Starting phenix.real_space_refine on Wed Jul 30 17:42:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v1z_31631/07_2025/7v1z_31631.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v1z_31631/07_2025/7v1z_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7v1z_31631/07_2025/7v1z_31631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v1z_31631/07_2025/7v1z_31631.map" model { file = "/net/cci-nas-00/data/ceres_data/7v1z_31631/07_2025/7v1z_31631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v1z_31631/07_2025/7v1z_31631.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.79, per 1000 atoms: 0.62 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: 2.96 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.59 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: 3.38 Time building geometry restraints manager: 3.50 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: 0.03 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: 1.980 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 29.810 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.560 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.21), 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 TRP 0.012 0.001 TRP B 454 HIS 0.006 0.001 HIS B 191 PHE 0.024 0.001 PHE A 374 TYR 0.012 0.001 TYR C 328 ARG 0.003 0.000 ARG D 112 Details of bonding type rmsd hydrogen bonds : bond 0.17415 ( 539) hydrogen bonds : angle 5.23521 ( 1500) covalent geometry : bond 0.00274 (12868) covalent geometry : angle 0.57814 (17396) *********************** 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 : 1.747 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: 1.6396 time to fit residues: 437.3737 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 : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 0.0470 chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- 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 ** 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 = 0.3680 r_free = 0.3680 target = 0.137926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.110574 restraints weight = 16600.081| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.77 r_work: 0.3205 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12868 Z= 0.106 Angle : 0.502 6.030 17396 Z= 0.267 Chirality : 0.042 0.140 1908 Planarity : 0.004 0.038 2208 Dihedral : 3.959 16.410 1740 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.48 % Allowed : 10.31 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.21), residues: 1576 helix: 2.27 (0.22), residues: 528 sheet: 1.35 (0.38), residues: 188 loop : 0.06 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 178 HIS 0.010 0.001 HIS C 191 PHE 0.011 0.001 PHE C 400 TYR 0.014 0.001 TYR A 328 ARG 0.004 0.000 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 539) hydrogen bonds : angle 4.29394 ( 1500) covalent geometry : bond 0.00235 (12868) covalent geometry : angle 0.50239 (17396) *********************** 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 170 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.7880 (mtpt) cc_final: 0.7513 (mttt) REVERT: A 228 LYS cc_start: 0.7297 (mtmp) cc_final: 0.6910 (mmmt) REVERT: A 355 ASP cc_start: 0.8543 (t70) cc_final: 0.8118 (t0) REVERT: A 510 ASN cc_start: 0.7505 (m-40) cc_final: 0.7298 (m110) REVERT: B 460 TYR cc_start: 0.8966 (t80) cc_final: 0.8709 (t80) REVERT: B 462 MET cc_start: 0.8504 (mmt) cc_final: 0.8221 (mmm) REVERT: C 120 ASP cc_start: 0.8297 (m-30) cc_final: 0.8004 (m-30) REVERT: C 224 GLU cc_start: 0.8068 (tp30) cc_final: 0.7443 (tm-30) REVERT: C 320 GLN cc_start: 0.8359 (tp-100) cc_final: 0.8113 (tm-30) REVERT: C 373 ARG cc_start: 0.8277 (mtp85) cc_final: 0.7918 (mmm160) REVERT: C 542 ASP cc_start: 0.8574 (t0) cc_final: 0.8302 (t0) REVERT: D 232 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6977 (tm-30) outliers start: 20 outliers final: 10 residues processed: 167 average time/residue: 1.6215 time to fit residues: 289.5797 Evaluate side-chains 140 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LYS 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 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 91 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 ** C 300 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 = 0.3586 r_free = 0.3586 target = 0.130525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.102593 restraints weight = 17100.169| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.01 r_work: 0.3084 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12868 Z= 0.171 Angle : 0.569 6.410 17396 Z= 0.301 Chirality : 0.044 0.138 1908 Planarity : 0.004 0.039 2208 Dihedral : 4.218 16.639 1740 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.52 % Allowed : 11.28 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.21), residues: 1576 helix: 2.18 (0.22), residues: 528 sheet: 0.67 (0.37), residues: 196 loop : 0.01 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 178 HIS 0.011 0.001 HIS C 191 PHE 0.018 0.002 PHE D 374 TYR 0.016 0.002 TYR A 328 ARG 0.004 0.000 ARG C 371 Details of bonding type rmsd hydrogen bonds : bond 0.05156 ( 539) hydrogen bonds : angle 4.43784 ( 1500) covalent geometry : bond 0.00413 (12868) covalent geometry : angle 0.56900 (17396) *********************** 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 173 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.558 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7597 (mttt) REVERT: A 228 LYS cc_start: 0.7530 (mtmp) cc_final: 0.7037 (mmmt) REVERT: A 355 ASP cc_start: 0.8674 (t70) cc_final: 0.8216 (t0) REVERT: A 373 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7937 (mtp180) REVERT: A 510 ASN cc_start: 0.7327 (m-40) cc_final: 0.7095 (m-40) REVERT: B 184 ASP cc_start: 0.7555 (t0) cc_final: 0.7275 (t0) REVERT: B 460 TYR cc_start: 0.9063 (t80) cc_final: 0.8823 (t80) REVERT: B 462 MET cc_start: 0.8657 (mmt) cc_final: 0.8397 (mmm) REVERT: C 190 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7392 (mt0) REVERT: C 195 GLU cc_start: 0.7741 (mp0) cc_final: 0.7308 (mp0) REVERT: C 224 GLU cc_start: 0.8173 (tp30) cc_final: 0.7506 (tm-30) REVERT: C 362 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: C 373 ARG cc_start: 0.8312 (mtp85) cc_final: 0.7938 (mmm160) REVERT: D 205 LYS cc_start: 0.8021 (mptt) cc_final: 0.7700 (tppt) REVERT: D 232 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: D 352 HIS cc_start: 0.7739 (t70) cc_final: 0.7530 (t-90) outliers start: 34 outliers final: 13 residues processed: 162 average time/residue: 1.5676 time to fit residues: 272.8395 Evaluate side-chains 137 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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 373 ARG Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 512 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ** C 300 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 = 0.3611 r_free = 0.3611 target = 0.132306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.104855 restraints weight = 16976.412| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.00 r_work: 0.3149 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12868 Z= 0.109 Angle : 0.491 7.304 17396 Z= 0.260 Chirality : 0.041 0.140 1908 Planarity : 0.003 0.038 2208 Dihedral : 3.987 15.527 1740 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.30 % Allowed : 14.39 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.21), residues: 1576 helix: 2.32 (0.22), residues: 528 sheet: 0.64 (0.38), residues: 204 loop : 0.15 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 178 HIS 0.011 0.001 HIS C 191 PHE 0.011 0.001 PHE D 374 TYR 0.016 0.001 TYR A 328 ARG 0.002 0.000 ARG D 469 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 539) hydrogen bonds : angle 4.12896 ( 1500) covalent geometry : bond 0.00255 (12868) covalent geometry : angle 0.49076 (17396) *********************** 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 174 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.353 Fit side-chains revert: symmetry clash REVERT: A 106 ARG cc_start: 0.6891 (ptm-80) cc_final: 0.6617 (ptm-80) REVERT: A 225 LYS cc_start: 0.7955 (mtpt) cc_final: 0.7616 (mttt) REVERT: A 228 LYS cc_start: 0.7540 (mtmp) cc_final: 0.7084 (mmmt) REVERT: A 355 ASP cc_start: 0.8614 (t70) cc_final: 0.8234 (t0) REVERT: A 469 ARG cc_start: 0.8694 (ppp80) cc_final: 0.8409 (ptt90) REVERT: B 460 TYR cc_start: 0.9044 (t80) cc_final: 0.8794 (t80) REVERT: B 462 MET cc_start: 0.8652 (mmt) cc_final: 0.8398 (mmm) REVERT: C 120 ASP cc_start: 0.8253 (m-30) cc_final: 0.7938 (m-30) REVERT: C 190 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7369 (mt0) REVERT: C 191 HIS cc_start: 0.7538 (OUTLIER) cc_final: 0.6826 (t-90) REVERT: C 195 GLU cc_start: 0.7780 (mp0) cc_final: 0.7533 (mp0) REVERT: C 224 GLU cc_start: 0.8166 (tp30) cc_final: 0.7509 (tm-30) REVERT: C 348 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8117 (tm-30) REVERT: C 362 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7569 (tt0) REVERT: C 373 ARG cc_start: 0.8262 (mtp85) cc_final: 0.7900 (mmm160) REVERT: D 205 LYS cc_start: 0.8000 (mptt) cc_final: 0.7683 (tppt) outliers start: 31 outliers final: 15 residues processed: 165 average time/residue: 1.5201 time to fit residues: 269.2893 Evaluate side-chains 145 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 357 LEU 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 191 HIS Chi-restraints excluded: chain C residue 362 GLU 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 182 LYS Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 442 MET 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 68 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 ** C 300 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 = 0.3580 r_free = 0.3580 target = 0.130317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.103888 restraints weight = 16901.836| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.83 r_work: 0.3081 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12868 Z= 0.180 Angle : 0.573 8.124 17396 Z= 0.302 Chirality : 0.044 0.143 1908 Planarity : 0.004 0.040 2208 Dihedral : 4.225 17.428 1740 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.52 % Allowed : 15.73 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1576 helix: 2.20 (0.22), residues: 528 sheet: 0.51 (0.39), residues: 180 loop : -0.02 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 464 HIS 0.024 0.002 HIS C 191 PHE 0.017 0.002 PHE D 374 TYR 0.016 0.002 TYR A 328 ARG 0.003 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.05082 ( 539) hydrogen bonds : angle 4.34119 ( 1500) covalent geometry : bond 0.00439 (12868) covalent geometry : angle 0.57316 (17396) *********************** 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 163 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.350 Fit side-chains REVERT: A 106 ARG cc_start: 0.7180 (ptm-80) cc_final: 0.6768 (ptm-80) REVERT: A 225 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7611 (mttt) REVERT: A 228 LYS cc_start: 0.7575 (mtmp) cc_final: 0.7127 (mmmt) REVERT: A 289 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6141 (mp10) REVERT: A 355 ASP cc_start: 0.8691 (t70) cc_final: 0.8294 (t0) REVERT: A 469 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8505 (ptt90) REVERT: B 184 ASP cc_start: 0.7587 (t0) cc_final: 0.7345 (t0) REVERT: B 460 TYR cc_start: 0.9063 (t80) cc_final: 0.8824 (t80) REVERT: B 462 MET cc_start: 0.8674 (mmt) cc_final: 0.8445 (mmm) REVERT: C 224 GLU cc_start: 0.8143 (tp30) cc_final: 0.7481 (tm-30) REVERT: C 362 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: C 373 ARG cc_start: 0.8238 (mtp85) cc_final: 0.7897 (mmm160) outliers start: 34 outliers final: 20 residues processed: 154 average time/residue: 1.5864 time to fit residues: 262.1122 Evaluate side-chains 144 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 442 MET 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 362 GLU 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 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 379 LYS 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 145 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 ** C 300 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 = 0.3553 r_free = 0.3553 target = 0.128092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.100200 restraints weight = 17024.855| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.80 r_work: 0.3042 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12868 Z= 0.237 Angle : 0.640 8.830 17396 Z= 0.336 Chirality : 0.046 0.147 1908 Planarity : 0.005 0.044 2208 Dihedral : 4.518 18.715 1740 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.49 % Allowed : 15.50 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1576 helix: 1.94 (0.22), residues: 524 sheet: 0.98 (0.44), residues: 148 loop : -0.30 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 464 HIS 0.006 0.001 HIS B 191 PHE 0.016 0.002 PHE D 423 TYR 0.019 0.002 TYR A 328 ARG 0.005 0.001 ARG D 545 Details of bonding type rmsd hydrogen bonds : bond 0.05969 ( 539) hydrogen bonds : angle 4.52760 ( 1500) covalent geometry : bond 0.00586 (12868) covalent geometry : angle 0.64008 (17396) *********************** 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 179 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 1.499 Fit side-chains REVERT: A 190 GLN cc_start: 0.8421 (mp10) cc_final: 0.8155 (mm-40) REVERT: A 225 LYS cc_start: 0.8009 (mtpt) cc_final: 0.7653 (mttt) REVERT: A 228 LYS cc_start: 0.7658 (mtmp) cc_final: 0.7179 (mmmt) REVERT: A 355 ASP cc_start: 0.8734 (t70) cc_final: 0.8326 (t0) REVERT: A 469 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8499 (ptt90) REVERT: A 485 HIS cc_start: 0.9055 (OUTLIER) cc_final: 0.8757 (t-170) REVERT: B 106 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7603 (ttp80) REVERT: B 184 ASP cc_start: 0.7605 (t0) cc_final: 0.7388 (t0) REVERT: B 460 TYR cc_start: 0.9043 (t80) cc_final: 0.8808 (t80) REVERT: C 190 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7174 (mt0) REVERT: C 195 GLU cc_start: 0.7842 (mp0) cc_final: 0.7451 (mp0) REVERT: C 200 GLU cc_start: 0.7232 (tt0) cc_final: 0.6833 (tt0) REVERT: C 348 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: C 362 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: C 373 ARG cc_start: 0.8288 (mtp85) cc_final: 0.7864 (mmm160) REVERT: D 117 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8463 (mtp180) REVERT: D 232 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: D 525 MET cc_start: 0.9119 (tpp) cc_final: 0.8800 (tpp) outliers start: 47 outliers final: 18 residues processed: 170 average time/residue: 1.5197 time to fit residues: 277.5113 Evaluate side-chains 150 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 469 ARG Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 190 GLN 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 117 ARG 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 379 LYS 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 101 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 102 optimal weight: 0.0040 chunk 86 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 123 optimal weight: 0.3980 chunk 147 optimal weight: 5.9990 chunk 70 optimal weight: 0.0670 overall best weight: 0.3730 ------------------------------------------------------------------------------- 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 C 300 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.132945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.105622 restraints weight = 16678.626| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.76 r_work: 0.3132 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12868 Z= 0.096 Angle : 0.499 10.173 17396 Z= 0.261 Chirality : 0.041 0.141 1908 Planarity : 0.003 0.038 2208 Dihedral : 4.019 15.068 1740 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.63 % Allowed : 17.36 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.21), residues: 1576 helix: 2.30 (0.22), residues: 524 sheet: 0.42 (0.39), residues: 188 loop : 0.02 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 454 HIS 0.013 0.001 HIS C 191 PHE 0.009 0.001 PHE A 374 TYR 0.014 0.001 TYR A 328 ARG 0.004 0.000 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 539) hydrogen bonds : angle 4.03794 ( 1500) covalent geometry : bond 0.00218 (12868) covalent geometry : angle 0.49852 (17396) *********************** 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 159 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 1.397 Fit side-chains REVERT: A 190 GLN cc_start: 0.8358 (mp10) cc_final: 0.8083 (mm-40) REVERT: A 228 LYS cc_start: 0.7509 (mtmp) cc_final: 0.6826 (mmmt) REVERT: A 232 GLU cc_start: 0.7522 (pp20) cc_final: 0.7057 (mp0) REVERT: A 355 ASP cc_start: 0.8646 (t70) cc_final: 0.8380 (t0) REVERT: B 460 TYR cc_start: 0.9030 (t80) cc_final: 0.8799 (t80) REVERT: B 502 GLU cc_start: 0.6799 (pm20) cc_final: 0.6519 (mp0) REVERT: C 195 GLU cc_start: 0.7807 (mp0) cc_final: 0.7508 (mp0) REVERT: C 200 GLU cc_start: 0.7141 (tt0) cc_final: 0.6717 (tt0) REVERT: C 373 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7782 (mmm160) outliers start: 22 outliers final: 11 residues processed: 153 average time/residue: 1.6009 time to fit residues: 262.6741 Evaluate side-chains 136 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 379 LYS 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 104 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 114 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.131112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.103446 restraints weight = 16741.148| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.78 r_work: 0.3100 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12868 Z= 0.126 Angle : 0.528 9.777 17396 Z= 0.275 Chirality : 0.042 0.140 1908 Planarity : 0.004 0.038 2208 Dihedral : 4.053 16.023 1740 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.71 % Allowed : 17.58 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.21), residues: 1576 helix: 2.26 (0.22), residues: 528 sheet: 1.02 (0.43), residues: 148 loop : -0.11 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 395 HIS 0.011 0.001 HIS C 191 PHE 0.013 0.001 PHE D 374 TYR 0.015 0.001 TYR A 328 ARG 0.002 0.000 ARG A 469 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 539) hydrogen bonds : angle 4.11914 ( 1500) covalent geometry : bond 0.00302 (12868) covalent geometry : angle 0.52821 (17396) *********************** 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 154 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.396 Fit side-chains REVERT: A 190 GLN cc_start: 0.8386 (mp10) cc_final: 0.8148 (mm-40) REVERT: A 228 LYS cc_start: 0.7542 (mtmp) cc_final: 0.6829 (mmmt) REVERT: A 232 GLU cc_start: 0.7642 (pp20) cc_final: 0.7150 (mp0) REVERT: A 355 ASP cc_start: 0.8703 (t70) cc_final: 0.8426 (t0) REVERT: A 485 HIS cc_start: 0.8980 (OUTLIER) cc_final: 0.8757 (t-90) REVERT: B 106 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7602 (ttp80) REVERT: B 502 GLU cc_start: 0.6851 (pm20) cc_final: 0.6575 (mp0) REVERT: C 120 ASP cc_start: 0.8268 (m-30) cc_final: 0.7949 (m-30) REVERT: C 191 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7194 (t-90) REVERT: C 195 GLU cc_start: 0.7816 (mp0) cc_final: 0.7444 (mp0) REVERT: C 320 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8162 (tp40) REVERT: C 348 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: C 373 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7814 (mmm160) outliers start: 23 outliers final: 13 residues processed: 149 average time/residue: 1.8676 time to fit residues: 299.6653 Evaluate side-chains 139 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 A residue 485 HIS 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 348 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 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 34 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.128045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.100770 restraints weight = 16785.148| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.87 r_work: 0.3059 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12868 Z= 0.228 Angle : 0.635 11.541 17396 Z= 0.332 Chirality : 0.046 0.146 1908 Planarity : 0.004 0.044 2208 Dihedral : 4.420 18.665 1740 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.08 % Allowed : 17.88 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1576 helix: 1.98 (0.22), residues: 528 sheet: 1.06 (0.43), residues: 140 loop : -0.33 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 464 HIS 0.026 0.002 HIS C 191 PHE 0.016 0.002 PHE D 423 TYR 0.026 0.002 TYR C 192 ARG 0.004 0.001 ARG D 545 Details of bonding type rmsd hydrogen bonds : bond 0.05752 ( 539) hydrogen bonds : angle 4.45439 ( 1500) covalent geometry : bond 0.00565 (12868) covalent geometry : angle 0.63485 (17396) *********************** 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 157 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 1.471 Fit side-chains REVERT: A 106 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6938 (ptm-80) REVERT: A 190 GLN cc_start: 0.8387 (mp10) cc_final: 0.8169 (mm-40) REVERT: A 228 LYS cc_start: 0.7598 (mtmp) cc_final: 0.6826 (mmmt) REVERT: A 232 GLU cc_start: 0.7639 (pp20) cc_final: 0.7092 (mp0) REVERT: A 355 ASP cc_start: 0.8762 (t70) cc_final: 0.8422 (t0) REVERT: A 485 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.8774 (t-170) REVERT: B 184 ASP cc_start: 0.7552 (t0) cc_final: 0.7319 (t0) REVERT: C 200 GLU cc_start: 0.7327 (tt0) cc_final: 0.6856 (tt0) REVERT: C 320 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8201 (tp40) REVERT: C 348 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: C 373 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7886 (mmm160) outliers start: 28 outliers final: 14 residues processed: 151 average time/residue: 1.7166 time to fit residues: 278.9819 Evaluate side-chains 139 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG 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 A residue 485 HIS Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 348 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 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 52 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 130 optimal weight: 0.0970 chunk 69 optimal weight: 0.0970 chunk 64 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.132356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.104991 restraints weight = 16660.898| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.78 r_work: 0.3124 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12868 Z= 0.098 Angle : 0.514 10.911 17396 Z= 0.269 Chirality : 0.041 0.140 1908 Planarity : 0.004 0.040 2208 Dihedral : 4.041 15.528 1740 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.11 % Allowed : 18.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1576 helix: 2.23 (0.22), residues: 528 sheet: 0.99 (0.43), residues: 148 loop : -0.11 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 395 HIS 0.008 0.001 HIS B 191 PHE 0.011 0.001 PHE A 374 TYR 0.015 0.001 TYR A 328 ARG 0.006 0.000 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 539) hydrogen bonds : angle 4.07670 ( 1500) covalent geometry : bond 0.00219 (12868) covalent geometry : angle 0.51444 (17396) ********************** 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 146 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.583 Fit side-chains REVERT: A 106 ARG cc_start: 0.6852 (ptm-80) cc_final: 0.6578 (ptm-80) REVERT: A 228 LYS cc_start: 0.7514 (mtmp) cc_final: 0.6761 (mmmt) REVERT: A 232 GLU cc_start: 0.7608 (pp20) cc_final: 0.7160 (mp0) REVERT: A 289 GLN cc_start: 0.6785 (OUTLIER) cc_final: 0.6365 (mp10) REVERT: A 355 ASP cc_start: 0.8638 (t70) cc_final: 0.8435 (t0) REVERT: B 184 ASP cc_start: 0.7503 (t0) cc_final: 0.7266 (t0) REVERT: C 120 ASP cc_start: 0.8194 (m-30) cc_final: 0.7903 (m-30) REVERT: C 200 GLU cc_start: 0.7242 (tt0) cc_final: 0.6849 (tt0) REVERT: C 320 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8158 (tp40) REVERT: C 356 MET cc_start: 0.8674 (mtp) cc_final: 0.8464 (mtp) REVERT: C 373 ARG cc_start: 0.8202 (mtp85) cc_final: 0.7789 (mmm160) outliers start: 15 outliers final: 11 residues processed: 143 average time/residue: 1.5223 time to fit residues: 234.6315 Evaluate side-chains 135 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 157 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 153 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 149 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 427 ASN B 429 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 = 0.3603 r_free = 0.3603 target = 0.131752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.104527 restraints weight = 16715.277| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.76 r_work: 0.3115 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3376 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= 0.111 Angle : 0.532 10.750 17396 Z= 0.276 Chirality : 0.041 0.139 1908 Planarity : 0.004 0.038 2208 Dihedral : 3.982 15.683 1740 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.96 % Allowed : 19.21 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.21), residues: 1576 helix: 2.27 (0.22), residues: 528 sheet: 1.06 (0.43), residues: 148 loop : -0.10 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 395 HIS 0.011 0.001 HIS C 191 PHE 0.011 0.001 PHE A 374 TYR 0.014 0.001 TYR A 328 ARG 0.005 0.000 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 539) hydrogen bonds : angle 4.06483 ( 1500) covalent geometry : bond 0.00263 (12868) covalent geometry : angle 0.53234 (17396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9181.32 seconds wall clock time: 159 minutes 49.70 seconds (9589.70 seconds total)