Starting phenix.real_space_refine on Sun Dec 29 10:12:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u2t_26319/12_2024/7u2t_26319.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2t_26319/12_2024/7u2t_26319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u2t_26319/12_2024/7u2t_26319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2t_26319/12_2024/7u2t_26319.map" model { file = "/net/cci-nas-00/data/ceres_data/7u2t_26319/12_2024/7u2t_26319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2t_26319/12_2024/7u2t_26319.cif" } resolution = 3.25 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= 0.007 sd= 0.158 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 88 5.16 5 C 6524 2.51 5 N 1728 2.21 5 O 1960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 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: 10300 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2547 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 5 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "A" 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 Restraints were copied for chains: C, B, D Time building chain proxies: 5.13, per 1000 atoms: 0.50 Number of scatterers: 10300 At special positions: 0 Unit cell: (117.16, 117.16, 63.8, 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 88 16.00 O 1960 8.00 N 1728 7.00 C 6524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.02 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.05 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 238 " distance=2.07 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 292 " distance=2.02 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 290 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 446 " distance=2.05 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 NAG-ASN " NAG A 501 " - " ASN A 235 " " NAG A 502 " - " ASN A 88 " " NAG B 501 " - " ASN B 235 " " NAG B 502 " - " ASN B 88 " " NAG C 501 " - " ASN C 235 " " NAG C 502 " - " ASN C 88 " " NAG D 501 " - " ASN D 235 " " NAG D 502 " - " ASN D 88 " Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.3 seconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 24 sheets defined 3.9% alpha, 42.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.711A pdb=" N ILE A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.711A pdb=" N ILE B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.711A pdb=" N ILE C 108 " --> pdb=" O ASN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.711A pdb=" N ILE D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.662A pdb=" N SER A 444 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS A 102 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER A 442 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.808A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 157 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER A 160 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE A 174 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 185 removed outlier: 3.778A pdb=" N SER A 180 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA A 204 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR A 215 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU A 206 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 234 removed outlier: 6.579A pdb=" N GLU A 259 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 284 removed outlier: 5.046A pdb=" N CYS A 279 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 291 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS A 281 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR A 289 " --> pdb=" O CYS A 281 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU A 287 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 353 removed outlier: 7.021A pdb=" N LYS A 369 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY A 395 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE A 371 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 389 " --> pdb=" O TRP A 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.662A pdb=" N SER B 444 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS B 102 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER B 442 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.808A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 157 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER B 160 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE B 174 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 180 through 185 removed outlier: 3.778A pdb=" N SER B 180 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 204 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR B 215 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU B 206 " --> pdb=" O THR B 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 234 removed outlier: 6.579A pdb=" N GLU B 259 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 277 through 284 removed outlier: 5.046A pdb=" N CYS B 279 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL B 291 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS B 281 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR B 289 " --> pdb=" O CYS B 281 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU B 287 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 350 through 353 removed outlier: 7.021A pdb=" N LYS B 369 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY B 395 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE B 371 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 389 " --> pdb=" O TRP B 375 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.662A pdb=" N SER C 444 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS C 102 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER C 442 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.808A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR C 157 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER C 160 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE C 174 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 180 through 185 removed outlier: 3.778A pdb=" N SER C 180 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA C 204 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR C 215 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU C 206 " --> pdb=" O THR C 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 232 through 234 removed outlier: 6.579A pdb=" N GLU C 259 " --> pdb=" O ILE C 263 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 277 through 284 removed outlier: 5.046A pdb=" N CYS C 279 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL C 291 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS C 281 " --> pdb=" O THR C 289 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR C 289 " --> pdb=" O CYS C 281 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU C 287 " --> pdb=" O PRO C 283 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 350 through 353 removed outlier: 7.021A pdb=" N LYS C 369 " --> pdb=" O GLY C 395 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY C 395 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE C 371 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 389 " --> pdb=" O TRP C 375 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.662A pdb=" N SER D 444 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS D 102 " --> pdb=" O SER D 442 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER D 442 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.808A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR D 157 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER D 160 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE D 174 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 180 through 185 removed outlier: 3.778A pdb=" N SER D 180 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA D 204 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR D 215 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU D 206 " --> pdb=" O THR D 213 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 232 through 234 removed outlier: 6.579A pdb=" N GLU D 259 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 277 through 284 removed outlier: 5.047A pdb=" N CYS D 279 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL D 291 " --> pdb=" O CYS D 279 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS D 281 " --> pdb=" O THR D 289 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR D 289 " --> pdb=" O CYS D 281 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU D 287 " --> pdb=" O PRO D 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 350 through 353 removed outlier: 7.021A pdb=" N LYS D 369 " --> pdb=" O GLY D 395 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY D 395 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE D 371 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 389 " --> pdb=" O TRP D 375 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 936 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: 3.27 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2811 1.33 - 1.47: 2977 1.47 - 1.60: 4648 1.60 - 1.73: 0 1.73 - 1.86: 112 Bond restraints: 10548 Sorted by residual: bond pdb=" N GLU A 119 " pdb=" CA GLU A 119 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.97e+01 bond pdb=" N GLU C 119 " pdb=" CA GLU C 119 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.97e+01 bond pdb=" N GLU D 119 " pdb=" CA GLU D 119 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.97e+01 bond pdb=" N GLU B 119 " pdb=" CA GLU B 119 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.97e+01 bond pdb=" N CYS D 281 " pdb=" CA CYS D 281 " ideal model delta sigma weight residual 1.454 1.498 -0.043 1.23e-02 6.61e+03 1.25e+01 ... (remaining 10543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 11694 1.83 - 3.66: 2109 3.66 - 5.49: 373 5.49 - 7.32: 95 7.32 - 9.15: 25 Bond angle restraints: 14296 Sorted by residual: angle pdb=" C GLY B 197 " pdb=" N PRO B 198 " pdb=" CA PRO B 198 " ideal model delta sigma weight residual 119.78 128.93 -9.15 1.03e+00 9.43e-01 7.90e+01 angle pdb=" C GLY A 197 " pdb=" N PRO A 198 " pdb=" CA PRO A 198 " ideal model delta sigma weight residual 119.78 128.93 -9.15 1.03e+00 9.43e-01 7.90e+01 angle pdb=" C GLY C 197 " pdb=" N PRO C 198 " pdb=" CA PRO C 198 " ideal model delta sigma weight residual 119.78 128.93 -9.15 1.03e+00 9.43e-01 7.90e+01 angle pdb=" C GLY D 197 " pdb=" N PRO D 198 " pdb=" CA PRO D 198 " ideal model delta sigma weight residual 119.78 128.90 -9.12 1.03e+00 9.43e-01 7.84e+01 angle pdb=" C SER D 153 " pdb=" N PRO D 154 " pdb=" CA PRO D 154 " ideal model delta sigma weight residual 119.56 127.23 -7.67 1.02e+00 9.61e-01 5.65e+01 ... (remaining 14291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 5963 15.12 - 30.24: 218 30.24 - 45.35: 51 45.35 - 60.47: 28 60.47 - 75.59: 16 Dihedral angle restraints: 6276 sinusoidal: 2512 harmonic: 3764 Sorted by residual: dihedral pdb=" C TYR B 402 " pdb=" N TYR B 402 " pdb=" CA TYR B 402 " pdb=" CB TYR B 402 " ideal model delta harmonic sigma weight residual -122.60 -111.67 -10.93 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" C TYR D 402 " pdb=" N TYR D 402 " pdb=" CA TYR D 402 " pdb=" CB TYR D 402 " ideal model delta harmonic sigma weight residual -122.60 -111.67 -10.93 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" C TYR C 402 " pdb=" N TYR C 402 " pdb=" CA TYR C 402 " pdb=" CB TYR C 402 " ideal model delta harmonic sigma weight residual -122.60 -111.67 -10.93 0 2.50e+00 1.60e-01 1.91e+01 ... (remaining 6273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 920 0.071 - 0.142: 467 0.142 - 0.214: 121 0.214 - 0.285: 48 0.285 - 0.356: 16 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CB VAL A 83 " pdb=" CA VAL A 83 " pdb=" CG1 VAL A 83 " pdb=" CG2 VAL A 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.99 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB VAL B 83 " pdb=" CA VAL B 83 " pdb=" CG1 VAL B 83 " pdb=" CG2 VAL B 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.99 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB VAL C 83 " pdb=" CA VAL C 83 " pdb=" CG1 VAL C 83 " pdb=" CG2 VAL C 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.99 0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 1569 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 502 " 0.260 2.00e-02 2.50e+03 2.22e-01 6.16e+02 pdb=" C7 NAG D 502 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG D 502 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG D 502 " -0.385 2.00e-02 2.50e+03 pdb=" O7 NAG D 502 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 502 " 0.260 2.00e-02 2.50e+03 2.22e-01 6.16e+02 pdb=" C7 NAG B 502 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG B 502 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG B 502 " -0.385 2.00e-02 2.50e+03 pdb=" O7 NAG B 502 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " 0.260 2.00e-02 2.50e+03 2.22e-01 6.16e+02 pdb=" C7 NAG C 502 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " -0.385 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " 0.024 2.00e-02 2.50e+03 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 72 2.60 - 3.17: 8370 3.17 - 3.75: 15352 3.75 - 4.32: 23570 4.32 - 4.90: 38409 Nonbonded interactions: 85773 Sorted by model distance: nonbonded pdb=" SG CYS D 281 " pdb=" SG CYS D 290 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS B 281 " pdb=" SG CYS B 290 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS C 281 " pdb=" SG CYS C 290 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS B 92 " pdb=" SG CYS B 417 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS C 92 " pdb=" SG CYS C 417 " model vdw 2.022 3.760 ... (remaining 85768 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' 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.730 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 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 : 0.014 0.075 10548 Z= 0.891 Angle : 1.542 9.154 14296 Z= 1.083 Chirality : 0.095 0.356 1572 Planarity : 0.013 0.222 1804 Dihedral : 10.503 75.590 3844 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.42 % Favored : 96.27 % Rotamer: Outliers : 1.77 % Allowed : 1.77 % Favored : 96.45 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1288 helix: None (None), residues: 0 sheet: 1.06 (0.24), residues: 444 loop : -0.43 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP B 179 HIS 0.003 0.002 HIS D 275 PHE 0.021 0.004 PHE D 406 TYR 0.033 0.005 TYR D 276 ARG 0.005 0.001 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 297 time to evaluate : 1.134 Fit side-chains REVERT: A 119 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7433 (mp0) REVERT: A 220 ARG cc_start: 0.7414 (ttt180) cc_final: 0.7160 (mmt90) REVERT: B 119 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7433 (mp0) REVERT: B 220 ARG cc_start: 0.7414 (ttt180) cc_final: 0.7162 (mmt90) REVERT: C 220 ARG cc_start: 0.7414 (ttt180) cc_final: 0.7155 (mmt90) REVERT: D 220 ARG cc_start: 0.7398 (ttt180) cc_final: 0.7066 (mmt90) outliers start: 20 outliers final: 8 residues processed: 313 average time/residue: 0.2795 time to fit residues: 116.0368 Evaluate side-chains 185 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 185 HIS A 189 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS B 131 GLN B 185 HIS B 189 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 HIS C 131 GLN C 185 HIS C 189 ASN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS D 131 GLN D 185 HIS D 189 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10548 Z= 0.218 Angle : 0.583 3.979 14296 Z= 0.327 Chirality : 0.049 0.148 1572 Planarity : 0.005 0.034 1804 Dihedral : 7.263 59.345 1588 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 0.62 % Favored : 99.07 % Rotamer: Outliers : 1.86 % Allowed : 9.40 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.22), residues: 1288 helix: -2.51 (0.30), residues: 24 sheet: 0.85 (0.22), residues: 508 loop : 0.12 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 179 HIS 0.006 0.003 HIS A 275 PHE 0.018 0.002 PHE C 406 TYR 0.009 0.001 TYR A 316 ARG 0.004 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7476 (ttt180) cc_final: 0.7057 (mpt180) REVERT: A 390 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7843 (ttmm) REVERT: B 220 ARG cc_start: 0.7482 (ttt180) cc_final: 0.7070 (mpt180) REVERT: B 390 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7842 (ttmm) REVERT: C 220 ARG cc_start: 0.7481 (ttt180) cc_final: 0.7068 (mpt180) REVERT: D 220 ARG cc_start: 0.7490 (ttt180) cc_final: 0.7075 (mpt180) REVERT: D 390 LYS cc_start: 0.8225 (ttpt) cc_final: 0.7844 (ttmm) outliers start: 21 outliers final: 17 residues processed: 202 average time/residue: 0.2426 time to fit residues: 68.6630 Evaluate side-chains 171 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 359 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 0.0870 chunk 99 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS B 185 HIS C 185 HIS D 185 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10548 Z= 0.281 Angle : 0.546 3.730 14296 Z= 0.304 Chirality : 0.049 0.148 1572 Planarity : 0.005 0.039 1804 Dihedral : 6.178 56.782 1576 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.55 % Favored : 98.14 % Rotamer: Outliers : 2.84 % Allowed : 11.08 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.23), residues: 1288 helix: -3.04 (0.24), residues: 24 sheet: 0.80 (0.21), residues: 556 loop : 0.13 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 179 HIS 0.006 0.002 HIS A 275 PHE 0.017 0.003 PHE A 406 TYR 0.006 0.001 TYR D 316 ARG 0.003 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8076 (ptm160) cc_final: 0.7795 (ptm-80) REVERT: A 220 ARG cc_start: 0.7505 (ttt180) cc_final: 0.7075 (mpt180) REVERT: B 118 ARG cc_start: 0.8080 (ptm160) cc_final: 0.7795 (ptm-80) REVERT: B 220 ARG cc_start: 0.7512 (ttt180) cc_final: 0.7084 (mpt180) REVERT: B 227 GLN cc_start: 0.8952 (mt0) cc_final: 0.8671 (mt0) REVERT: C 220 ARG cc_start: 0.7506 (ttt180) cc_final: 0.7079 (mpt180) REVERT: C 227 GLN cc_start: 0.8950 (mt0) cc_final: 0.8662 (mt0) REVERT: D 220 ARG cc_start: 0.7517 (ttt180) cc_final: 0.7093 (mpt180) REVERT: D 227 GLN cc_start: 0.8919 (mt0) cc_final: 0.8694 (mt0) outliers start: 32 outliers final: 22 residues processed: 193 average time/residue: 0.2946 time to fit residues: 75.0042 Evaluate side-chains 178 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10548 Z= 0.245 Angle : 0.508 3.873 14296 Z= 0.280 Chirality : 0.048 0.147 1572 Planarity : 0.004 0.039 1804 Dihedral : 5.985 55.421 1576 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.31 % Allowed : 0.93 % Favored : 98.76 % Rotamer: Outliers : 2.75 % Allowed : 12.77 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.23), residues: 1288 helix: -3.18 (0.21), residues: 24 sheet: 0.70 (0.22), residues: 520 loop : -0.13 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 179 HIS 0.005 0.002 HIS D 275 PHE 0.016 0.002 PHE A 406 TYR 0.007 0.001 TYR C 274 ARG 0.005 0.001 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7498 (ttt180) cc_final: 0.7040 (mpt180) REVERT: A 390 LYS cc_start: 0.8370 (ttpt) cc_final: 0.7942 (ttmm) REVERT: B 118 ARG cc_start: 0.8084 (ptm160) cc_final: 0.7881 (ptm-80) REVERT: B 220 ARG cc_start: 0.7506 (ttt180) cc_final: 0.7053 (mpt180) REVERT: B 227 GLN cc_start: 0.8894 (mt0) cc_final: 0.8620 (mt0) REVERT: B 228 GLU cc_start: 0.8995 (mp0) cc_final: 0.8741 (mm-30) REVERT: B 265 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7746 (tptp) REVERT: B 372 GLU cc_start: 0.8363 (pt0) cc_final: 0.8105 (pt0) REVERT: B 376 ASP cc_start: 0.7143 (t0) cc_final: 0.6711 (t0) REVERT: B 380 TRP cc_start: 0.8262 (t-100) cc_final: 0.8043 (t-100) REVERT: B 390 LYS cc_start: 0.8331 (ttpt) cc_final: 0.7919 (ttmm) REVERT: C 220 ARG cc_start: 0.7500 (ttt180) cc_final: 0.7049 (mpt180) REVERT: C 227 GLN cc_start: 0.8887 (mt0) cc_final: 0.8617 (mt0) REVERT: C 228 GLU cc_start: 0.8938 (mp0) cc_final: 0.8710 (mm-30) REVERT: C 380 TRP cc_start: 0.8255 (t-100) cc_final: 0.8044 (t-100) REVERT: D 220 ARG cc_start: 0.7511 (ttt180) cc_final: 0.7062 (mpt180) REVERT: D 227 GLN cc_start: 0.8894 (mt0) cc_final: 0.8539 (mt0) REVERT: D 265 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7745 (tptp) REVERT: D 380 TRP cc_start: 0.8266 (t-100) cc_final: 0.8056 (t-100) REVERT: D 390 LYS cc_start: 0.8357 (ttpt) cc_final: 0.7944 (ttmm) outliers start: 31 outliers final: 19 residues processed: 198 average time/residue: 0.2692 time to fit residues: 72.0264 Evaluate side-chains 177 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 0.4980 chunk 114 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 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 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10548 Z= 0.189 Angle : 0.480 3.900 14296 Z= 0.265 Chirality : 0.047 0.144 1572 Planarity : 0.004 0.040 1804 Dihedral : 5.875 54.821 1576 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 0.93 % Favored : 98.76 % Rotamer: Outliers : 2.84 % Allowed : 11.97 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.23), residues: 1288 helix: -3.06 (0.21), residues: 24 sheet: 0.60 (0.22), residues: 528 loop : -0.11 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 179 HIS 0.005 0.002 HIS B 275 PHE 0.015 0.002 PHE A 121 TYR 0.008 0.001 TYR A 316 ARG 0.004 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7493 (ttt180) cc_final: 0.7044 (mpt180) REVERT: A 376 ASP cc_start: 0.7201 (t0) cc_final: 0.6797 (t0) REVERT: B 220 ARG cc_start: 0.7494 (ttt180) cc_final: 0.7058 (mpt180) REVERT: B 227 GLN cc_start: 0.8905 (mt0) cc_final: 0.8584 (mt0) REVERT: B 376 ASP cc_start: 0.7164 (t0) cc_final: 0.6763 (t0) REVERT: C 128 GLU cc_start: 0.8026 (pt0) cc_final: 0.7755 (pt0) REVERT: C 220 ARG cc_start: 0.7494 (ttt180) cc_final: 0.7048 (mpt180) REVERT: C 227 GLN cc_start: 0.8897 (mt0) cc_final: 0.8577 (mt0) REVERT: C 376 ASP cc_start: 0.7157 (t0) cc_final: 0.6739 (t0) REVERT: D 128 GLU cc_start: 0.8034 (pt0) cc_final: 0.7762 (pt0) REVERT: D 220 ARG cc_start: 0.7504 (ttt180) cc_final: 0.7068 (mpt180) REVERT: D 227 GLN cc_start: 0.8886 (mt0) cc_final: 0.8580 (mt0) REVERT: D 376 ASP cc_start: 0.7180 (t0) cc_final: 0.6776 (t0) outliers start: 32 outliers final: 16 residues processed: 192 average time/residue: 0.2506 time to fit residues: 66.0117 Evaluate side-chains 178 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 127 optimal weight: 8.9990 chunk 106 optimal weight: 0.0370 chunk 59 optimal weight: 8.9990 chunk 10 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN C 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10548 Z= 0.157 Angle : 0.460 3.657 14296 Z= 0.254 Chirality : 0.046 0.144 1572 Planarity : 0.004 0.040 1804 Dihedral : 5.793 54.444 1576 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.24 % Favored : 98.45 % Rotamer: Outliers : 2.66 % Allowed : 12.15 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.23), residues: 1288 helix: -2.91 (0.23), residues: 24 sheet: 0.55 (0.22), residues: 528 loop : -0.11 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 179 HIS 0.005 0.002 HIS C 275 PHE 0.014 0.002 PHE B 121 TYR 0.009 0.001 TYR A 316 ARG 0.004 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7508 (ttt180) cc_final: 0.7088 (mpt180) REVERT: A 376 ASP cc_start: 0.7204 (t0) cc_final: 0.6818 (t0) REVERT: B 220 ARG cc_start: 0.7512 (ttt180) cc_final: 0.7085 (mpt180) REVERT: B 376 ASP cc_start: 0.7172 (t0) cc_final: 0.6778 (t0) REVERT: C 128 GLU cc_start: 0.7994 (pt0) cc_final: 0.7700 (pt0) REVERT: C 220 ARG cc_start: 0.7511 (ttt180) cc_final: 0.7084 (mpt180) REVERT: C 376 ASP cc_start: 0.7133 (t0) cc_final: 0.6741 (t0) REVERT: D 128 GLU cc_start: 0.8007 (pt0) cc_final: 0.7720 (pt0) REVERT: D 220 ARG cc_start: 0.7541 (ttt180) cc_final: 0.7112 (mpt180) REVERT: D 227 GLN cc_start: 0.8648 (mt0) cc_final: 0.8425 (mt0) REVERT: D 376 ASP cc_start: 0.7187 (t0) cc_final: 0.6795 (t0) REVERT: D 398 GLU cc_start: 0.7087 (tp30) cc_final: 0.6351 (tt0) outliers start: 30 outliers final: 18 residues processed: 182 average time/residue: 0.2726 time to fit residues: 66.5453 Evaluate side-chains 169 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10548 Z= 0.196 Angle : 0.474 3.885 14296 Z= 0.261 Chirality : 0.047 0.146 1572 Planarity : 0.004 0.040 1804 Dihedral : 5.818 55.315 1576 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.24 % Favored : 98.45 % Rotamer: Outliers : 2.04 % Allowed : 12.50 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.23), residues: 1288 helix: -3.04 (0.21), residues: 24 sheet: 0.45 (0.22), residues: 556 loop : -0.05 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 179 HIS 0.005 0.002 HIS B 275 PHE 0.015 0.002 PHE B 121 TYR 0.007 0.001 TYR A 316 ARG 0.007 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7395 (ttt180) cc_final: 0.6962 (mpt180) REVERT: A 376 ASP cc_start: 0.7213 (t0) cc_final: 0.6839 (t0) REVERT: B 220 ARG cc_start: 0.7392 (ttt180) cc_final: 0.6980 (mpt180) REVERT: B 228 GLU cc_start: 0.8967 (mp0) cc_final: 0.8685 (mm-30) REVERT: B 376 ASP cc_start: 0.7192 (t0) cc_final: 0.6816 (t0) REVERT: C 220 ARG cc_start: 0.7411 (ttt180) cc_final: 0.6983 (mpt180) REVERT: C 228 GLU cc_start: 0.8905 (mp0) cc_final: 0.8662 (mm-30) REVERT: C 376 ASP cc_start: 0.7364 (t0) cc_final: 0.6995 (t0) REVERT: D 220 ARG cc_start: 0.7431 (ttt180) cc_final: 0.7003 (mpt180) REVERT: D 376 ASP cc_start: 0.7208 (t0) cc_final: 0.6826 (t0) outliers start: 23 outliers final: 19 residues processed: 167 average time/residue: 0.2519 time to fit residues: 57.3266 Evaluate side-chains 178 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 273 ASN C 273 ASN D 227 GLN D 273 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10548 Z= 0.191 Angle : 0.469 3.741 14296 Z= 0.258 Chirality : 0.047 0.162 1572 Planarity : 0.004 0.040 1804 Dihedral : 5.785 55.056 1576 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.55 % Favored : 98.14 % Rotamer: Outliers : 1.77 % Allowed : 13.21 % Favored : 85.02 % 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: 0.19 (0.24), residues: 1288 helix: -3.01 (0.21), residues: 24 sheet: 0.54 (0.22), residues: 564 loop : -0.01 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 179 HIS 0.005 0.002 HIS D 275 PHE 0.014 0.002 PHE B 121 TYR 0.011 0.001 TYR C 274 ARG 0.006 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7667 (ttt180) cc_final: 0.6951 (mpt180) REVERT: A 376 ASP cc_start: 0.7256 (t0) cc_final: 0.6909 (t0) REVERT: B 128 GLU cc_start: 0.7923 (pt0) cc_final: 0.7602 (pt0) REVERT: B 220 ARG cc_start: 0.7664 (ttt180) cc_final: 0.6966 (mpt180) REVERT: B 228 GLU cc_start: 0.8956 (mp0) cc_final: 0.8718 (mm-30) REVERT: B 376 ASP cc_start: 0.7240 (t0) cc_final: 0.6895 (t0) REVERT: B 398 GLU cc_start: 0.7100 (tp30) cc_final: 0.6351 (tt0) REVERT: C 220 ARG cc_start: 0.7666 (ttt180) cc_final: 0.6968 (mpt180) REVERT: C 228 GLU cc_start: 0.8920 (mp0) cc_final: 0.8668 (mm-30) REVERT: C 312 TYR cc_start: 0.8557 (p90) cc_final: 0.8352 (p90) REVERT: C 376 ASP cc_start: 0.7393 (t0) cc_final: 0.7061 (t0) REVERT: D 128 GLU cc_start: 0.7945 (pt0) cc_final: 0.7631 (pt0) REVERT: D 220 ARG cc_start: 0.7670 (ttt180) cc_final: 0.6978 (mpt180) REVERT: D 376 ASP cc_start: 0.7253 (t0) cc_final: 0.6898 (t0) REVERT: D 398 GLU cc_start: 0.7093 (tp30) cc_final: 0.6363 (tt0) outliers start: 20 outliers final: 19 residues processed: 193 average time/residue: 0.2614 time to fit residues: 68.6638 Evaluate side-chains 179 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 125 optimal weight: 0.4980 chunk 76 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10548 Z= 0.157 Angle : 0.459 3.618 14296 Z= 0.253 Chirality : 0.047 0.153 1572 Planarity : 0.004 0.039 1804 Dihedral : 5.735 54.679 1576 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.32 % Favored : 98.37 % Rotamer: Outliers : 1.86 % Allowed : 13.83 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1288 helix: -2.92 (0.22), residues: 24 sheet: 0.63 (0.23), residues: 536 loop : -0.11 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 179 HIS 0.005 0.001 HIS C 275 PHE 0.013 0.002 PHE B 121 TYR 0.007 0.001 TYR A 316 ARG 0.006 0.000 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7656 (ttt180) cc_final: 0.6967 (mpt180) REVERT: A 277 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: A 376 ASP cc_start: 0.7298 (t0) cc_final: 0.6907 (t0) REVERT: B 220 ARG cc_start: 0.7669 (ttt180) cc_final: 0.6987 (mpt180) REVERT: B 376 ASP cc_start: 0.7264 (t0) cc_final: 0.6905 (t0) REVERT: C 220 ARG cc_start: 0.7662 (ttt180) cc_final: 0.6964 (mpt180) REVERT: C 312 TYR cc_start: 0.8479 (p90) cc_final: 0.8239 (p90) REVERT: C 376 ASP cc_start: 0.7399 (t0) cc_final: 0.7057 (t0) REVERT: D 220 ARG cc_start: 0.7684 (ttt180) cc_final: 0.7012 (mpt180) REVERT: D 376 ASP cc_start: 0.7293 (t0) cc_final: 0.6896 (t0) outliers start: 21 outliers final: 19 residues processed: 179 average time/residue: 0.2522 time to fit residues: 61.7893 Evaluate side-chains 175 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.7802 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10548 Z= 0.198 Angle : 0.477 3.679 14296 Z= 0.262 Chirality : 0.048 0.145 1572 Planarity : 0.004 0.039 1804 Dihedral : 5.784 55.209 1576 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.41 % Favored : 97.28 % Rotamer: Outliers : 1.86 % Allowed : 14.89 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.24), residues: 1288 helix: -3.01 (0.21), residues: 24 sheet: 0.51 (0.22), residues: 564 loop : -0.02 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 179 HIS 0.005 0.002 HIS C 275 PHE 0.014 0.002 PHE C 121 TYR 0.008 0.001 TYR A 274 ARG 0.007 0.001 ARG B 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7675 (ttt180) cc_final: 0.6966 (mpt180) REVERT: A 277 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: A 376 ASP cc_start: 0.7331 (t0) cc_final: 0.6938 (t0) REVERT: B 220 ARG cc_start: 0.7674 (ttt180) cc_final: 0.6998 (mpt180) REVERT: B 227 GLN cc_start: 0.8792 (mt0) cc_final: 0.8461 (mt0) REVERT: B 376 ASP cc_start: 0.7313 (t0) cc_final: 0.6921 (t0) REVERT: B 392 ASP cc_start: 0.8102 (p0) cc_final: 0.7442 (p0) REVERT: C 220 ARG cc_start: 0.7677 (ttt180) cc_final: 0.6993 (mpt180) REVERT: C 312 TYR cc_start: 0.8484 (p90) cc_final: 0.8250 (p90) REVERT: C 376 ASP cc_start: 0.7433 (t0) cc_final: 0.7087 (t0) REVERT: D 220 ARG cc_start: 0.7690 (ttt180) cc_final: 0.7015 (mpt180) REVERT: D 376 ASP cc_start: 0.7321 (t0) cc_final: 0.6920 (t0) outliers start: 21 outliers final: 20 residues processed: 168 average time/residue: 0.2374 time to fit residues: 55.8905 Evaluate side-chains 177 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 275 HIS Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.7980 chunk 15 optimal weight: 0.0570 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.150122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.118321 restraints weight = 11549.060| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.39 r_work: 0.3080 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10548 Z= 0.163 Angle : 0.469 3.609 14296 Z= 0.259 Chirality : 0.047 0.145 1572 Planarity : 0.004 0.039 1804 Dihedral : 5.753 54.988 1576 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.71 % Favored : 97.98 % Rotamer: Outliers : 1.86 % Allowed : 15.78 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1288 helix: -2.93 (0.22), residues: 24 sheet: 0.62 (0.23), residues: 536 loop : -0.12 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 179 HIS 0.005 0.001 HIS C 275 PHE 0.013 0.002 PHE C 121 TYR 0.009 0.001 TYR A 316 ARG 0.006 0.001 ARG B 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2408.31 seconds wall clock time: 45 minutes 2.23 seconds (2702.23 seconds total)