Starting phenix.real_space_refine on Tue Dec 31 07:12:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sq8_25379/12_2024/7sq8_25379_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sq8_25379/12_2024/7sq8_25379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.598 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sq8_25379/12_2024/7sq8_25379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sq8_25379/12_2024/7sq8_25379.map" model { file = "/net/cci-nas-00/data/ceres_data/7sq8_25379/12_2024/7sq8_25379_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sq8_25379/12_2024/7sq8_25379_neut.cif" } resolution = 2.598 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= 0.007 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: 5 Type Number sf(0) Gaussians S 96 5.16 5 Na 1 4.78 5 C 9904 2.51 5 N 2500 2.21 5 O 2616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15117 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3749 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 13, 'TRANS': 449} Chain breaks: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, F, G, H Time building chain proxies: 8.22, per 1000 atoms: 0.54 Number of scatterers: 15117 At special positions: 0 Unit cell: (108.73, 108.73, 114.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 Na 1 11.00 O 2616 8.00 N 2500 7.00 C 9904 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 230 " " NAG F 1 " - " ASN B 230 " " NAG G 1 " - " ASN C 230 " " NAG H 1 " - " ASN D 230 " Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.8 seconds 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 66.5% alpha, 20.7% 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 41 through 48 Processing helix chain 'A' and resid 51 through 58 removed outlier: 3.867A pdb=" N ARG A 57 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 106 removed outlier: 4.073A pdb=" N MET A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 138 Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 297 through 338 removed outlier: 3.523A pdb=" N TRP A 335 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 352 through 377 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.622A pdb=" N CYS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.889A pdb=" N LEU A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 448 removed outlier: 4.030A pdb=" N LEU A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 3.997A pdb=" N VAL A 434 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 4.064A pdb=" N ARG A 455 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 469 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.819A pdb=" N THR A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 508 Processing helix chain 'A' and resid 508 through 526 Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 51 through 58 removed outlier: 3.867A pdb=" N ARG B 57 " --> pdb=" O CYS B 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 106 removed outlier: 4.073A pdb=" N MET B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 138 Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 297 through 338 removed outlier: 3.523A pdb=" N TRP B 335 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 349 Processing helix chain 'B' and resid 352 through 377 Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.622A pdb=" N CYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.889A pdb=" N LEU B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 448 removed outlier: 4.030A pdb=" N LEU B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 3.998A pdb=" N VAL B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 removed outlier: 4.064A pdb=" N ARG B 455 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 469 Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.813A pdb=" N THR B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 508 Processing helix chain 'B' and resid 508 through 526 Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 51 through 58 removed outlier: 3.867A pdb=" N ARG C 57 " --> pdb=" O CYS C 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 58 " --> pdb=" O ASP C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 106 removed outlier: 4.073A pdb=" N MET C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 138 Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 297 through 338 removed outlier: 3.523A pdb=" N TRP C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 349 Processing helix chain 'C' and resid 352 through 377 Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.622A pdb=" N CYS C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 3.889A pdb=" N LEU C 405 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 448 removed outlier: 4.030A pdb=" N LEU C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 3.998A pdb=" N VAL C 434 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 455 removed outlier: 4.064A pdb=" N ARG C 455 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 469 Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.837A pdb=" N THR C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 508 Processing helix chain 'C' and resid 508 through 526 Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 51 through 58 removed outlier: 3.867A pdb=" N ARG D 57 " --> pdb=" O CYS D 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 58 " --> pdb=" O ASP D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 106 removed outlier: 4.072A pdb=" N MET D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 138 Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 297 through 338 removed outlier: 3.523A pdb=" N TRP D 335 " --> pdb=" O VAL D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 349 Processing helix chain 'D' and resid 352 through 377 Processing helix chain 'D' and resid 382 through 401 removed outlier: 3.622A pdb=" N CYS D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.889A pdb=" N LEU D 405 " --> pdb=" O VAL D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 448 removed outlier: 4.030A pdb=" N LEU D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 3.998A pdb=" N VAL D 434 " --> pdb=" O CYS D 430 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 455 removed outlier: 4.063A pdb=" N ARG D 455 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 469 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.814A pdb=" N THR D 476 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 508 Processing helix chain 'D' and resid 508 through 526 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP A 252 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP A 252 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ARG A 168 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 231 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS A 166 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE A 233 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA A 164 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 removed outlier: 3.596A pdb=" N ASP A 176 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP B 252 " --> pdb=" O ASN B 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP B 252 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ARG B 168 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL B 231 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS B 166 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE B 233 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA B 164 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.596A pdb=" N ASP B 176 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP C 252 " --> pdb=" O ASN C 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP C 252 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG C 168 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL C 231 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS C 166 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE C 233 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA C 164 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 175 through 176 removed outlier: 3.596A pdb=" N ASP C 176 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP D 252 " --> pdb=" O ASN D 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP D 252 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG D 168 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL D 231 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS D 166 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE D 233 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA D 164 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 175 through 176 removed outlier: 3.597A pdb=" N ASP D 176 " --> pdb=" O THR D 181 " (cutoff:3.500A) 1132 hydrogen bonds defined for protein. 3288 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: 5.50 Time building geometry restraints manager: 4.52 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: 3190 1.33 - 1.45: 3635 1.45 - 1.57: 8511 1.57 - 1.69: 4 1.69 - 1.81: 132 Bond restraints: 15472 Sorted by residual: bond pdb=" CA ASP A 196 " pdb=" C ASP A 196 " ideal model delta sigma weight residual 1.523 1.574 -0.051 1.06e-02 8.90e+03 2.32e+01 bond pdb=" CA ASP D 196 " pdb=" C ASP D 196 " ideal model delta sigma weight residual 1.523 1.574 -0.051 1.06e-02 8.90e+03 2.31e+01 bond pdb=" CA ASP B 196 " pdb=" C ASP B 196 " ideal model delta sigma weight residual 1.523 1.573 -0.051 1.06e-02 8.90e+03 2.28e+01 bond pdb=" CA ASP C 196 " pdb=" C ASP C 196 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.06e-02 8.90e+03 2.26e+01 bond pdb=" C ASP C 196 " pdb=" N PRO C 197 " ideal model delta sigma weight residual 1.335 1.377 -0.043 1.15e-02 7.56e+03 1.37e+01 ... (remaining 15467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 20177 1.29 - 2.57: 653 2.57 - 3.86: 126 3.86 - 5.14: 20 5.14 - 6.43: 4 Bond angle restraints: 20980 Sorted by residual: angle pdb=" C ALA B 58 " pdb=" N LYS B 59 " pdb=" CA LYS B 59 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C ALA C 58 " pdb=" N LYS C 59 " pdb=" CA LYS C 59 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C ALA A 58 " pdb=" N LYS A 59 " pdb=" CA LYS A 59 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C ALA D 58 " pdb=" N LYS D 59 " pdb=" CA LYS D 59 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" N ALA C 482 " pdb=" CA ALA C 482 " pdb=" C ALA C 482 " ideal model delta sigma weight residual 110.97 114.61 -3.64 1.09e+00 8.42e-01 1.12e+01 ... (remaining 20975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 8320 17.30 - 34.59: 689 34.59 - 51.89: 120 51.89 - 69.18: 11 69.18 - 86.48: 20 Dihedral angle restraints: 9160 sinusoidal: 3724 harmonic: 5436 Sorted by residual: dihedral pdb=" CG ARG D 419 " pdb=" CD ARG D 419 " pdb=" NE ARG D 419 " pdb=" CZ ARG D 419 " ideal model delta sinusoidal sigma weight residual -90.00 -131.89 41.89 2 1.50e+01 4.44e-03 9.51e+00 dihedral pdb=" CG ARG C 419 " pdb=" CD ARG C 419 " pdb=" NE ARG C 419 " pdb=" CZ ARG C 419 " ideal model delta sinusoidal sigma weight residual -90.00 -131.84 41.84 2 1.50e+01 4.44e-03 9.49e+00 dihedral pdb=" CG ARG B 419 " pdb=" CD ARG B 419 " pdb=" NE ARG B 419 " pdb=" CZ ARG B 419 " ideal model delta sinusoidal sigma weight residual -90.00 -131.80 41.80 2 1.50e+01 4.44e-03 9.48e+00 ... (remaining 9157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1991 0.052 - 0.104: 367 0.104 - 0.156: 66 0.156 - 0.208: 0 0.208 - 0.260: 12 Chirality restraints: 2436 Sorted by residual: chirality pdb=" CA HIS D 486 " pdb=" N HIS D 486 " pdb=" C HIS D 486 " pdb=" CB HIS D 486 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA HIS C 486 " pdb=" N HIS C 486 " pdb=" C HIS C 486 " pdb=" CB HIS C 486 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA HIS A 486 " pdb=" N HIS A 486 " pdb=" C HIS A 486 " pdb=" CB HIS A 486 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 2433 not shown) Planarity restraints: 2572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 471 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" C ASP D 471 " 0.024 2.00e-02 2.50e+03 pdb=" O ASP D 471 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP D 472 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 471 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C ASP B 471 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP B 471 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP B 472 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 471 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.65e+00 pdb=" C ASP C 471 " 0.022 2.00e-02 2.50e+03 pdb=" O ASP C 471 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP C 472 " -0.007 2.00e-02 2.50e+03 ... (remaining 2569 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 994 2.74 - 3.28: 15338 3.28 - 3.82: 25994 3.82 - 4.36: 30876 4.36 - 4.90: 52933 Nonbonded interactions: 126135 Sorted by model distance: nonbonded pdb=" OD1 ASP C 134 " pdb=" OH TYR C 218 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP D 134 " pdb=" OH TYR D 218 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP A 134 " pdb=" OH TYR A 218 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP B 134 " pdb=" OH TYR B 218 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP A 384 " pdb=" OH TYR B 450 " model vdw 2.243 3.040 ... (remaining 126130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 40 through 527) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.450 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: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 34.420 Find NCS groups from input model: 0.530 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:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.004 0.051 15472 Z= 0.229 Angle : 0.554 6.426 20980 Z= 0.325 Chirality : 0.044 0.260 2436 Planarity : 0.003 0.028 2568 Dihedral : 13.318 86.476 5656 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.20), residues: 1828 helix: 2.07 (0.16), residues: 1140 sheet: 1.05 (0.34), residues: 252 loop : -0.70 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 398 HIS 0.003 0.001 HIS B 103 PHE 0.011 0.001 PHE A 505 TYR 0.015 0.001 TYR C 497 ARG 0.002 0.000 ARG D 419 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.721 Fit side-chains REVERT: A 322 ARG cc_start: 0.6572 (mtp-110) cc_final: 0.6359 (ttm170) REVERT: A 324 PHE cc_start: 0.6479 (t80) cc_final: 0.6165 (t80) REVERT: B 322 ARG cc_start: 0.6555 (mtp-110) cc_final: 0.6333 (ttm170) REVERT: B 324 PHE cc_start: 0.6414 (t80) cc_final: 0.6098 (t80) REVERT: C 322 ARG cc_start: 0.6553 (mtp-110) cc_final: 0.6337 (ttm170) REVERT: C 324 PHE cc_start: 0.6428 (t80) cc_final: 0.6101 (t80) REVERT: D 324 PHE cc_start: 0.6446 (t80) cc_final: 0.6118 (t80) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 1.0976 time to fit residues: 232.6380 Evaluate side-chains 129 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 226 HIS A 352 ASN A 483 GLN B 194 GLN B 226 HIS B 352 ASN B 483 GLN C 194 GLN C 226 HIS C 352 ASN C 483 GLN D 194 GLN D 226 HIS D 352 ASN D 483 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15472 Z= 0.355 Angle : 0.618 4.827 20980 Z= 0.335 Chirality : 0.046 0.147 2436 Planarity : 0.005 0.039 2568 Dihedral : 5.082 33.938 2208 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.36 % Allowed : 5.86 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.19), residues: 1828 helix: 2.11 (0.15), residues: 1100 sheet: 1.00 (0.34), residues: 252 loop : -0.48 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 398 HIS 0.004 0.002 HIS B 174 PHE 0.018 0.002 PHE B 474 TYR 0.016 0.002 TYR C 497 ARG 0.004 0.001 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 1.681 Fit side-chains REVERT: A 322 ARG cc_start: 0.6667 (mtp-110) cc_final: 0.6393 (ttm170) REVERT: A 324 PHE cc_start: 0.6428 (t80) cc_final: 0.6200 (t80) REVERT: A 483 GLN cc_start: 0.6005 (OUTLIER) cc_final: 0.4682 (mm110) REVERT: B 322 ARG cc_start: 0.6642 (mtp-110) cc_final: 0.6348 (ttm170) REVERT: B 324 PHE cc_start: 0.6412 (t80) cc_final: 0.6194 (t80) REVERT: B 483 GLN cc_start: 0.5998 (OUTLIER) cc_final: 0.4683 (mm110) REVERT: C 322 ARG cc_start: 0.6629 (mtp-110) cc_final: 0.6343 (ttm170) REVERT: C 324 PHE cc_start: 0.6388 (t80) cc_final: 0.6175 (t80) REVERT: C 483 GLN cc_start: 0.6007 (OUTLIER) cc_final: 0.4711 (mm-40) REVERT: D 324 PHE cc_start: 0.6440 (t80) cc_final: 0.6175 (t80) REVERT: D 483 GLN cc_start: 0.6011 (OUTLIER) cc_final: 0.4690 (mm110) outliers start: 39 outliers final: 16 residues processed: 162 average time/residue: 1.1504 time to fit residues: 209.2580 Evaluate side-chains 145 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 483 GLN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 chunk 113 optimal weight: 0.0020 chunk 46 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15472 Z= 0.300 Angle : 0.575 4.772 20980 Z= 0.314 Chirality : 0.044 0.142 2436 Planarity : 0.004 0.032 2568 Dihedral : 4.935 30.991 2208 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.29 % Allowed : 7.97 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.19), residues: 1828 helix: 2.06 (0.15), residues: 1120 sheet: 1.08 (0.33), residues: 252 loop : -0.50 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 398 HIS 0.004 0.001 HIS A 234 PHE 0.016 0.002 PHE C 474 TYR 0.015 0.002 TYR C 497 ARG 0.003 0.001 ARG D 200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 1.528 Fit side-chains REVERT: A 322 ARG cc_start: 0.6702 (mtp-110) cc_final: 0.6452 (ttm110) REVERT: A 324 PHE cc_start: 0.6405 (t80) cc_final: 0.6195 (t80) REVERT: A 371 MET cc_start: 0.7968 (mtp) cc_final: 0.7583 (mtm) REVERT: B 322 ARG cc_start: 0.6692 (mtp-110) cc_final: 0.6425 (ttm110) REVERT: C 322 ARG cc_start: 0.6659 (mtp-110) cc_final: 0.6400 (ttm110) outliers start: 38 outliers final: 16 residues processed: 160 average time/residue: 1.1136 time to fit residues: 200.4063 Evaluate side-chains 139 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 483 GLN C 483 GLN D 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15472 Z= 0.269 Angle : 0.557 6.167 20980 Z= 0.303 Chirality : 0.043 0.138 2436 Planarity : 0.004 0.031 2568 Dihedral : 4.813 29.716 2208 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.66 % Allowed : 8.39 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.19), residues: 1828 helix: 2.14 (0.15), residues: 1120 sheet: 1.19 (0.33), residues: 252 loop : -0.52 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 398 HIS 0.004 0.001 HIS B 234 PHE 0.015 0.002 PHE C 474 TYR 0.015 0.002 TYR C 497 ARG 0.003 0.001 ARG D 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 1.697 Fit side-chains REVERT: A 283 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7084 (tt0) REVERT: A 322 ARG cc_start: 0.6694 (mtp-110) cc_final: 0.6457 (ttm110) REVERT: B 283 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7073 (tt0) REVERT: B 322 ARG cc_start: 0.6681 (mtp-110) cc_final: 0.6421 (ttm110) REVERT: B 371 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7717 (mtm) REVERT: C 283 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: C 322 ARG cc_start: 0.6630 (mtp-110) cc_final: 0.6399 (ttm110) REVERT: C 371 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7716 (mtm) REVERT: D 283 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7124 (tt0) outliers start: 44 outliers final: 16 residues processed: 159 average time/residue: 1.2186 time to fit residues: 216.4478 Evaluate side-chains 142 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.9980 chunk 100 optimal weight: 0.0270 chunk 2 optimal weight: 0.0770 chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 151 optimal weight: 0.3980 chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 ASN B 469 ASN C 469 ASN D 469 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15472 Z= 0.134 Angle : 0.464 5.882 20980 Z= 0.254 Chirality : 0.039 0.126 2436 Planarity : 0.003 0.036 2568 Dihedral : 4.206 25.511 2208 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.63 % Allowed : 10.33 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.19), residues: 1828 helix: 2.35 (0.15), residues: 1140 sheet: 1.39 (0.34), residues: 252 loop : -0.81 (0.25), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 491 HIS 0.003 0.001 HIS D 526 PHE 0.013 0.001 PHE A 474 TYR 0.012 0.001 TYR A 497 ARG 0.002 0.000 ARG D 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.766 Fit side-chains REVERT: A 175 VAL cc_start: 0.7472 (t) cc_final: 0.7235 (m) REVERT: A 322 ARG cc_start: 0.6644 (mtp-110) cc_final: 0.6366 (ttm110) REVERT: B 175 VAL cc_start: 0.7469 (t) cc_final: 0.7235 (m) REVERT: B 322 ARG cc_start: 0.6602 (mtp-110) cc_final: 0.6380 (ttm110) REVERT: B 371 MET cc_start: 0.7969 (mtm) cc_final: 0.7665 (mtm) REVERT: C 175 VAL cc_start: 0.7446 (t) cc_final: 0.7209 (m) REVERT: C 322 ARG cc_start: 0.6590 (mtp-110) cc_final: 0.6368 (ttm110) REVERT: C 371 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7623 (mtm) REVERT: D 175 VAL cc_start: 0.7448 (t) cc_final: 0.7215 (m) outliers start: 27 outliers final: 4 residues processed: 146 average time/residue: 1.2666 time to fit residues: 205.9376 Evaluate side-chains 120 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 74 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 327 GLN B 226 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15472 Z= 0.321 Angle : 0.587 6.525 20980 Z= 0.317 Chirality : 0.044 0.138 2436 Planarity : 0.004 0.033 2568 Dihedral : 4.878 30.624 2208 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.66 % Allowed : 9.96 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 1828 helix: 2.31 (0.15), residues: 1116 sheet: 1.42 (0.34), residues: 252 loop : -0.56 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 398 HIS 0.004 0.002 HIS A 234 PHE 0.016 0.002 PHE D 235 TYR 0.016 0.002 TYR B 497 ARG 0.004 0.001 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 2.163 Fit side-chains REVERT: A 283 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7078 (tt0) REVERT: A 322 ARG cc_start: 0.6706 (mtp-110) cc_final: 0.6471 (ttm110) REVERT: B 283 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7032 (tt0) REVERT: B 322 ARG cc_start: 0.6687 (mtp-110) cc_final: 0.6423 (ttm110) REVERT: B 371 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7674 (mtm) REVERT: C 283 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6998 (tt0) REVERT: C 322 ARG cc_start: 0.6663 (mtp-110) cc_final: 0.6410 (ttm110) REVERT: C 371 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7711 (mtm) REVERT: D 283 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7059 (tt0) outliers start: 44 outliers final: 12 residues processed: 159 average time/residue: 1.3028 time to fit residues: 231.6202 Evaluate side-chains 140 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15472 Z= 0.254 Angle : 0.550 6.346 20980 Z= 0.299 Chirality : 0.042 0.132 2436 Planarity : 0.004 0.034 2568 Dihedral : 4.755 29.473 2208 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.23 % Allowed : 10.99 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 1828 helix: 2.34 (0.15), residues: 1116 sheet: 1.37 (0.34), residues: 252 loop : -0.62 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 398 HIS 0.004 0.001 HIS D 526 PHE 0.024 0.002 PHE C 324 TYR 0.016 0.002 TYR D 497 ARG 0.003 0.001 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 1.683 Fit side-chains REVERT: A 252 ASP cc_start: 0.7384 (m-30) cc_final: 0.7169 (m-30) REVERT: A 283 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7017 (tt0) REVERT: A 322 ARG cc_start: 0.6676 (mtp-110) cc_final: 0.6455 (ttm110) REVERT: B 283 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6998 (tt0) REVERT: B 322 ARG cc_start: 0.6681 (mtp-110) cc_final: 0.6417 (ttm110) REVERT: B 371 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7662 (mtm) REVERT: C 283 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6965 (tt0) REVERT: C 322 ARG cc_start: 0.6637 (mtp-110) cc_final: 0.6398 (ttm110) REVERT: C 371 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7701 (mtm) REVERT: D 283 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6984 (tt0) outliers start: 37 outliers final: 15 residues processed: 141 average time/residue: 1.2650 time to fit residues: 198.2016 Evaluate side-chains 140 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.3980 chunk 70 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15472 Z= 0.206 Angle : 0.518 6.520 20980 Z= 0.283 Chirality : 0.041 0.128 2436 Planarity : 0.003 0.035 2568 Dihedral : 4.595 29.117 2208 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.17 % Allowed : 11.11 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.19), residues: 1828 helix: 2.41 (0.15), residues: 1120 sheet: 1.40 (0.34), residues: 252 loop : -0.55 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 398 HIS 0.004 0.001 HIS D 526 PHE 0.031 0.001 PHE B 324 TYR 0.016 0.001 TYR D 497 ARG 0.003 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 1.763 Fit side-chains REVERT: A 283 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6976 (tt0) REVERT: A 322 ARG cc_start: 0.6669 (mtp-110) cc_final: 0.6456 (ttm110) REVERT: B 283 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6906 (tt0) REVERT: B 322 ARG cc_start: 0.6676 (mtp-110) cc_final: 0.6417 (ttm110) REVERT: B 371 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7650 (mtm) REVERT: C 283 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6916 (tt0) REVERT: C 322 ARG cc_start: 0.6627 (mtp-110) cc_final: 0.6402 (ttm110) REVERT: C 371 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7696 (mtm) REVERT: D 283 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6953 (tt0) outliers start: 36 outliers final: 13 residues processed: 151 average time/residue: 1.2515 time to fit residues: 210.6840 Evaluate side-chains 146 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 165 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 327 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15472 Z= 0.158 Angle : 0.484 6.110 20980 Z= 0.265 Chirality : 0.039 0.126 2436 Planarity : 0.003 0.036 2568 Dihedral : 4.304 26.255 2208 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.21 % Allowed : 11.78 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.19), residues: 1828 helix: 2.43 (0.15), residues: 1140 sheet: 1.53 (0.34), residues: 252 loop : -0.95 (0.25), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 398 HIS 0.003 0.001 HIS A 226 PHE 0.036 0.001 PHE C 324 TYR 0.014 0.001 TYR A 497 ARG 0.002 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.737 Fit side-chains REVERT: A 283 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6901 (tt0) REVERT: A 322 ARG cc_start: 0.6631 (mtp-110) cc_final: 0.6373 (ttm110) REVERT: B 322 ARG cc_start: 0.6637 (mtp-110) cc_final: 0.6406 (ttm110) REVERT: B 371 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7639 (mtm) REVERT: C 283 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6834 (tt0) REVERT: C 322 ARG cc_start: 0.6601 (mtp-110) cc_final: 0.6315 (ttm110) REVERT: C 371 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7676 (mtm) REVERT: D 283 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6882 (tt0) outliers start: 20 outliers final: 9 residues processed: 138 average time/residue: 1.2537 time to fit residues: 192.2967 Evaluate side-chains 133 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 168 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 226 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15472 Z= 0.153 Angle : 0.479 5.689 20980 Z= 0.262 Chirality : 0.039 0.127 2436 Planarity : 0.003 0.036 2568 Dihedral : 4.175 23.085 2208 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.91 % Allowed : 12.26 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.19), residues: 1828 helix: 2.50 (0.15), residues: 1140 sheet: 1.61 (0.34), residues: 252 loop : -0.96 (0.25), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 398 HIS 0.004 0.001 HIS B 226 PHE 0.035 0.001 PHE A 324 TYR 0.015 0.001 TYR A 497 ARG 0.002 0.000 ARG A 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.729 Fit side-chains REVERT: A 283 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6899 (tt0) REVERT: A 322 ARG cc_start: 0.6653 (mtp-110) cc_final: 0.6398 (ttm110) REVERT: B 283 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6797 (tt0) REVERT: B 322 ARG cc_start: 0.6614 (mtp-110) cc_final: 0.6330 (ttm110) REVERT: B 371 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7677 (mtm) REVERT: C 322 ARG cc_start: 0.6613 (mtp-110) cc_final: 0.6336 (ttm110) REVERT: C 371 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7677 (mtm) outliers start: 15 outliers final: 9 residues processed: 133 average time/residue: 1.2351 time to fit residues: 183.2084 Evaluate side-chains 138 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 128 optimal weight: 0.7980 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.144023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.103265 restraints weight = 16191.549| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.68 r_work: 0.2806 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15472 Z= 0.312 Angle : 0.592 6.539 20980 Z= 0.319 Chirality : 0.044 0.141 2436 Planarity : 0.004 0.034 2568 Dihedral : 4.823 28.872 2208 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.57 % Allowed : 11.71 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.19), residues: 1828 helix: 2.38 (0.15), residues: 1116 sheet: 1.43 (0.33), residues: 252 loop : -0.81 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 398 HIS 0.004 0.002 HIS D 103 PHE 0.033 0.002 PHE C 324 TYR 0.016 0.002 TYR D 497 ARG 0.004 0.001 ARG A 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4178.57 seconds wall clock time: 76 minutes 38.78 seconds (4598.78 seconds total)