Starting phenix.real_space_refine on Wed Mar 4 05:24:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r5m_14331/03_2026/7r5m_14331.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r5m_14331/03_2026/7r5m_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 { model { file = "/net/cci-nas-00/data/ceres_data/7r5m_14331/03_2026/7r5m_14331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r5m_14331/03_2026/7r5m_14331.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r5m_14331/03_2026/7r5m_14331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r5m_14331/03_2026/7r5m_14331.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.91, per 1000 atoms: 0.26 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: 0.84 Conformation dependent library (CDL) restraints added in 533.7 milliseconds 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: 0.42 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: 1.71 Time building geometry restraints manager: 1.20 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: 0.01 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.440 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.760 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG H 278 TYR 0.021 0.003 TYR F 316 PHE 0.017 0.002 PHE F 408 TRP 0.013 0.002 TRP B 442 HIS 0.006 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00642 (11454) covalent geometry : angle 0.94465 (15507) hydrogen bonds : bond 0.18894 ( 596) hydrogen bonds : angle 6.05898 ( 1758) *********************** 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 : 0.438 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: 0.1059 time to fit residues: 38.3703 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 : 0.363 ------------------------------------------------------------------------------- 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 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.177534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.127902 restraints weight = 14302.545| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.38 r_work: 0.3142 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 11454 Z= 0.115 Angle : 0.530 6.054 15507 Z= 0.275 Chirality : 0.044 0.157 1887 Planarity : 0.004 0.039 1959 Dihedral : 3.879 39.145 1537 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.67 % Allowed : 7.80 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.23), residues: 1437 helix: 2.24 (0.22), residues: 594 sheet: 0.04 (0.33), residues: 192 loop : -1.36 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 339 TYR 0.011 0.001 TYR B 365 PHE 0.011 0.001 PHE G 384 TRP 0.010 0.002 TRP G 305 HIS 0.001 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00258 (11454) covalent geometry : angle 0.53001 (15507) hydrogen bonds : bond 0.03972 ( 596) hydrogen bonds : angle 3.79692 ( 1758) *********************** 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 232 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 329 ILE cc_start: 0.7577 (mm) cc_final: 0.7332 (mm) REVERT: A 366 GLN cc_start: 0.7268 (mm110) cc_final: 0.6906 (mm-40) REVERT: B 329 ILE cc_start: 0.7442 (mm) cc_final: 0.7198 (mm) REVERT: B 444 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7843 (ttp-170) REVERT: B 451 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7704 (mm-30) REVERT: G 329 ILE cc_start: 0.7537 (mm) cc_final: 0.7322 (mm) REVERT: H 334 LYS cc_start: 0.7182 (mttm) cc_final: 0.6976 (mtpt) REVERT: J 293 LEU cc_start: 0.7405 (pp) cc_final: 0.6894 (pp) REVERT: K 334 LYS cc_start: 0.7378 (mttm) cc_final: 0.7129 (mtpt) REVERT: L 334 LYS cc_start: 0.7530 (mttm) cc_final: 0.7170 (mptt) REVERT: M 322 GLU cc_start: 0.7325 (tt0) cc_final: 0.6871 (tt0) REVERT: M 406 GLN cc_start: 0.7824 (tt0) cc_final: 0.7610 (tp40) outliers start: 21 outliers final: 18 residues processed: 226 average time/residue: 0.1117 time to fit residues: 34.5301 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 : 0.451 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 18 optimal weight: 0.0060 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 269 GLN F 307 ASN F 325 ASN J 307 ASN M 283 ASN M 307 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.168070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.118085 restraints weight = 14591.814| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.29 r_work: 0.3024 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11454 Z= 0.151 Angle : 0.564 5.984 15507 Z= 0.290 Chirality : 0.045 0.145 1887 Planarity : 0.004 0.038 1959 Dihedral : 4.259 37.804 1537 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.78 % Allowed : 9.63 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.22), residues: 1437 helix: 2.24 (0.21), residues: 612 sheet: 0.44 (0.31), residues: 207 loop : -1.26 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 339 TYR 0.012 0.001 TYR B 365 PHE 0.013 0.002 PHE G 384 TRP 0.011 0.002 TRP G 305 HIS 0.002 0.001 HIS F 286 Details of bonding type rmsd covalent geometry : bond 0.00371 (11454) covalent geometry : angle 0.56357 (15507) hydrogen bonds : bond 0.05101 ( 596) hydrogen bonds : angle 3.73728 ( 1758) *********************** 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 253 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 329 ILE cc_start: 0.7517 (mm) cc_final: 0.7243 (tp) REVERT: B 329 ILE cc_start: 0.7540 (mm) cc_final: 0.7157 (tp) REVERT: G 329 ILE cc_start: 0.7458 (mm) cc_final: 0.7084 (pt) REVERT: H 334 LYS cc_start: 0.7459 (mttm) cc_final: 0.7253 (mtpt) REVERT: H 451 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.5417 (mp0) REVERT: J 293 LEU cc_start: 0.7490 (pp) cc_final: 0.6930 (pp) REVERT: J 337 GLU cc_start: 0.6451 (mm-30) cc_final: 0.6170 (mm-30) REVERT: J 339 ARG cc_start: 0.8089 (mtp180) cc_final: 0.7831 (mtp180) REVERT: K 451 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.5504 (mp0) REVERT: L 334 LYS cc_start: 0.7743 (mttm) cc_final: 0.7499 (mtpt) REVERT: L 451 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.5367 (mp0) REVERT: M 406 GLN cc_start: 0.7836 (tt0) cc_final: 0.7617 (tp40) outliers start: 35 outliers final: 22 residues processed: 240 average time/residue: 0.1192 time to fit residues: 38.7986 Evaluate side-chains 218 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain F residue 283 ASN Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain G residue 235 MET Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 424 ILE Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain J residue 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 48 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 76 optimal weight: 0.0000 chunk 71 optimal weight: 0.0870 chunk 145 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 94 optimal weight: 0.1980 chunk 146 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.4566 ------------------------------------------------------------------------------- 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 283 ASN F 307 ASN G 269 GLN J 283 ASN J 307 ASN M 283 ASN M 307 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.168589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.119346 restraints weight = 14511.285| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.37 r_work: 0.2991 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11454 Z= 0.127 Angle : 0.517 5.920 15507 Z= 0.266 Chirality : 0.043 0.162 1887 Planarity : 0.004 0.040 1959 Dihedral : 4.053 36.556 1537 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.78 % Allowed : 11.22 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.22), residues: 1437 helix: 2.54 (0.20), residues: 612 sheet: 0.60 (0.30), residues: 219 loop : -1.24 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 297 TYR 0.009 0.001 TYR B 365 PHE 0.014 0.001 PHE A 253 TRP 0.009 0.002 TRP G 305 HIS 0.002 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00309 (11454) covalent geometry : angle 0.51739 (15507) hydrogen bonds : bond 0.04223 ( 596) hydrogen bonds : angle 3.50716 ( 1758) *********************** 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 242 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: F 283 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.6882 (p0) REVERT: H 334 LYS cc_start: 0.7499 (mttm) cc_final: 0.7275 (mtpt) REVERT: H 451 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.5376 (mp0) REVERT: J 293 LEU cc_start: 0.7488 (pp) cc_final: 0.6939 (pp) REVERT: J 339 ARG cc_start: 0.8132 (mtp180) cc_final: 0.7808 (mtp180) REVERT: K 451 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.5427 (mp0) REVERT: L 334 LYS cc_start: 0.7743 (mttm) cc_final: 0.7496 (mttm) REVERT: M 339 ARG cc_start: 0.7862 (mtp-110) cc_final: 0.7634 (mtp180) REVERT: M 406 GLN cc_start: 0.7808 (tt0) cc_final: 0.7606 (tp40) outliers start: 35 outliers final: 26 residues processed: 228 average time/residue: 0.1082 time to fit residues: 33.9678 Evaluate side-chains 221 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 283 ASN Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain G residue 235 MET Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 404 VAL 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 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 M residue 283 ASN Chi-restraints excluded: chain M residue 291 VAL 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 67 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 283 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.168475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.119045 restraints weight = 14266.013| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.51 r_work: 0.3038 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3543 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= 0.124 Angle : 0.508 5.867 15507 Z= 0.263 Chirality : 0.043 0.136 1887 Planarity : 0.004 0.043 1959 Dihedral : 4.004 35.801 1537 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.39 % Allowed : 13.21 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.22), residues: 1437 helix: 2.75 (0.20), residues: 609 sheet: 0.70 (0.29), residues: 219 loop : -1.21 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 297 TYR 0.009 0.001 TYR B 365 PHE 0.014 0.002 PHE A 253 TRP 0.008 0.002 TRP G 305 HIS 0.002 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00300 (11454) covalent geometry : angle 0.50760 (15507) hydrogen bonds : bond 0.04076 ( 596) hydrogen bonds : angle 3.41626 ( 1758) *********************** 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 231 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: F 283 ASN cc_start: 0.7405 (OUTLIER) cc_final: 0.6961 (p0) REVERT: H 334 LYS cc_start: 0.7534 (mttm) cc_final: 0.7291 (mtpt) REVERT: H 349 LYS cc_start: 0.7724 (mtmt) cc_final: 0.7482 (mtpp) REVERT: H 451 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.5393 (mp0) REVERT: H 455 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8447 (mm-30) REVERT: J 339 ARG cc_start: 0.8139 (mtp180) cc_final: 0.7805 (mtp180) REVERT: J 393 PHE cc_start: 0.6503 (m-80) cc_final: 0.6276 (m-80) REVERT: K 297 ARG cc_start: 0.7509 (tpp80) cc_final: 0.7291 (tpp80) REVERT: K 379 PRO cc_start: 0.8040 (Cg_exo) cc_final: 0.7820 (Cg_endo) REVERT: K 451 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.5469 (mp0) REVERT: L 334 LYS cc_start: 0.7690 (mttm) cc_final: 0.7419 (mtpt) REVERT: M 322 GLU cc_start: 0.7226 (tt0) cc_final: 0.6782 (tt0) REVERT: M 339 ARG cc_start: 0.7866 (mtp-110) cc_final: 0.7650 (mtp180) outliers start: 30 outliers final: 21 residues processed: 222 average time/residue: 0.1141 time to fit residues: 34.6940 Evaluate side-chains 212 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 B residue 404 VAL Chi-restraints excluded: chain F residue 283 ASN Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 375 MET Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain H residue 451 GLU Chi-restraints excluded: chain J residue 274 SER Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain 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 414 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 119 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 283 ASN ** F 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN J 283 ASN J 307 ASN M 283 ASN ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.167713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.118753 restraints weight = 14419.890| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.46 r_work: 0.3024 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11454 Z= 0.133 Angle : 0.512 5.868 15507 Z= 0.264 Chirality : 0.043 0.136 1887 Planarity : 0.004 0.037 1959 Dihedral : 4.042 35.397 1537 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.70 % Allowed : 13.84 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.22), residues: 1437 helix: 2.77 (0.20), residues: 609 sheet: 0.72 (0.29), residues: 219 loop : -1.24 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 297 TYR 0.007 0.001 TYR B 365 PHE 0.015 0.002 PHE A 253 TRP 0.009 0.002 TRP G 305 HIS 0.002 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00328 (11454) covalent geometry : angle 0.51176 (15507) hydrogen bonds : bond 0.04269 ( 596) hydrogen bonds : angle 3.40781 ( 1758) *********************** 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 238 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: F 283 ASN cc_start: 0.7372 (OUTLIER) cc_final: 0.6923 (p0) REVERT: H 334 LYS cc_start: 0.7547 (mttm) cc_final: 0.7286 (mtpt) REVERT: H 349 LYS cc_start: 0.7713 (mtmt) cc_final: 0.7459 (mtpp) REVERT: H 451 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.5284 (mp0) REVERT: H 455 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8411 (mm-30) REVERT: J 339 ARG cc_start: 0.8111 (mtp180) cc_final: 0.7763 (mtp180) REVERT: K 297 ARG cc_start: 0.7476 (tpp80) cc_final: 0.7264 (tpp80) REVERT: K 379 PRO cc_start: 0.7948 (Cg_exo) cc_final: 0.7711 (Cg_endo) REVERT: K 451 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.5398 (mp0) REVERT: L 334 LYS cc_start: 0.7674 (mttm) cc_final: 0.7413 (mtpt) REVERT: L 336 VAL cc_start: 0.8375 (m) cc_final: 0.8069 (t) REVERT: L 455 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8718 (mm-30) REVERT: M 322 GLU cc_start: 0.7172 (tt0) cc_final: 0.6680 (tt0) REVERT: M 339 ARG cc_start: 0.7844 (mtp-110) cc_final: 0.7633 (mtp180) outliers start: 34 outliers final: 26 residues processed: 227 average time/residue: 0.1119 time to fit residues: 34.7480 Evaluate side-chains 216 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 B residue 404 VAL Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 283 ASN 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 G residue 404 VAL 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 274 SER Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain K residue 348 VAL Chi-restraints excluded: chain K residue 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 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 54 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 83 optimal weight: 0.0070 chunk 56 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.9204 ------------------------------------------------------------------------------- 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 ** 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 = 0.3845 r_free = 0.3845 target = 0.169207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.119305 restraints weight = 14558.941| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.27 r_work: 0.3050 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11454 Z= 0.102 Angle : 0.479 5.823 15507 Z= 0.248 Chirality : 0.042 0.129 1887 Planarity : 0.004 0.038 1959 Dihedral : 3.869 34.572 1537 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.47 % Allowed : 15.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.22), residues: 1437 helix: 2.95 (0.20), residues: 609 sheet: 0.70 (0.28), residues: 219 loop : -1.13 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 297 TYR 0.008 0.001 TYR B 365 PHE 0.015 0.001 PHE J 393 TRP 0.008 0.001 TRP A 442 HIS 0.001 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00242 (11454) covalent geometry : angle 0.47876 (15507) hydrogen bonds : bond 0.03469 ( 596) hydrogen bonds : angle 3.25610 ( 1758) *********************** 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 229 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: F 283 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.6941 (p0) REVERT: F 322 GLU cc_start: 0.7215 (tt0) cc_final: 0.6667 (tt0) REVERT: F 393 PHE cc_start: 0.6219 (m-80) cc_final: 0.6018 (m-80) REVERT: H 334 LYS cc_start: 0.7506 (mttm) cc_final: 0.7265 (mtpt) REVERT: H 349 LYS cc_start: 0.7670 (mtmt) cc_final: 0.7446 (mtpp) REVERT: H 455 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8403 (mm-30) REVERT: J 339 ARG cc_start: 0.8138 (mtp180) cc_final: 0.7774 (mtp180) REVERT: K 336 VAL cc_start: 0.8516 (m) cc_final: 0.8232 (t) REVERT: K 451 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.5350 (mp0) REVERT: L 334 LYS cc_start: 0.7651 (mttm) cc_final: 0.7410 (mtpt) REVERT: L 336 VAL cc_start: 0.8370 (m) cc_final: 0.8088 (t) REVERT: L 455 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8727 (mm-30) REVERT: M 322 GLU cc_start: 0.7185 (tt0) cc_final: 0.6682 (tt0) REVERT: M 339 ARG cc_start: 0.7850 (mtp-110) cc_final: 0.7630 (mtp180) outliers start: 31 outliers final: 22 residues processed: 220 average time/residue: 0.1156 time to fit residues: 34.8181 Evaluate side-chains 213 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 283 ASN 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 J residue 280 ASP Chi-restraints excluded: chain J residue 307 ASN Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 392 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 L residue 455 GLU Chi-restraints excluded: chain M residue 283 ASN 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 78 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 73 optimal weight: 0.2980 chunk 140 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 0.1980 chunk 123 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 283 ASN ** F 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN J 283 ASN J 307 ASN ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.170584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.120556 restraints weight = 14601.609| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.43 r_work: 0.3069 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3776 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= 0.090 Angle : 0.459 5.761 15507 Z= 0.237 Chirality : 0.041 0.128 1887 Planarity : 0.004 0.038 1959 Dihedral : 3.732 34.328 1537 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.91 % Allowed : 15.67 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.22), residues: 1437 helix: 3.07 (0.21), residues: 609 sheet: 0.71 (0.28), residues: 219 loop : -0.98 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 297 TYR 0.008 0.001 TYR B 365 PHE 0.014 0.001 PHE M 393 TRP 0.007 0.001 TRP B 442 HIS 0.002 0.000 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00212 (11454) covalent geometry : angle 0.45898 (15507) hydrogen bonds : bond 0.03038 ( 596) hydrogen bonds : angle 3.15278 ( 1758) *********************** 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 225 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: B 359 LYS cc_start: 0.7534 (ptpp) cc_final: 0.6807 (ptpt) REVERT: F 322 GLU cc_start: 0.7250 (tt0) cc_final: 0.6770 (tt0) REVERT: H 334 LYS cc_start: 0.7568 (mttm) cc_final: 0.7332 (mtpt) REVERT: H 349 LYS cc_start: 0.7664 (mtmt) cc_final: 0.7454 (mtpp) REVERT: H 455 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8433 (mm-30) REVERT: J 293 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7144 (pp) REVERT: J 337 GLU cc_start: 0.6535 (mm-30) cc_final: 0.6310 (mm-30) REVERT: J 339 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7780 (mtp180) REVERT: K 336 VAL cc_start: 0.8441 (m) cc_final: 0.8183 (t) REVERT: K 451 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6638 (mt-10) REVERT: L 334 LYS cc_start: 0.7601 (mttm) cc_final: 0.7376 (mtpt) REVERT: L 336 VAL cc_start: 0.8334 (m) cc_final: 0.8091 (t) REVERT: L 455 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8736 (mm-30) REVERT: M 322 GLU cc_start: 0.7200 (tt0) cc_final: 0.6711 (tt0) REVERT: M 339 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.7650 (mtp180) outliers start: 24 outliers final: 17 residues processed: 215 average time/residue: 0.1143 time to fit residues: 33.4461 Evaluate side-chains 205 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 283 ASN 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 G residue 385 THR Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 307 ASN Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 392 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 455 GLU Chi-restraints excluded: chain M residue 283 ASN 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 1 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 283 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.167702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.117872 restraints weight = 14419.938| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.27 r_work: 0.3019 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11454 Z= 0.141 Angle : 0.519 5.824 15507 Z= 0.268 Chirality : 0.043 0.129 1887 Planarity : 0.004 0.038 1959 Dihedral : 3.984 34.163 1537 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.23 % Allowed : 15.91 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.22), residues: 1437 helix: 2.84 (0.20), residues: 609 sheet: 0.70 (0.28), residues: 219 loop : -1.06 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 297 TYR 0.007 0.001 TYR B 365 PHE 0.019 0.002 PHE F 393 TRP 0.009 0.002 TRP G 305 HIS 0.003 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00352 (11454) covalent geometry : angle 0.51888 (15507) hydrogen bonds : bond 0.04353 ( 596) hydrogen bonds : angle 3.31901 ( 1758) *********************** 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 229 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: F 322 GLU cc_start: 0.7291 (tt0) cc_final: 0.6680 (tt0) REVERT: H 334 LYS cc_start: 0.7634 (mttm) cc_final: 0.7386 (mtpt) REVERT: H 350 GLU cc_start: 0.6394 (tp30) cc_final: 0.6033 (tp30) REVERT: H 455 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8382 (mm-30) REVERT: J 283 ASN cc_start: 0.7249 (p0) cc_final: 0.7027 (m-40) REVERT: J 293 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7180 (pp) REVERT: J 337 GLU cc_start: 0.6528 (mm-30) cc_final: 0.6285 (mm-30) REVERT: J 406 GLN cc_start: 0.7913 (tt0) cc_final: 0.7657 (tp40) REVERT: K 336 VAL cc_start: 0.8556 (m) cc_final: 0.8324 (t) REVERT: K 451 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.5363 (mp0) REVERT: L 334 LYS cc_start: 0.7681 (mttm) cc_final: 0.7448 (mtpt) REVERT: L 336 VAL cc_start: 0.8413 (m) cc_final: 0.8162 (t) REVERT: L 455 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8761 (mm-30) REVERT: M 322 GLU cc_start: 0.7190 (tt0) cc_final: 0.6587 (tt0) REVERT: M 339 ARG cc_start: 0.7874 (mtp-110) cc_final: 0.7644 (mtp180) outliers start: 28 outliers final: 22 residues processed: 220 average time/residue: 0.1166 time to fit residues: 34.7568 Evaluate side-chains 216 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 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 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 L residue 455 GLU Chi-restraints excluded: chain M residue 283 ASN 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 53 optimal weight: 0.0570 chunk 55 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 112 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN ** F 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3855 r_free = 0.3855 target = 0.169922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.121279 restraints weight = 14558.330| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.42 r_work: 0.3059 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11454 Z= 0.094 Angle : 0.469 5.747 15507 Z= 0.242 Chirality : 0.041 0.127 1887 Planarity : 0.004 0.039 1959 Dihedral : 3.751 33.242 1537 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.99 % Allowed : 16.79 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.22), residues: 1437 helix: 3.03 (0.21), residues: 609 sheet: 0.74 (0.28), residues: 219 loop : -0.91 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 297 TYR 0.008 0.001 TYR B 365 PHE 0.017 0.001 PHE F 393 TRP 0.008 0.001 TRP B 442 HIS 0.003 0.001 HIS M 286 Details of bonding type rmsd covalent geometry : bond 0.00222 (11454) covalent geometry : angle 0.46938 (15507) hydrogen bonds : bond 0.03107 ( 596) hydrogen bonds : angle 3.12097 ( 1758) ********************** 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 220 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: F 322 GLU cc_start: 0.7228 (tt0) cc_final: 0.6776 (tt0) REVERT: H 334 LYS cc_start: 0.7578 (mttm) cc_final: 0.7359 (mtpt) REVERT: H 336 VAL cc_start: 0.8478 (m) cc_final: 0.8195 (t) REVERT: H 350 GLU cc_start: 0.6378 (tp30) cc_final: 0.6011 (tp30) REVERT: H 455 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8381 (mm-30) REVERT: J 283 ASN cc_start: 0.7273 (p0) cc_final: 0.7053 (m-40) REVERT: J 284 LYS cc_start: 0.8585 (tppt) cc_final: 0.8283 (tppt) REVERT: J 293 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7120 (pp) REVERT: J 337 GLU cc_start: 0.6523 (mm-30) cc_final: 0.6299 (mm-30) REVERT: J 406 GLN cc_start: 0.7946 (tt0) cc_final: 0.7745 (tp40) REVERT: K 336 VAL cc_start: 0.8482 (m) cc_final: 0.8252 (t) REVERT: K 451 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6657 (mt-10) REVERT: L 334 LYS cc_start: 0.7611 (mttm) cc_final: 0.7398 (mtpt) REVERT: L 336 VAL cc_start: 0.8371 (m) cc_final: 0.8151 (t) REVERT: M 283 ASN cc_start: 0.7487 (OUTLIER) cc_final: 0.7036 (m-40) REVERT: M 288 THR cc_start: 0.8148 (m) cc_final: 0.7785 (m) REVERT: M 322 GLU cc_start: 0.7217 (tt0) cc_final: 0.6706 (tt0) REVERT: M 339 ARG cc_start: 0.7873 (mtp-110) cc_final: 0.7651 (mtp180) outliers start: 25 outliers final: 20 residues processed: 212 average time/residue: 0.1153 time to fit residues: 33.3166 Evaluate side-chains 212 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 F residue 424 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain H residue 414 THR Chi-restraints excluded: chain J residue 280 ASP Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 307 ASN Chi-restraints excluded: chain J residue 315 ASN Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 392 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 333 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.168846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.119195 restraints weight = 14536.277| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.51 r_work: 0.3016 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4016 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= 0.118 Angle : 0.493 5.780 15507 Z= 0.254 Chirality : 0.042 0.132 1887 Planarity : 0.004 0.037 1959 Dihedral : 3.825 33.211 1537 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.15 % Allowed : 16.87 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.22), residues: 1437 helix: 2.93 (0.20), residues: 609 sheet: 0.75 (0.28), residues: 219 loop : -0.90 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 297 TYR 0.007 0.001 TYR B 365 PHE 0.016 0.001 PHE F 393 TRP 0.008 0.001 TRP G 305 HIS 0.002 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00292 (11454) covalent geometry : angle 0.49262 (15507) hydrogen bonds : bond 0.03729 ( 596) hydrogen bonds : angle 3.18706 ( 1758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2801.99 seconds wall clock time: 48 minutes 34.60 seconds (2914.60 seconds total)