 (0.28), residues: 219 loop : -0.85 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 419 HIS 0.002 0.000 HIS B 252 PHE 0.018 0.001 PHE F 393 TYR 0.008 0.001 TYR B 365 ARG 0.004 0.000 ARG H 297 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 596) hydrogen bonds : angle 3.14545 ( 1758) covalent geometry : bond 0.00224 (11454) covalent geometry : angle 0.46215 (15507) *********************** 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 222 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 349 LYS cc_start: 0.8067 (mtmt) cc_final: 0.7833 (tttt) REVERT: B 359 LYS cc_start: 0.7571 (ptpp) cc_final: 0.6773 (ptpt) REVERT: F 322 GLU cc_start: 0.7302 (tt0) cc_final: 0.6896 (tt0) REVERT: F 337 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6080 (mm-30) REVERT: G 445 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8265 (mm-30) REVERT: H 336 VAL cc_start: 0.8445 (m) cc_final: 0.8148 (t) REVERT: H 451 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.5324 (mp0) REVERT: H 455 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8488 (mm-30) REVERT: J 339 ARG cc_start: 0.8124 (mtp180) cc_final: 0.7776 (mtp180) REVERT: K 336 VAL cc_start: 0.8422 (m) cc_final: 0.8152 (t) REVERT: K 349 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7140 (mtpp) REVERT: K 451 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.5465 (mp0) REVERT: L 278 ARG cc_start: 0.7426 (mtp180) cc_final: 0.6853 (ttp-170) REVERT: L 336 VAL cc_start: 0.8342 (m) cc_final: 0.8070 (t) REVERT: L 455 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8801 (mm-30) REVERT: M 322 GLU cc_start: 0.7205 (tt0) cc_final: 0.6814 (tt0) outliers start: 25 outliers final: 17 residues processed: 215 average time/residue: 0.2846 time to fit residues: 83.3584 Evaluate side-chains 206 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 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 333 VAL 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 M residue 283 ASN Chi-restraints excluded: chain M residue 291 VAL Chi-restraints excluded: chain M residue 333 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.170832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.120752 restraints weight = 14279.362| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.26 r_work: 0.3096 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3872 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= 0.107 Angle : 0.479 5.782 15507 Z= 0.247 Chirality : 0.042 0.125 1887 Planarity : 0.004 0.037 1959 Dihedral : 3.690 33.873 1537 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.91 % Allowed : 16.07 % Favored : 82.02 % 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: 1.72 (0.22), residues: 1437 helix: 3.06 (0.21), residues: 609 sheet: 0.86 (0.28), residues: 219 loop : -0.82 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 305 HIS 0.003 0.001 HIS M 286 PHE 0.016 0.001 PHE F 393 TYR 0.008 0.001 TYR B 365 ARG 0.005 0.000 ARG H 297 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 596) hydrogen bonds : angle 3.16582 ( 1758) covalent geometry : bond 0.00262 (11454) covalent geometry : angle 0.47919 (15507) ********************** 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 221 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: A 349 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7859 (tttt) REVERT: A 445 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8423 (mm-30) REVERT: B 359 LYS cc_start: 0.7576 (ptpp) cc_final: 0.6897 (ptpt) REVERT: F 322 GLU cc_start: 0.7423 (tt0) cc_final: 0.7015 (tt0) REVERT: F 337 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6155 (mm-30) REVERT: G 445 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8451 (mm-30) REVERT: H 336 VAL cc_start: 0.8473 (m) cc_final: 0.8176 (t) REVERT: H 451 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.5610 (mp0) REVERT: H 455 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8568 (mm-30) REVERT: J 406 GLN cc_start: 0.7964 (tt0) cc_final: 0.7740 (tp40) REVERT: K 336 VAL cc_start: 0.8474 (m) cc_final: 0.8215 (t) REVERT: K 451 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.5621 (mp0) REVERT: L 278 ARG cc_start: 0.7466 (mtp180) cc_final: 0.7028 (ttp-170) REVERT: L 334 LYS cc_start: 0.7973 (mttm) cc_final: 0.7494 (mtpt) REVERT: L 336 VAL cc_start: 0.8357 (m) cc_final: 0.8122 (t) REVERT: L 455 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8911 (mm-30) REVERT: M 322 GLU cc_start: 0.7378 (tt0) cc_final: 0.6999 (tt0) outliers start: 24 outliers final: 21 residues processed: 215 average time/residue: 0.2830 time to fit residues: 81.9429 Evaluate side-chains 213 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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 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 307 ASN Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 333 VAL 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 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 41 optimal weight: 0.0570 chunk 11 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 143 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN ** F 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN G 392 GLN ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.169612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.125447 restraints weight = 14427.642| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.93 r_work: 0.3167 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 11454 Z= 0.131 Angle : 0.789 59.199 15507 Z= 0.462 Chirality : 0.043 0.489 1887 Planarity : 0.004 0.091 1959 Dihedral : 3.716 33.851 1537 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.83 % Allowed : 16.31 % Favored : 81.86 % Cbeta Deviations : 0.07 % 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: 1.73 (0.22), residues: 1437 helix: 3.06 (0.21), residues: 609 sheet: 0.86 (0.28), residues: 219 loop : -0.81 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 305 HIS 0.003 0.001 HIS M 286 PHE 0.015 0.001 PHE F 393 TYR 0.007 0.001 TYR B 365 ARG 0.004 0.000 ARG H 297 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 596) hydrogen bonds : angle 3.18225 ( 1758) covalent geometry : bond 0.00294 (11454) covalent geometry : angle 0.78900 (15507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7232.86 seconds wall clock time: 127 minutes 1.67 seconds (7621.67 seconds total)