Starting phenix.real_space_refine on Sun Dec 29 15:18:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vtk_21380/12_2024/6vtk_21380.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vtk_21380/12_2024/6vtk_21380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vtk_21380/12_2024/6vtk_21380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vtk_21380/12_2024/6vtk_21380.map" model { file = "/net/cci-nas-00/data/ceres_data/6vtk_21380/12_2024/6vtk_21380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vtk_21380/12_2024/6vtk_21380.cif" } resolution = 2.82 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= 0.066 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 81 5.16 5 C 6846 2.51 5 N 1725 2.21 5 O 2034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10686 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3534 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 425} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 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 Time building chain proxies: 7.91, per 1000 atoms: 0.74 Number of scatterers: 10686 At special positions: 0 Unit cell: (97.544, 94.256, 132.616, 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 81 16.00 O 2034 8.00 N 1725 7.00 C 6846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 195 " distance=2.02 Simple disulfide: pdb=" SG CYS A 173 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 366 " distance=2.05 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 362 " distance=2.04 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 360 " distance=2.04 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 344 " distance=2.04 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 336 " distance=2.03 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 601 " - " ASN A 394 " " NAG A 602 " - " ASN A 367 " " NAG B 601 " - " ASN B 394 " " NAG B 602 " - " ASN B 367 " " NAG C 601 " - " ASN C 394 " " NAG C 602 " - " ASN C 367 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 12 sheets defined 42.4% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 18 through 26 removed outlier: 3.584A pdb=" N SER A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 35 removed outlier: 3.754A pdb=" N ILE A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 70 removed outlier: 4.120A pdb=" N VAL A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.570A pdb=" N ARG A 103 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 104 " --> pdb=" O PHE A 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 104' Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 134 through 142 removed outlier: 3.762A pdb=" N LYS A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 214 through 217 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.503A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 323 removed outlier: 3.723A pdb=" N ASP A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS A 313 " --> pdb=" O CYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.719A pdb=" N LYS A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 355 removed outlier: 3.548A pdb=" N GLU A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.520A pdb=" N LEU A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.941A pdb=" N GLY A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 441 removed outlier: 3.588A pdb=" N PHE A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.588A pdb=" N ILE A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 461 " --> pdb=" O TYR A 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 26 removed outlier: 3.584A pdb=" N SER C 24 " --> pdb=" O GLN C 20 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.753A pdb=" N ILE C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 70 removed outlier: 4.120A pdb=" N VAL C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 48 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.571A pdb=" N ARG C 103 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 104 " --> pdb=" O PHE C 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 100 through 104' Processing helix chain 'C' and resid 105 through 112 Processing helix chain 'C' and resid 134 through 142 removed outlier: 3.761A pdb=" N LYS C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 214 through 217 Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.503A pdb=" N GLY C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 323 removed outlier: 3.723A pdb=" N ASP C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS C 313 " --> pdb=" O CYS C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.718A pdb=" N LYS C 342 " --> pdb=" O PRO C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 355 removed outlier: 3.549A pdb=" N GLU C 354 " --> pdb=" O ASP C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 393 removed outlier: 3.521A pdb=" N LEU C 389 " --> pdb=" O SER C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 removed outlier: 3.941A pdb=" N GLY C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 441 removed outlier: 3.588A pdb=" N PHE C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 462 removed outlier: 3.588A pdb=" N ILE C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS C 461 " --> pdb=" O TYR C 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.584A pdb=" N SER B 24 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.753A pdb=" N ILE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 70 removed outlier: 4.120A pdb=" N VAL B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.571A pdb=" N ARG B 103 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 104 " --> pdb=" O PHE B 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 104' Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.762A pdb=" N LYS B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 214 through 217 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.503A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 323 removed outlier: 3.723A pdb=" N ASP B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS B 313 " --> pdb=" O CYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 344 removed outlier: 3.718A pdb=" N LYS B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 355 removed outlier: 3.548A pdb=" N GLU B 354 " --> pdb=" O ASP B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 removed outlier: 3.521A pdb=" N LEU B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.941A pdb=" N GLY B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 441 removed outlier: 3.588A pdb=" N PHE B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.588A pdb=" N ILE B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 461 " --> pdb=" O TYR B 457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 81 removed outlier: 4.254A pdb=" N PHE A 270 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU A 278 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N LEU A 414 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N ARG A 280 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N TYR A 416 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 12.557A pdb=" N ILE A 282 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N THR A 418 " --> pdb=" O ILE A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.085A pdb=" N LYS A 194 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASN A 95 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 74 through 81 Processing sheet with id=AA6, first strand: chain 'C' and resid 74 through 81 removed outlier: 4.254A pdb=" N PHE C 270 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU C 278 " --> pdb=" O GLU C 412 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N LEU C 414 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N ARG C 280 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N TYR C 416 " --> pdb=" O ARG C 280 " (cutoff:3.500A) removed outlier: 12.556A pdb=" N ILE C 282 " --> pdb=" O TYR C 416 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N THR C 418 " --> pdb=" O ILE C 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AA8, first strand: chain 'C' and resid 185 through 190 removed outlier: 7.085A pdb=" N LYS C 194 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASN C 95 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 74 through 81 Processing sheet with id=AB1, first strand: chain 'B' and resid 74 through 81 removed outlier: 4.254A pdb=" N PHE B 270 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU B 278 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N LEU B 414 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N ARG B 280 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N TYR B 416 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 12.557A pdb=" N ILE B 282 " --> pdb=" O TYR B 416 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N THR B 418 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB3, first strand: chain 'B' and resid 185 through 190 removed outlier: 7.086A pdb=" N LYS B 194 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASN B 95 " --> pdb=" O LYS B 194 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1350 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: 3.35 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3398 1.34 - 1.46: 2101 1.46 - 1.58: 5325 1.58 - 1.70: 0 1.70 - 1.82: 111 Bond restraints: 10935 Sorted by residual: bond pdb=" C1 NAG C 602 " pdb=" O5 NAG C 602 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.16e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" C1 NAG B 602 " pdb=" O5 NAG B 602 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.95e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.34e+00 ... (remaining 10930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 14253 1.90 - 3.81: 501 3.81 - 5.71: 48 5.71 - 7.61: 15 7.61 - 9.52: 6 Bond angle restraints: 14823 Sorted by residual: angle pdb=" C GLN B 202 " pdb=" N ASP B 203 " pdb=" CA ASP B 203 " ideal model delta sigma weight residual 122.40 127.24 -4.84 1.45e+00 4.76e-01 1.11e+01 angle pdb=" C GLN A 202 " pdb=" N ASP A 203 " pdb=" CA ASP A 203 " ideal model delta sigma weight residual 122.40 127.19 -4.79 1.45e+00 4.76e-01 1.09e+01 angle pdb=" C GLN C 202 " pdb=" N ASP C 203 " pdb=" CA ASP C 203 " ideal model delta sigma weight residual 122.40 127.17 -4.77 1.45e+00 4.76e-01 1.08e+01 angle pdb=" N ILE A 442 " pdb=" CA ILE A 442 " pdb=" C ILE A 442 " ideal model delta sigma weight residual 113.53 110.62 2.91 9.80e-01 1.04e+00 8.82e+00 angle pdb=" N ILE C 442 " pdb=" CA ILE C 442 " pdb=" C ILE C 442 " ideal model delta sigma weight residual 113.53 110.66 2.87 9.80e-01 1.04e+00 8.55e+00 ... (remaining 14818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 6286 15.13 - 30.27: 282 30.27 - 45.40: 38 45.40 - 60.54: 8 60.54 - 75.67: 7 Dihedral angle restraints: 6621 sinusoidal: 2706 harmonic: 3915 Sorted by residual: dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS A 360 " pdb=" CB CYS A 360 " ideal model delta sinusoidal sigma weight residual -86.00 -157.87 71.87 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" CB CYS A 173 " pdb=" SG CYS A 173 " pdb=" SG CYS A 180 " pdb=" CB CYS A 180 " ideal model delta sinusoidal sigma weight residual -86.00 -27.54 -58.46 1 1.00e+01 1.00e-02 4.58e+01 dihedral pdb=" CA CYS B 366 " pdb=" C CYS B 366 " pdb=" N ASN B 367 " pdb=" CA ASN B 367 " ideal model delta harmonic sigma weight residual 180.00 150.50 29.50 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 6618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 962 0.035 - 0.070: 461 0.070 - 0.106: 138 0.106 - 0.141: 61 0.141 - 0.176: 13 Chirality restraints: 1635 Sorted by residual: chirality pdb=" CA CYS B 366 " pdb=" N CYS B 366 " pdb=" C CYS B 366 " pdb=" CB CYS B 366 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA CYS A 366 " pdb=" N CYS A 366 " pdb=" C CYS A 366 " pdb=" CB CYS A 366 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA CYS C 366 " pdb=" N CYS C 366 " pdb=" C CYS C 366 " pdb=" CB CYS C 366 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 1632 not shown) Planarity restraints: 1926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 230 " -0.016 2.00e-02 2.50e+03 1.44e-02 4.15e+00 pdb=" CG TYR B 230 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 230 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 230 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 230 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 230 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 230 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 230 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 230 " -0.016 2.00e-02 2.50e+03 1.44e-02 4.12e+00 pdb=" CG TYR A 230 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 230 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 230 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 230 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 230 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 230 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 230 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 230 " 0.015 2.00e-02 2.50e+03 1.43e-02 4.09e+00 pdb=" CG TYR C 230 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR C 230 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR C 230 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 230 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C 230 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 230 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 230 " 0.003 2.00e-02 2.50e+03 ... (remaining 1923 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 53 2.59 - 3.17: 8127 3.17 - 3.75: 15316 3.75 - 4.32: 23283 4.32 - 4.90: 38430 Nonbonded interactions: 85209 Sorted by model distance: nonbonded pdb=" SG CYS B 94 " pdb=" SG CYS B 195 " model vdw 2.016 3.760 nonbonded pdb=" SG CYS C 94 " pdb=" SG CYS C 195 " model vdw 2.017 3.760 nonbonded pdb=" SG CYS B 324 " pdb=" SG CYS B 336 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS C 324 " pdb=" SG CYS C 336 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS C 313 " pdb=" SG CYS C 360 " model vdw 2.035 3.760 ... (remaining 85204 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' } 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.320 Find NCS groups from input model: 0.370 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:14.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 : 0.005 0.055 10935 Z= 0.342 Angle : 0.818 9.518 14823 Z= 0.455 Chirality : 0.048 0.176 1635 Planarity : 0.005 0.049 1920 Dihedral : 9.132 75.671 4092 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -4.44 (0.18), residues: 1332 helix: -4.97 (0.06), residues: 456 sheet: -1.42 (0.31), residues: 279 loop : -1.80 (0.21), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 47 HIS 0.004 0.001 HIS B 164 PHE 0.020 0.002 PHE A 264 TYR 0.033 0.002 TYR B 230 ARG 0.003 0.001 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.235 Fit side-chains REVERT: A 106 LYS cc_start: 0.8437 (ttmt) cc_final: 0.8161 (ttmm) REVERT: A 124 GLU cc_start: 0.7165 (pt0) cc_final: 0.6453 (pm20) REVERT: C 124 GLU cc_start: 0.7189 (pt0) cc_final: 0.6648 (pm20) REVERT: B 106 LYS cc_start: 0.8437 (ttmt) cc_final: 0.8210 (ttmm) REVERT: B 108 ASP cc_start: 0.7926 (m-30) cc_final: 0.7523 (m-30) REVERT: B 124 GLU cc_start: 0.6984 (pt0) cc_final: 0.6296 (pm20) REVERT: B 453 PHE cc_start: 0.7296 (m-10) cc_final: 0.7075 (m-10) outliers start: 0 outliers final: 1 residues processed: 202 average time/residue: 1.4204 time to fit residues: 306.4991 Evaluate side-chains 103 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN C 120 ASN C 421 GLN B 202 GLN B 421 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10935 Z= 0.273 Angle : 0.648 7.466 14823 Z= 0.341 Chirality : 0.043 0.211 1635 Planarity : 0.005 0.062 1920 Dihedral : 6.240 51.755 1586 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.58 % Allowed : 8.18 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.80 (0.20), residues: 1332 helix: -2.62 (0.18), residues: 489 sheet: -1.03 (0.30), residues: 273 loop : -1.35 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 234 HIS 0.002 0.001 HIS B 164 PHE 0.013 0.002 PHE C 158 TYR 0.016 0.002 TYR B 230 ARG 0.009 0.001 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.252 Fit side-chains REVERT: A 322 CYS cc_start: 0.4554 (p) cc_final: 0.4235 (t) REVERT: C 124 GLU cc_start: 0.7204 (pt0) cc_final: 0.6683 (pm20) REVERT: B 122 ARG cc_start: 0.7863 (mtm110) cc_final: 0.7602 (mtm110) REVERT: B 391 LYS cc_start: 0.8455 (mtpp) cc_final: 0.8252 (tttm) outliers start: 18 outliers final: 5 residues processed: 116 average time/residue: 1.4522 time to fit residues: 180.4494 Evaluate side-chains 96 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain B residue 363 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 HIS B 121 ASN B 202 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10935 Z= 0.333 Angle : 0.625 8.950 14823 Z= 0.326 Chirality : 0.044 0.191 1635 Planarity : 0.005 0.053 1920 Dihedral : 5.931 49.177 1584 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.41 % Allowed : 10.82 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.79 (0.21), residues: 1332 helix: -1.23 (0.22), residues: 489 sheet: -0.77 (0.30), residues: 273 loop : -1.17 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 234 HIS 0.003 0.001 HIS C 33 PHE 0.011 0.002 PHE A 93 TYR 0.019 0.002 TYR B 425 ARG 0.009 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.094 Fit side-chains REVERT: A 137 GLU cc_start: 0.7171 (tp30) cc_final: 0.6946 (tp30) REVERT: C 124 GLU cc_start: 0.7061 (pt0) cc_final: 0.6602 (pm20) REVERT: B 391 LYS cc_start: 0.8401 (mtpp) cc_final: 0.8013 (ttmm) outliers start: 16 outliers final: 6 residues processed: 102 average time/residue: 1.5184 time to fit residues: 165.5404 Evaluate side-chains 91 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain B residue 376 SER 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: 2.9990 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10935 Z= 0.237 Angle : 0.561 7.543 14823 Z= 0.293 Chirality : 0.042 0.149 1635 Planarity : 0.004 0.071 1920 Dihedral : 5.721 50.087 1584 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.41 % Allowed : 11.35 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.24 (0.22), residues: 1332 helix: -0.55 (0.24), residues: 489 sheet: -0.68 (0.30), residues: 273 loop : -0.97 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 47 HIS 0.002 0.001 HIS A 251 PHE 0.010 0.001 PHE B 158 TYR 0.014 0.001 TYR C 457 ARG 0.011 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.300 Fit side-chains REVERT: A 137 GLU cc_start: 0.7232 (tp30) cc_final: 0.6989 (tp30) REVERT: A 280 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7732 (ttp-110) REVERT: C 124 GLU cc_start: 0.7010 (pt0) cc_final: 0.6475 (pm20) REVERT: C 450 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7575 (tt) REVERT: B 391 LYS cc_start: 0.8454 (mtpp) cc_final: 0.8020 (ttmm) outliers start: 16 outliers final: 7 residues processed: 96 average time/residue: 1.5668 time to fit residues: 160.8449 Evaluate side-chains 91 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10935 Z= 0.319 Angle : 0.597 9.350 14823 Z= 0.309 Chirality : 0.043 0.175 1635 Planarity : 0.004 0.055 1920 Dihedral : 5.755 49.349 1584 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.76 % Allowed : 11.87 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.04 (0.22), residues: 1332 helix: -0.30 (0.24), residues: 489 sheet: -0.58 (0.30), residues: 273 loop : -0.95 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 47 HIS 0.003 0.001 HIS C 33 PHE 0.011 0.002 PHE A 264 TYR 0.014 0.002 TYR A 457 ARG 0.011 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 1.390 Fit side-chains REVERT: A 137 GLU cc_start: 0.7226 (tp30) cc_final: 0.6953 (tp30) REVERT: A 280 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7728 (ttp-110) REVERT: C 124 GLU cc_start: 0.7014 (pt0) cc_final: 0.6493 (pm20) REVERT: C 318 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7721 (mm) REVERT: C 450 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7584 (tt) outliers start: 20 outliers final: 8 residues processed: 97 average time/residue: 1.5487 time to fit residues: 161.0649 Evaluate side-chains 93 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 10 optimal weight: 0.0970 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10935 Z= 0.223 Angle : 0.554 7.953 14823 Z= 0.289 Chirality : 0.042 0.164 1635 Planarity : 0.004 0.074 1920 Dihedral : 5.642 49.742 1584 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.41 % Allowed : 12.66 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.84 (0.22), residues: 1332 helix: -0.07 (0.24), residues: 489 sheet: -0.54 (0.30), residues: 273 loop : -0.84 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 47 HIS 0.002 0.001 HIS B 111 PHE 0.012 0.001 PHE C 93 TYR 0.016 0.001 TYR C 457 ARG 0.014 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 1.213 Fit side-chains REVERT: A 52 MET cc_start: 0.7076 (mtm) cc_final: 0.6872 (mtm) REVERT: A 137 GLU cc_start: 0.7164 (tp30) cc_final: 0.6906 (tp30) REVERT: A 222 MET cc_start: 0.9052 (ttm) cc_final: 0.8692 (ttm) REVERT: A 280 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7719 (ttp-110) REVERT: C 124 GLU cc_start: 0.6916 (pt0) cc_final: 0.6628 (pm20) REVERT: C 450 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7613 (tt) REVERT: B 391 LYS cc_start: 0.8474 (ttmm) cc_final: 0.8243 (tttm) outliers start: 16 outliers final: 9 residues processed: 97 average time/residue: 1.5656 time to fit residues: 162.2678 Evaluate side-chains 91 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10935 Z= 0.242 Angle : 0.559 8.341 14823 Z= 0.291 Chirality : 0.042 0.167 1635 Planarity : 0.004 0.055 1920 Dihedral : 5.602 49.993 1584 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.85 % Allowed : 12.58 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.64 (0.23), residues: 1332 helix: 0.10 (0.24), residues: 489 sheet: -0.44 (0.30), residues: 273 loop : -0.74 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 47 HIS 0.002 0.001 HIS B 111 PHE 0.011 0.001 PHE C 93 TYR 0.015 0.001 TYR C 457 ARG 0.008 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 1.288 Fit side-chains REVERT: A 134 LYS cc_start: 0.7969 (tppt) cc_final: 0.7321 (tmmt) REVERT: A 137 GLU cc_start: 0.7167 (tp30) cc_final: 0.6893 (tp30) REVERT: A 280 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7720 (ttp-110) REVERT: C 124 GLU cc_start: 0.6959 (pt0) cc_final: 0.6638 (pm20) REVERT: C 318 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7721 (mm) REVERT: C 450 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7627 (tt) REVERT: B 318 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7654 (mp) REVERT: B 391 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8234 (tttm) REVERT: B 426 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7516 (mt-10) outliers start: 21 outliers final: 12 residues processed: 101 average time/residue: 1.5814 time to fit residues: 170.7427 Evaluate side-chains 99 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 426 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10935 Z= 0.239 Angle : 0.563 8.714 14823 Z= 0.293 Chirality : 0.042 0.142 1635 Planarity : 0.004 0.071 1920 Dihedral : 5.588 49.927 1584 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.93 % Allowed : 12.84 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.51 (0.23), residues: 1332 helix: 0.25 (0.25), residues: 489 sheet: -0.39 (0.30), residues: 273 loop : -0.70 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 47 HIS 0.002 0.001 HIS B 111 PHE 0.011 0.001 PHE C 93 TYR 0.015 0.001 TYR C 457 ARG 0.017 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 1.114 Fit side-chains REVERT: A 134 LYS cc_start: 0.7965 (tppt) cc_final: 0.7290 (tmmt) REVERT: A 137 GLU cc_start: 0.7158 (tp30) cc_final: 0.6903 (tp30) REVERT: A 280 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7693 (ttp-110) REVERT: C 124 GLU cc_start: 0.6934 (pt0) cc_final: 0.6628 (pm20) REVERT: C 318 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7715 (mm) REVERT: B 318 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7493 (mm) REVERT: B 391 LYS cc_start: 0.8470 (ttmm) cc_final: 0.8253 (tttm) REVERT: B 426 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7517 (mt-10) outliers start: 22 outliers final: 12 residues processed: 101 average time/residue: 1.5262 time to fit residues: 164.7356 Evaluate side-chains 97 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 426 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10935 Z= 0.277 Angle : 0.584 8.826 14823 Z= 0.303 Chirality : 0.042 0.150 1635 Planarity : 0.004 0.056 1920 Dihedral : 5.605 49.695 1584 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.76 % Allowed : 13.28 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.49 (0.23), residues: 1332 helix: 0.28 (0.25), residues: 489 sheet: -0.37 (0.30), residues: 273 loop : -0.69 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 47 HIS 0.002 0.001 HIS B 111 PHE 0.011 0.001 PHE B 93 TYR 0.014 0.001 TYR C 457 ARG 0.008 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.310 Fit side-chains REVERT: A 134 LYS cc_start: 0.7941 (tppt) cc_final: 0.7281 (tmmt) REVERT: A 137 GLU cc_start: 0.7204 (tp30) cc_final: 0.6925 (tp30) REVERT: A 280 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7725 (ttp-110) REVERT: A 460 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.7968 (mp) REVERT: C 49 LEU cc_start: 0.8635 (mt) cc_final: 0.8233 (mm) REVERT: C 124 GLU cc_start: 0.6887 (pt0) cc_final: 0.6509 (pm20) REVERT: C 318 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7723 (mm) REVERT: B 318 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7631 (mp) REVERT: B 391 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8260 (tttm) REVERT: B 426 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7525 (mt-10) outliers start: 20 outliers final: 12 residues processed: 96 average time/residue: 1.6046 time to fit residues: 165.1759 Evaluate side-chains 97 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 426 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10935 Z= 0.219 Angle : 0.559 7.982 14823 Z= 0.291 Chirality : 0.041 0.141 1635 Planarity : 0.004 0.055 1920 Dihedral : 5.527 49.935 1584 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.58 % Allowed : 13.46 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.34 (0.23), residues: 1332 helix: 0.45 (0.25), residues: 489 sheet: -0.34 (0.30), residues: 273 loop : -0.63 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 47 HIS 0.002 0.001 HIS B 111 PHE 0.011 0.001 PHE C 93 TYR 0.014 0.001 TYR C 457 ARG 0.008 0.000 ARG B 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 1.301 Fit side-chains REVERT: A 134 LYS cc_start: 0.7914 (tppt) cc_final: 0.7290 (tmmt) REVERT: A 137 GLU cc_start: 0.7124 (tp30) cc_final: 0.6859 (tp30) REVERT: A 280 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7767 (ttp-110) REVERT: A 460 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.7937 (mp) REVERT: C 49 LEU cc_start: 0.8621 (mt) cc_final: 0.8225 (mm) REVERT: C 124 GLU cc_start: 0.6892 (pt0) cc_final: 0.6649 (pm20) REVERT: B 318 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7483 (mm) REVERT: B 391 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8252 (tttm) REVERT: B 426 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7515 (mt-10) outliers start: 18 outliers final: 11 residues processed: 96 average time/residue: 1.5992 time to fit residues: 164.0045 Evaluate side-chains 94 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 426 GLU 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: 0.9980 chunk 29 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112416 restraints weight = 13928.929| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.53 r_work: 0.3289 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10935 Z= 0.254 Angle : 0.576 8.434 14823 Z= 0.299 Chirality : 0.042 0.146 1635 Planarity : 0.004 0.055 1920 Dihedral : 5.562 49.887 1584 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.50 % Allowed : 13.46 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.31 (0.23), residues: 1332 helix: 0.47 (0.25), residues: 489 sheet: -0.32 (0.30), residues: 273 loop : -0.60 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 47 HIS 0.002 0.001 HIS B 111 PHE 0.011 0.001 PHE B 93 TYR 0.014 0.001 TYR C 457 ARG 0.008 0.000 ARG B 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3714.67 seconds wall clock time: 67 minutes 38.10 seconds (4058.10 seconds total)