Starting phenix.real_space_refine on Wed Mar 4 09:38:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v1z_31631/03_2026/7v1z_31631.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v1z_31631/03_2026/7v1z_31631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v1z_31631/03_2026/7v1z_31631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v1z_31631/03_2026/7v1z_31631.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v1z_31631/03_2026/7v1z_31631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v1z_31631/03_2026/7v1z_31631.map" } resolution = 2.98 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 64 5.16 5 C 8088 2.51 5 N 2112 2.21 5 O 2324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 12588 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3147 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3147 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3147 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3147 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 2.72, per 1000 atoms: 0.22 Number of scatterers: 12588 At special positions: 0 Unit cell: (115.132, 83.928, 152.792, 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 64 16.00 O 2324 8.00 N 2112 7.00 C 8088 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: 0.94 Conformation dependent library (CDL) restraints added in 576.3 milliseconds 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 15 sheets defined 42.0% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 104 through 123 Processing helix chain 'A' and resid 165 through 180 removed outlier: 3.627A pdb=" N LEU A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.625A pdb=" N SER A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 239 removed outlier: 3.742A pdb=" N VAL A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.798A pdb=" N LEU A 294 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 308 removed outlier: 3.612A pdb=" N LEU A 307 " --> pdb=" O SER A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 340 Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 394 through 399 removed outlier: 3.679A pdb=" N GLY A 399 " --> pdb=" O TRP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 425 removed outlier: 3.863A pdb=" N LEU A 407 " --> pdb=" O THR A 403 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLY A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 444 removed outlier: 3.549A pdb=" N MET A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 511 removed outlier: 3.505A pdb=" N ASN A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 544 removed outlier: 3.518A pdb=" N LYS A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 123 removed outlier: 3.575A pdb=" N SER B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 180 removed outlier: 4.271A pdb=" N SER B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 226 through 239 Processing helix chain 'B' and resid 290 through 294 removed outlier: 3.571A pdb=" N LEU B 294 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 325 through 340 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 394 through 399 removed outlier: 3.619A pdb=" N GLY B 399 " --> pdb=" O TRP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 425 removed outlier: 3.815A pdb=" N LEU B 407 " --> pdb=" O THR B 403 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 423 " --> pdb=" O GLN B 419 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN B 425 " --> pdb=" O GLY B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 444 Processing helix chain 'B' and resid 504 through 511 removed outlier: 3.515A pdb=" N ILE B 508 " --> pdb=" O ASP B 504 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN B 509 " --> pdb=" O THR B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 544 removed outlier: 4.094A pdb=" N ASP B 544 " --> pdb=" O GLU B 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 123 removed outlier: 3.725A pdb=" N LEU C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 180 removed outlier: 3.864A pdb=" N SER C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 209 through 215 removed outlier: 3.887A pdb=" N SER C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 239 removed outlier: 3.628A pdb=" N GLU C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.709A pdb=" N LEU C 294 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 325 through 340 Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.543A pdb=" N TYR C 346 " --> pdb=" O LYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 395 removed outlier: 3.515A pdb=" N LYS C 394 " --> pdb=" O ASN C 391 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TRP C 395 " --> pdb=" O SER C 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 391 through 395' Processing helix chain 'C' and resid 403 through 425 removed outlier: 3.771A pdb=" N LEU C 407 " --> pdb=" O THR C 403 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU C 422 " --> pdb=" O TYR C 418 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C 423 " --> pdb=" O GLN C 419 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN C 425 " --> pdb=" O GLY C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 444 Processing helix chain 'C' and resid 504 through 511 Processing helix chain 'C' and resid 530 through 544 removed outlier: 3.603A pdb=" N ASP C 544 " --> pdb=" O GLU C 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'D' and resid 164 through 180 removed outlier: 3.911A pdb=" N SER D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 209 through 215 removed outlier: 3.523A pdb=" N SER D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 239 Processing helix chain 'D' and resid 289 through 294 removed outlier: 3.717A pdb=" N LEU D 294 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 325 through 340 Processing helix chain 'D' and resid 342 through 354 Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 394 through 399 removed outlier: 3.791A pdb=" N GLY D 399 " --> pdb=" O TRP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 424 removed outlier: 3.925A pdb=" N LEU D 407 " --> pdb=" O THR D 403 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLY D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU D 422 " --> pdb=" O TYR D 418 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE D 423 " --> pdb=" O GLN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 444 Processing helix chain 'D' and resid 504 through 511 removed outlier: 3.509A pdb=" N ILE D 508 " --> pdb=" O ASP D 504 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN D 509 " --> pdb=" O THR D 505 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN D 510 " --> pdb=" O GLU D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 544 removed outlier: 3.883A pdb=" N ASP D 544 " --> pdb=" O GLU D 540 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 5.318A pdb=" N GLU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 133 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP A 139 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 492 " --> pdb=" O ALA A 489 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 162 removed outlier: 4.211A pdb=" N PHE A 400 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AA4, first strand: chain 'A' and resid 375 through 377 Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.545A pdb=" N VAL B 152 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL B 133 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 492 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA7, first strand: chain 'B' and resid 375 through 377 Processing sheet with id=AA8, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.611A pdb=" N VAL C 152 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 133 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C 492 " --> pdb=" O ALA C 489 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AB1, first strand: chain 'C' and resid 200 through 201 Processing sheet with id=AB2, first strand: chain 'C' and resid 375 through 377 Processing sheet with id=AB3, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.520A pdb=" N VAL D 152 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL D 133 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP D 139 " --> pdb=" O VAL D 131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 160 through 161 Processing sheet with id=AB5, first strand: chain 'D' and resid 200 through 201 removed outlier: 3.607A pdb=" N TYR D 201 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 375 through 377 539 hydrogen bonds defined for protein. 1500 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: 1.87 Time building geometry restraints manager: 1.26 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: 3349 1.33 - 1.45: 2277 1.45 - 1.57: 7134 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 12868 Sorted by residual: bond pdb=" C ALA A 124 " pdb=" N PRO A 125 " ideal model delta sigma weight residual 1.336 1.368 -0.032 1.23e-02 6.61e+03 6.94e+00 bond pdb=" CA ALA A 124 " pdb=" C ALA A 124 " ideal model delta sigma weight residual 1.528 1.555 -0.027 1.13e-02 7.83e+03 5.83e+00 bond pdb=" C GLU B 365 " pdb=" N PRO B 366 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.34e-02 5.57e+03 5.27e+00 bond pdb=" CA LEU D 115 " pdb=" C LEU D 115 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.27e-02 6.20e+03 4.90e+00 bond pdb=" C LEU D 115 " pdb=" O LEU D 115 " ideal model delta sigma weight residual 1.236 1.213 0.023 1.15e-02 7.56e+03 4.09e+00 ... (remaining 12863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 17167 2.15 - 4.30: 207 4.30 - 6.45: 19 6.45 - 8.60: 2 8.60 - 10.75: 1 Bond angle restraints: 17396 Sorted by residual: angle pdb=" C GLU B 365 " pdb=" N PRO B 366 " pdb=" CA PRO B 366 " ideal model delta sigma weight residual 119.78 114.06 5.72 1.03e+00 9.43e-01 3.08e+01 angle pdb=" N ALA A 124 " pdb=" CA ALA A 124 " pdb=" C ALA A 124 " ideal model delta sigma weight residual 109.57 115.45 -5.88 1.23e+00 6.61e-01 2.29e+01 angle pdb=" N SER A 402 " pdb=" CA SER A 402 " pdb=" C SER A 402 " ideal model delta sigma weight residual 108.79 115.59 -6.80 1.53e+00 4.27e-01 1.97e+01 angle pdb=" N THR A 472 " pdb=" CA THR A 472 " pdb=" C THR A 472 " ideal model delta sigma weight residual 111.36 115.74 -4.38 1.09e+00 8.42e-01 1.61e+01 angle pdb=" N SER B 484 " pdb=" CA SER B 484 " pdb=" C SER B 484 " ideal model delta sigma weight residual 109.23 115.33 -6.10 1.55e+00 4.16e-01 1.55e+01 ... (remaining 17391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6972 17.70 - 35.39: 616 35.39 - 53.09: 114 53.09 - 70.79: 15 70.79 - 88.49: 11 Dihedral angle restraints: 7728 sinusoidal: 3108 harmonic: 4620 Sorted by residual: dihedral pdb=" CB GLU A 363 " pdb=" CG GLU A 363 " pdb=" CD GLU A 363 " pdb=" OE1 GLU A 363 " ideal model delta sinusoidal sigma weight residual 0.00 88.49 -88.49 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU C 291 " pdb=" CG GLU C 291 " pdb=" CD GLU C 291 " pdb=" OE1 GLU C 291 " ideal model delta sinusoidal sigma weight residual 0.00 86.36 -86.36 1 3.00e+01 1.11e-03 9.99e+00 dihedral pdb=" CB GLU A 540 " pdb=" CG GLU A 540 " pdb=" CD GLU A 540 " pdb=" OE1 GLU A 540 " ideal model delta sinusoidal sigma weight residual 0.00 85.72 -85.72 1 3.00e+01 1.11e-03 9.87e+00 ... (remaining 7725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1455 0.045 - 0.091: 307 0.091 - 0.136: 127 0.136 - 0.182: 11 0.182 - 0.227: 8 Chirality restraints: 1908 Sorted by residual: chirality pdb=" CA TYR B 369 " pdb=" N TYR B 369 " pdb=" C TYR B 369 " pdb=" CB TYR B 369 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASN A 370 " pdb=" N ASN A 370 " pdb=" C ASN A 370 " pdb=" CB ASN A 370 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA LYS A 381 " pdb=" N LYS A 381 " pdb=" C LYS A 381 " pdb=" CB LYS A 381 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1905 not shown) Planarity restraints: 2208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 124 " 0.033 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO A 125 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 124 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO D 125 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 125 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 125 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 374 " 0.016 2.00e-02 2.50e+03 1.14e-02 2.26e+00 pdb=" CG PHE A 374 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 374 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 374 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 374 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 374 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 374 " 0.005 2.00e-02 2.50e+03 ... (remaining 2205 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1106 2.75 - 3.28: 11933 3.28 - 3.82: 19773 3.82 - 4.36: 24061 4.36 - 4.90: 42368 Nonbonded interactions: 99241 Sorted by model distance: nonbonded pdb=" OE2 GLU C 137 " pdb=" OG SER C 140 " model vdw 2.207 3.040 nonbonded pdb=" O VAL D 441 " pdb=" OG1 THR D 445 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR A 358 " pdb=" OD2 ASP A 406 " model vdw 2.275 3.040 nonbonded pdb=" OE2 GLU A 137 " pdb=" OG SER A 140 " model vdw 2.286 3.040 nonbonded pdb=" OD1 ASP B 542 " pdb=" NH2 ARG B 545 " model vdw 2.318 3.120 ... (remaining 99236 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 'C' selection = chain 'D' } 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.520 Find NCS groups from input model: 0.190 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:7.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.003 0.035 12868 Z= 0.156 Angle : 0.578 10.746 17396 Z= 0.346 Chirality : 0.045 0.227 1908 Planarity : 0.004 0.051 2208 Dihedral : 13.828 88.487 4776 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.22 % Allowed : 0.82 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.19 (0.21), residues: 1576 helix: 1.90 (0.23), residues: 524 sheet: 1.29 (0.38), residues: 188 loop : 0.03 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 112 TYR 0.012 0.001 TYR C 328 PHE 0.024 0.001 PHE A 374 TRP 0.012 0.001 TRP B 454 HIS 0.006 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00274 (12868) covalent geometry : angle 0.57814 (17396) hydrogen bonds : bond 0.17415 ( 539) hydrogen bonds : angle 5.23521 ( 1500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 247 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.7639 (mtpt) cc_final: 0.7391 (mttm) REVERT: A 355 ASP cc_start: 0.7992 (t70) cc_final: 0.7518 (t0) REVERT: A 510 ASN cc_start: 0.7510 (m-40) cc_final: 0.7047 (m-40) REVERT: A 540 GLU cc_start: 0.8044 (tp30) cc_final: 0.7835 (tp30) REVERT: B 460 TYR cc_start: 0.8886 (t80) cc_final: 0.8600 (t80) REVERT: B 462 MET cc_start: 0.8043 (mmt) cc_final: 0.7767 (mmm) REVERT: C 120 ASP cc_start: 0.7950 (m-30) cc_final: 0.7679 (m-30) REVERT: C 224 GLU cc_start: 0.7348 (tp30) cc_final: 0.7144 (tm-30) REVERT: C 320 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7834 (tp40) REVERT: C 373 ARG cc_start: 0.7596 (mtp85) cc_final: 0.7266 (mmm160) REVERT: D 200 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6996 (mp0) outliers start: 3 outliers final: 0 residues processed: 250 average time/residue: 0.7314 time to fit residues: 194.5372 Evaluate side-chains 136 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN A 425 ASN A 481 HIS B 370 ASN C 191 HIS C 216 HIS C 300 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.135797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108432 restraints weight = 16788.634| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.75 r_work: 0.3168 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12868 Z= 0.127 Angle : 0.525 5.834 17396 Z= 0.280 Chirality : 0.042 0.140 1908 Planarity : 0.004 0.039 2208 Dihedral : 4.053 16.352 1740 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.71 % Allowed : 10.24 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.36 (0.21), residues: 1576 helix: 2.16 (0.22), residues: 532 sheet: 1.29 (0.38), residues: 188 loop : 0.05 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 106 TYR 0.014 0.001 TYR A 328 PHE 0.013 0.001 PHE D 374 TRP 0.020 0.001 TRP B 178 HIS 0.011 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00289 (12868) covalent geometry : angle 0.52498 (17396) hydrogen bonds : bond 0.04459 ( 539) hydrogen bonds : angle 4.39394 ( 1500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8496 (mp) REVERT: A 225 LYS cc_start: 0.7925 (mtpt) cc_final: 0.7576 (mttt) REVERT: A 228 LYS cc_start: 0.7321 (mtmp) cc_final: 0.6936 (mmmt) REVERT: A 355 ASP cc_start: 0.8580 (t70) cc_final: 0.8159 (t0) REVERT: A 510 ASN cc_start: 0.7500 (m-40) cc_final: 0.7288 (m110) REVERT: B 460 TYR cc_start: 0.9005 (t80) cc_final: 0.8701 (t80) REVERT: B 462 MET cc_start: 0.8538 (mmt) cc_final: 0.8289 (mmm) REVERT: C 120 ASP cc_start: 0.8351 (m-30) cc_final: 0.8027 (m-30) REVERT: C 224 GLU cc_start: 0.8026 (tp30) cc_final: 0.7457 (tm-30) REVERT: C 373 ARG cc_start: 0.8316 (mtp85) cc_final: 0.7970 (mmm160) REVERT: C 542 ASP cc_start: 0.8625 (t0) cc_final: 0.8359 (t0) REVERT: D 200 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7459 (mp0) REVERT: D 232 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.6999 (tm-30) outliers start: 23 outliers final: 12 residues processed: 163 average time/residue: 0.7585 time to fit residues: 131.6590 Evaluate side-chains 142 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 56 optimal weight: 0.0570 chunk 113 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN A 427 ASN C 191 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.105994 restraints weight = 17075.487| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.95 r_work: 0.3133 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12868 Z= 0.113 Angle : 0.496 5.909 17396 Z= 0.263 Chirality : 0.042 0.138 1908 Planarity : 0.004 0.038 2208 Dihedral : 3.960 15.090 1740 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.00 % Allowed : 11.87 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.42 (0.21), residues: 1576 helix: 2.32 (0.22), residues: 528 sheet: 0.75 (0.38), residues: 204 loop : 0.17 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 106 TYR 0.015 0.001 TYR A 328 PHE 0.012 0.001 PHE D 374 TRP 0.017 0.001 TRP B 178 HIS 0.011 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00263 (12868) covalent geometry : angle 0.49610 (17396) hydrogen bonds : bond 0.03956 ( 539) hydrogen bonds : angle 4.17871 ( 1500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8450 (mp) REVERT: A 225 LYS cc_start: 0.7952 (mtpt) cc_final: 0.7628 (mttt) REVERT: A 228 LYS cc_start: 0.7480 (mtmp) cc_final: 0.7045 (mmmt) REVERT: A 355 ASP cc_start: 0.8616 (t70) cc_final: 0.8270 (t0) REVERT: A 510 ASN cc_start: 0.7320 (m-40) cc_final: 0.7071 (m-40) REVERT: B 460 TYR cc_start: 0.9049 (t80) cc_final: 0.8791 (t80) REVERT: B 462 MET cc_start: 0.8575 (mmt) cc_final: 0.8300 (mmm) REVERT: C 120 ASP cc_start: 0.8312 (m-30) cc_final: 0.7997 (m-30) REVERT: C 190 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7434 (mt0) REVERT: C 195 GLU cc_start: 0.7773 (mp0) cc_final: 0.7413 (mp0) REVERT: C 224 GLU cc_start: 0.8129 (tp30) cc_final: 0.7478 (tm-30) REVERT: C 348 GLN cc_start: 0.8623 (tm-30) cc_final: 0.7997 (tp40) REVERT: C 362 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: C 373 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7891 (mmm160) REVERT: C 508 ILE cc_start: 0.8064 (mm) cc_final: 0.7803 (mt) REVERT: D 205 LYS cc_start: 0.7993 (mptt) cc_final: 0.7683 (tppt) outliers start: 27 outliers final: 13 residues processed: 162 average time/residue: 0.7004 time to fit residues: 121.1680 Evaluate side-chains 140 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 37 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN A 427 ASN C 191 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.128242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.101237 restraints weight = 17090.294| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.81 r_work: 0.3029 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12868 Z= 0.209 Angle : 0.607 7.364 17396 Z= 0.321 Chirality : 0.045 0.144 1908 Planarity : 0.004 0.038 2208 Dihedral : 4.383 17.726 1740 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.67 % Allowed : 13.95 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.07 (0.21), residues: 1576 helix: 2.16 (0.22), residues: 524 sheet: 0.60 (0.40), residues: 180 loop : -0.14 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 151 TYR 0.016 0.002 TYR A 328 PHE 0.018 0.002 PHE D 374 TRP 0.015 0.002 TRP C 464 HIS 0.011 0.002 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00514 (12868) covalent geometry : angle 0.60740 (17396) hydrogen bonds : bond 0.05708 ( 539) hydrogen bonds : angle 4.47063 ( 1500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.451 Fit side-chains REVERT: A 177 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8619 (mp) REVERT: A 225 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7645 (mttt) REVERT: A 228 LYS cc_start: 0.7615 (mtmp) cc_final: 0.7149 (mmmt) REVERT: A 355 ASP cc_start: 0.8772 (t70) cc_final: 0.8303 (t0) REVERT: A 373 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8050 (mtp180) REVERT: A 469 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8618 (ptt90) REVERT: A 510 ASN cc_start: 0.7376 (m-40) cc_final: 0.7117 (m-40) REVERT: B 460 TYR cc_start: 0.9070 (t80) cc_final: 0.8819 (t80) REVERT: B 462 MET cc_start: 0.8714 (mmt) cc_final: 0.8487 (mmm) REVERT: C 190 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7373 (mt0) REVERT: C 224 GLU cc_start: 0.8245 (tp30) cc_final: 0.7534 (tm-30) REVERT: C 362 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: C 373 ARG cc_start: 0.8199 (mtp85) cc_final: 0.7851 (mmm160) outliers start: 36 outliers final: 18 residues processed: 161 average time/residue: 0.6776 time to fit residues: 116.7767 Evaluate side-chains 142 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 35 optimal weight: 0.7980 chunk 106 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN A 427 ASN B 429 ASN C 191 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103392 restraints weight = 17091.949| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.79 r_work: 0.3066 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12868 Z= 0.132 Angle : 0.529 8.064 17396 Z= 0.279 Chirality : 0.042 0.143 1908 Planarity : 0.004 0.038 2208 Dihedral : 4.159 16.443 1740 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.37 % Allowed : 15.58 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.24 (0.21), residues: 1576 helix: 2.26 (0.22), residues: 524 sheet: 1.17 (0.44), residues: 148 loop : -0.07 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 117 TYR 0.016 0.001 TYR A 328 PHE 0.012 0.001 PHE D 374 TRP 0.010 0.001 TRP B 178 HIS 0.011 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00317 (12868) covalent geometry : angle 0.52853 (17396) hydrogen bonds : bond 0.04290 ( 539) hydrogen bonds : angle 4.22014 ( 1500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.512 Fit side-chains REVERT: A 177 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8563 (mp) REVERT: A 190 GLN cc_start: 0.8268 (mp10) cc_final: 0.8036 (mm-40) REVERT: A 225 LYS cc_start: 0.7946 (mtpt) cc_final: 0.7660 (mttt) REVERT: A 228 LYS cc_start: 0.7605 (mtmp) cc_final: 0.7115 (mmmt) REVERT: A 289 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.7077 (mm-40) REVERT: A 355 ASP cc_start: 0.8682 (t70) cc_final: 0.8299 (t0) REVERT: A 485 HIS cc_start: 0.9012 (OUTLIER) cc_final: 0.8794 (t-90) REVERT: A 510 ASN cc_start: 0.7333 (m-40) cc_final: 0.7073 (m-40) REVERT: B 460 TYR cc_start: 0.9071 (t80) cc_final: 0.8851 (t80) REVERT: B 462 MET cc_start: 0.8667 (mmt) cc_final: 0.8456 (mmm) REVERT: C 190 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: C 191 HIS cc_start: 0.7676 (OUTLIER) cc_final: 0.7030 (t-90) REVERT: C 195 GLU cc_start: 0.7781 (mp0) cc_final: 0.7476 (mp0) REVERT: C 224 GLU cc_start: 0.8200 (tp30) cc_final: 0.7511 (tm-30) REVERT: C 362 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: C 373 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7797 (mmm160) REVERT: D 232 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7028 (tm-30) outliers start: 32 outliers final: 16 residues processed: 154 average time/residue: 0.7332 time to fit residues: 120.3967 Evaluate side-chains 142 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 53 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN A 427 ASN B 150 ASN B 429 ASN C 191 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103158 restraints weight = 17076.012| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.83 r_work: 0.3071 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12868 Z= 0.130 Angle : 0.531 8.824 17396 Z= 0.278 Chirality : 0.042 0.141 1908 Planarity : 0.004 0.039 2208 Dihedral : 4.125 16.103 1740 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.74 % Allowed : 16.02 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.27 (0.21), residues: 1576 helix: 2.32 (0.22), residues: 524 sheet: 1.08 (0.44), residues: 148 loop : -0.06 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 545 TYR 0.015 0.001 TYR A 328 PHE 0.013 0.001 PHE D 374 TRP 0.008 0.001 TRP C 464 HIS 0.017 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00312 (12868) covalent geometry : angle 0.53103 (17396) hydrogen bonds : bond 0.04255 ( 539) hydrogen bonds : angle 4.17846 ( 1500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.462 Fit side-chains REVERT: A 177 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8592 (mp) REVERT: A 190 GLN cc_start: 0.8281 (mp10) cc_final: 0.8032 (mm-40) REVERT: A 225 LYS cc_start: 0.7896 (mtpt) cc_final: 0.7680 (mptt) REVERT: A 228 LYS cc_start: 0.7600 (mtmp) cc_final: 0.7108 (mmmt) REVERT: A 355 ASP cc_start: 0.8700 (t70) cc_final: 0.8320 (t0) REVERT: A 469 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8495 (ptt90) REVERT: A 485 HIS cc_start: 0.9007 (OUTLIER) cc_final: 0.8793 (t-90) REVERT: A 510 ASN cc_start: 0.7272 (m-40) cc_final: 0.7017 (m-40) REVERT: B 462 MET cc_start: 0.8666 (mmt) cc_final: 0.8460 (mmm) REVERT: C 190 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7403 (mt0) REVERT: C 195 GLU cc_start: 0.7775 (mp0) cc_final: 0.7549 (mp0) REVERT: C 224 GLU cc_start: 0.8188 (tp30) cc_final: 0.7478 (tm-30) REVERT: C 348 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: C 362 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: C 373 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7711 (mmm160) REVERT: D 232 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7014 (tm-30) outliers start: 37 outliers final: 17 residues processed: 160 average time/residue: 0.6734 time to fit residues: 115.6757 Evaluate side-chains 140 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 6 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN A 427 ASN B 429 ASN C 191 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.099883 restraints weight = 17028.292| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.96 r_work: 0.3068 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12868 Z= 0.218 Angle : 0.615 9.092 17396 Z= 0.324 Chirality : 0.045 0.145 1908 Planarity : 0.004 0.044 2208 Dihedral : 4.423 18.056 1740 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.74 % Allowed : 16.47 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.94 (0.21), residues: 1576 helix: 2.03 (0.22), residues: 524 sheet: 1.09 (0.43), residues: 140 loop : -0.27 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 545 TYR 0.022 0.002 TYR A 145 PHE 0.016 0.002 PHE D 374 TRP 0.014 0.002 TRP C 464 HIS 0.011 0.002 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00538 (12868) covalent geometry : angle 0.61458 (17396) hydrogen bonds : bond 0.05749 ( 539) hydrogen bonds : angle 4.47909 ( 1500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.523 Fit side-chains REVERT: A 177 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8652 (mp) REVERT: A 190 GLN cc_start: 0.8399 (mp10) cc_final: 0.8131 (mm-40) REVERT: A 225 LYS cc_start: 0.7963 (mtpt) cc_final: 0.7648 (mttt) REVERT: A 228 LYS cc_start: 0.7635 (mtmp) cc_final: 0.7163 (mmmt) REVERT: A 355 ASP cc_start: 0.8711 (t70) cc_final: 0.8276 (t0) REVERT: A 485 HIS cc_start: 0.9075 (OUTLIER) cc_final: 0.8786 (t-170) REVERT: A 510 ASN cc_start: 0.7325 (m-40) cc_final: 0.7053 (m-40) REVERT: B 106 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7725 (ttp80) REVERT: B 184 ASP cc_start: 0.7579 (t0) cc_final: 0.7338 (t0) REVERT: C 190 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7260 (mt0) REVERT: C 191 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.7076 (t-90) REVERT: C 200 GLU cc_start: 0.7271 (tt0) cc_final: 0.6847 (tt0) REVERT: C 348 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: C 362 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: C 373 ARG cc_start: 0.8159 (mtp85) cc_final: 0.7723 (mmm160) REVERT: D 232 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.6959 (tm-30) outliers start: 37 outliers final: 16 residues processed: 163 average time/residue: 0.7180 time to fit residues: 124.9448 Evaluate side-chains 146 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 138 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN A 427 ASN B 429 ASN C 190 GLN C 191 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.134161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.108655 restraints weight = 16602.464| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.77 r_work: 0.3119 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12868 Z= 0.106 Angle : 0.519 11.058 17396 Z= 0.272 Chirality : 0.041 0.143 1908 Planarity : 0.004 0.044 2208 Dihedral : 4.092 15.531 1740 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.85 % Allowed : 17.66 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.23 (0.21), residues: 1576 helix: 2.29 (0.22), residues: 524 sheet: 0.98 (0.44), residues: 148 loop : -0.06 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 545 TYR 0.025 0.001 TYR C 192 PHE 0.010 0.001 PHE A 374 TRP 0.010 0.001 TRP B 395 HIS 0.027 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00244 (12868) covalent geometry : angle 0.51944 (17396) hydrogen bonds : bond 0.03645 ( 539) hydrogen bonds : angle 4.15295 ( 1500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.427 Fit side-chains REVERT: A 190 GLN cc_start: 0.8429 (mp10) cc_final: 0.8175 (mm-40) REVERT: A 228 LYS cc_start: 0.7627 (mtmp) cc_final: 0.6938 (mmmt) REVERT: A 232 GLU cc_start: 0.7590 (pp20) cc_final: 0.7181 (mp0) REVERT: A 355 ASP cc_start: 0.8612 (t70) cc_final: 0.8352 (t0) REVERT: A 510 ASN cc_start: 0.7305 (m-40) cc_final: 0.7048 (m-40) REVERT: B 106 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7573 (ttp80) REVERT: C 195 GLU cc_start: 0.7720 (mp0) cc_final: 0.7461 (mp0) REVERT: C 200 GLU cc_start: 0.7255 (tt0) cc_final: 0.6874 (tt0) REVERT: C 320 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8212 (tp40) REVERT: C 373 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7688 (mmm160) REVERT: D 232 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7124 (tm-30) outliers start: 25 outliers final: 15 residues processed: 152 average time/residue: 0.6740 time to fit residues: 109.7758 Evaluate side-chains 141 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 120 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 113 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN A 427 ASN B 429 ASN C 191 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.132553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106050 restraints weight = 16686.863| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.86 r_work: 0.3122 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12868 Z= 0.140 Angle : 0.548 10.026 17396 Z= 0.288 Chirality : 0.042 0.143 1908 Planarity : 0.004 0.039 2208 Dihedral : 4.139 16.501 1740 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.71 % Allowed : 18.10 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.18 (0.21), residues: 1576 helix: 2.24 (0.22), residues: 524 sheet: 0.98 (0.44), residues: 148 loop : -0.09 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 545 TYR 0.016 0.001 TYR A 328 PHE 0.014 0.001 PHE D 374 TRP 0.008 0.001 TRP D 395 HIS 0.007 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00340 (12868) covalent geometry : angle 0.54828 (17396) hydrogen bonds : bond 0.04340 ( 539) hydrogen bonds : angle 4.22929 ( 1500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.401 Fit side-chains REVERT: A 190 GLN cc_start: 0.8463 (mp10) cc_final: 0.8151 (mm-40) REVERT: A 228 LYS cc_start: 0.7645 (mtmp) cc_final: 0.6924 (mmmt) REVERT: A 232 GLU cc_start: 0.7568 (pp20) cc_final: 0.7172 (mp0) REVERT: A 355 ASP cc_start: 0.8628 (t70) cc_final: 0.8349 (t0) REVERT: A 510 ASN cc_start: 0.7304 (m-40) cc_final: 0.7037 (m-40) REVERT: B 106 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7560 (ttp80) REVERT: C 195 GLU cc_start: 0.7728 (mp0) cc_final: 0.7448 (mp0) REVERT: C 200 GLU cc_start: 0.7276 (tt0) cc_final: 0.6874 (tt0) REVERT: C 320 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8176 (tp40) REVERT: C 373 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7699 (mmm160) REVERT: D 232 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7076 (tm-30) outliers start: 23 outliers final: 15 residues processed: 149 average time/residue: 0.7187 time to fit residues: 114.5105 Evaluate side-chains 138 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 61 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 0.0670 chunk 155 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 75 optimal weight: 0.1980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN A 427 ASN B 429 ASN ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.134590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108234 restraints weight = 16757.664| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.89 r_work: 0.3149 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12868 Z= 0.098 Angle : 0.507 10.436 17396 Z= 0.265 Chirality : 0.041 0.140 1908 Planarity : 0.003 0.039 2208 Dihedral : 3.938 14.930 1740 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.48 % Allowed : 18.62 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.33 (0.21), residues: 1576 helix: 2.35 (0.22), residues: 524 sheet: 1.01 (0.44), residues: 148 loop : 0.02 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 106 TYR 0.014 0.001 TYR A 328 PHE 0.011 0.001 PHE A 374 TRP 0.011 0.001 TRP B 395 HIS 0.011 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00225 (12868) covalent geometry : angle 0.50665 (17396) hydrogen bonds : bond 0.03370 ( 539) hydrogen bonds : angle 4.04711 ( 1500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.420 Fit side-chains REVERT: A 106 ARG cc_start: 0.6851 (ptm-80) cc_final: 0.6649 (ptm-80) REVERT: A 190 GLN cc_start: 0.8406 (mp10) cc_final: 0.8167 (mm-40) REVERT: A 228 LYS cc_start: 0.7602 (mtmp) cc_final: 0.6903 (mmmt) REVERT: A 232 GLU cc_start: 0.7569 (pp20) cc_final: 0.7190 (mp0) REVERT: A 355 ASP cc_start: 0.8594 (t70) cc_final: 0.8393 (t0) REVERT: A 469 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8197 (ptt90) REVERT: A 510 ASN cc_start: 0.7304 (m-40) cc_final: 0.7035 (m-40) REVERT: B 106 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7594 (ttp80) REVERT: C 120 ASP cc_start: 0.8232 (m-30) cc_final: 0.7956 (m-30) REVERT: C 191 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.7325 (t-90) REVERT: C 195 GLU cc_start: 0.7700 (mp0) cc_final: 0.7423 (mp0) REVERT: C 200 GLU cc_start: 0.7257 (tt0) cc_final: 0.6872 (tt0) REVERT: C 320 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8208 (tp40) REVERT: C 373 ARG cc_start: 0.7959 (mtp85) cc_final: 0.7654 (mmm160) REVERT: D 232 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: D 363 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8115 (pm20) outliers start: 20 outliers final: 11 residues processed: 149 average time/residue: 0.6843 time to fit residues: 109.2561 Evaluate side-chains 141 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 22 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 27 optimal weight: 0.0010 chunk 11 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 147 optimal weight: 0.0870 overall best weight: 0.7366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 425 ASN A 427 ASN B 429 ASN C 191 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.134326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.107399 restraints weight = 16760.985| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.89 r_work: 0.3150 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12868 Z= 0.107 Angle : 0.520 10.499 17396 Z= 0.270 Chirality : 0.041 0.138 1908 Planarity : 0.003 0.039 2208 Dihedral : 3.934 15.229 1740 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.19 % Allowed : 19.14 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.34 (0.21), residues: 1576 helix: 2.35 (0.22), residues: 524 sheet: 0.99 (0.44), residues: 148 loop : 0.03 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 545 TYR 0.022 0.001 TYR C 192 PHE 0.011 0.001 PHE A 374 TRP 0.009 0.001 TRP B 395 HIS 0.013 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00250 (12868) covalent geometry : angle 0.52005 (17396) hydrogen bonds : bond 0.03554 ( 539) hydrogen bonds : angle 4.05078 ( 1500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4024.13 seconds wall clock time: 69 minutes 18.56 seconds (4158.56 seconds total)