Starting phenix.real_space_refine on Fri Feb 14 23:32:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vtk_21380/02_2025/6vtk_21380.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vtk_21380/02_2025/6vtk_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_21380/02_2025/6vtk_21380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vtk_21380/02_2025/6vtk_21380.map" model { file = "/net/cci-nas-00/data/ceres_data/6vtk_21380/02_2025/6vtk_21380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vtk_21380/02_2025/6vtk_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-5592/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: 7.20, per 1000 atoms: 0.67 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: 2.76 Conformation dependent library (CDL) restraints added in 1.2 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: 1.40 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: 3.46 Time building geometry restraints manager: 3.23 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.450 Find NCS groups from input model: 0.220 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:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.050 ------------------------------------------------------------------------------- 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 : 1.115 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: 1.4221 time to fit residues: 306.4252 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 : 1.264 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.136309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.105875 restraints weight = 13870.623| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.61 r_work: 0.3313 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 1.171 Fit side-chains REVERT: A 122 ARG cc_start: 0.7885 (mtm110) cc_final: 0.7622 (mtp-110) REVERT: A 302 ASP cc_start: 0.8233 (m-30) cc_final: 0.8033 (t0) REVERT: A 322 CYS cc_start: 0.6075 (p) cc_final: 0.5059 (t) REVERT: C 124 GLU cc_start: 0.7320 (pt0) cc_final: 0.6341 (pm20) REVERT: B 122 ARG cc_start: 0.7935 (mtm110) cc_final: 0.7560 (mtm110) REVERT: B 137 GLU cc_start: 0.6875 (tp30) cc_final: 0.6639 (tp30) REVERT: B 391 LYS cc_start: 0.8546 (mtpp) cc_final: 0.8216 (tttm) REVERT: B 458 GLU cc_start: 0.6565 (tm-30) cc_final: 0.6308 (tm-30) outliers start: 18 outliers final: 5 residues processed: 116 average time/residue: 1.4910 time to fit residues: 185.2917 Evaluate side-chains 97 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 69 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 0.0570 chunk 125 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 101 optimal weight: 0.0770 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.4056 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.138118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107491 restraints weight = 13813.028| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.62 r_work: 0.3334 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10935 Z= 0.158 Angle : 0.532 5.870 14823 Z= 0.280 Chirality : 0.040 0.177 1635 Planarity : 0.004 0.050 1920 Dihedral : 5.722 51.365 1584 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.06 % Allowed : 11.17 % 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: -1.72 (0.21), residues: 1332 helix: -1.12 (0.22), residues: 489 sheet: -0.90 (0.30), residues: 273 loop : -1.09 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 47 HIS 0.001 0.000 HIS B 111 PHE 0.011 0.001 PHE B 158 TYR 0.012 0.001 TYR C 457 ARG 0.009 0.001 ARG C 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 106 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 1.192 Fit side-chains REVERT: A 137 GLU cc_start: 0.6799 (tp30) cc_final: 0.6532 (tp30) REVERT: A 280 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8204 (ttp-110) REVERT: A 450 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8065 (tt) REVERT: A 458 GLU cc_start: 0.6347 (tm-30) cc_final: 0.6138 (tm-30) REVERT: C 124 GLU cc_start: 0.7137 (pt0) cc_final: 0.6377 (pm20) REVERT: C 458 GLU cc_start: 0.6681 (tm-30) cc_final: 0.6403 (tm-30) REVERT: B 137 GLU cc_start: 0.6816 (tp30) cc_final: 0.6360 (tp30) REVERT: B 391 LYS cc_start: 0.8605 (mtpp) cc_final: 0.8257 (tttm) REVERT: B 438 MET cc_start: 0.8246 (mtm) cc_final: 0.8036 (mtp) outliers start: 12 outliers final: 4 residues processed: 103 average time/residue: 1.4331 time to fit residues: 158.3570 Evaluate side-chains 85 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ARG 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 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.0010 chunk 120 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.143070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.113416 restraints weight = 13959.023| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.56 r_work: 0.3313 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10935 Z= 0.228 Angle : 0.554 7.299 14823 Z= 0.288 Chirality : 0.041 0.153 1635 Planarity : 0.004 0.063 1920 Dihedral : 5.660 51.000 1584 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.32 % Allowed : 11.96 % Favored : 86.72 % 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: -1.13 (0.22), residues: 1332 helix: -0.41 (0.24), residues: 486 sheet: -0.67 (0.30), residues: 273 loop : -0.93 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 234 HIS 0.002 0.001 HIS B 111 PHE 0.009 0.001 PHE A 93 TYR 0.015 0.001 TYR A 457 ARG 0.013 0.001 ARG C 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 95 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 1.333 Fit side-chains REVERT: A 137 GLU cc_start: 0.6917 (tp30) cc_final: 0.6598 (tp30) REVERT: A 280 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8166 (ttp-110) REVERT: A 458 GLU cc_start: 0.6545 (tm-30) cc_final: 0.6333 (tm-30) REVERT: C 124 GLU cc_start: 0.7181 (pt0) cc_final: 0.6180 (pm20) REVERT: C 450 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7560 (tt) REVERT: C 458 GLU cc_start: 0.6461 (tm-30) cc_final: 0.6253 (tm-30) REVERT: B 137 GLU cc_start: 0.6799 (tp30) cc_final: 0.6449 (tp30) REVERT: B 339 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6893 (pt0) REVERT: B 458 GLU cc_start: 0.6464 (tm-30) cc_final: 0.6174 (tm-30) outliers start: 15 outliers final: 6 residues processed: 89 average time/residue: 1.6409 time to fit residues: 155.8443 Evaluate side-chains 87 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 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 107 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 0.0370 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.136203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.105440 restraints weight = 13867.995| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.63 r_work: 0.3301 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2634 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= 0.212 Angle : 0.529 7.174 14823 Z= 0.276 Chirality : 0.041 0.160 1635 Planarity : 0.004 0.054 1920 Dihedral : 5.556 50.380 1584 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.58 % Allowed : 11.96 % Favored : 86.46 % 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: -0.77 (0.23), residues: 1332 helix: -0.01 (0.24), residues: 489 sheet: -0.52 (0.30), residues: 273 loop : -0.79 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 234 HIS 0.002 0.001 HIS B 111 PHE 0.009 0.001 PHE C 93 TYR 0.014 0.001 TYR A 457 ARG 0.013 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 100 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 1.283 Fit side-chains REVERT: A 137 GLU cc_start: 0.6850 (tp30) cc_final: 0.6502 (tp30) REVERT: A 280 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8158 (ttp-110) REVERT: C 124 GLU cc_start: 0.7033 (pt0) cc_final: 0.6289 (pm20) REVERT: C 450 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7579 (tt) REVERT: B 137 GLU cc_start: 0.6794 (tp30) cc_final: 0.6427 (tp30) REVERT: B 339 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6894 (pt0) REVERT: B 391 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8159 (tttm) outliers start: 18 outliers final: 7 residues processed: 96 average time/residue: 1.5912 time to fit residues: 163.4045 Evaluate side-chains 86 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.0000 chunk 112 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.136336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.105505 restraints weight = 13907.740| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.65 r_work: 0.3306 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10935 Z= 0.198 Angle : 0.531 7.017 14823 Z= 0.278 Chirality : 0.041 0.154 1635 Planarity : 0.004 0.079 1920 Dihedral : 5.524 50.610 1584 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.50 % Allowed : 11.87 % Favored : 86.63 % 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: -0.47 (0.23), residues: 1332 helix: 0.28 (0.25), residues: 489 sheet: -0.43 (0.30), residues: 273 loop : -0.62 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 234 HIS 0.002 0.001 HIS B 111 PHE 0.012 0.001 PHE B 93 TYR 0.013 0.001 TYR A 457 ARG 0.014 0.001 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 100 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.427 Fit side-chains REVERT: A 137 GLU cc_start: 0.6878 (tp30) cc_final: 0.6519 (tp30) REVERT: A 280 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8118 (ttp-110) REVERT: C 124 GLU cc_start: 0.7033 (pt0) cc_final: 0.6148 (pm20) REVERT: C 318 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7784 (mm) REVERT: C 450 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7609 (tt) REVERT: B 137 GLU cc_start: 0.6771 (tp30) cc_final: 0.6392 (tp30) REVERT: B 339 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6879 (pt0) REVERT: B 391 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8221 (tttm) REVERT: B 458 GLU cc_start: 0.6600 (tm-30) cc_final: 0.6317 (tm-30) outliers start: 17 outliers final: 6 residues processed: 95 average time/residue: 1.6316 time to fit residues: 165.2389 Evaluate side-chains 87 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 376 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 27 optimal weight: 0.0570 chunk 56 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.142801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.112921 restraints weight = 14203.160| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.59 r_work: 0.3296 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10935 Z= 0.220 Angle : 0.539 8.199 14823 Z= 0.280 Chirality : 0.041 0.159 1635 Planarity : 0.004 0.055 1920 Dihedral : 5.499 50.378 1584 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.23 % Allowed : 12.40 % 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: -0.34 (0.23), residues: 1332 helix: 0.42 (0.25), residues: 489 sheet: -0.36 (0.30), residues: 273 loop : -0.58 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 234 HIS 0.002 0.001 HIS B 111 PHE 0.010 0.001 PHE B 93 TYR 0.011 0.001 TYR A 457 ARG 0.011 0.000 ARG C 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 99 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 1.168 Fit side-chains REVERT: A 134 LYS cc_start: 0.7657 (tppt) cc_final: 0.6940 (tmmt) REVERT: A 137 GLU cc_start: 0.6901 (tp30) cc_final: 0.6529 (tp30) REVERT: A 222 MET cc_start: 0.9316 (ttm) cc_final: 0.8988 (ttm) REVERT: A 280 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8123 (ttp-110) REVERT: C 124 GLU cc_start: 0.6872 (pt0) cc_final: 0.6242 (pm20) REVERT: B 137 GLU cc_start: 0.6768 (tp30) cc_final: 0.6384 (tp30) REVERT: B 391 LYS cc_start: 0.8601 (ttmm) cc_final: 0.8241 (tttm) outliers start: 14 outliers final: 7 residues processed: 96 average time/residue: 1.5976 time to fit residues: 163.7851 Evaluate side-chains 89 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 361 VAL Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 108 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 120 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.143191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.113455 restraints weight = 13923.926| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.55 r_work: 0.3309 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10935 Z= 0.208 Angle : 0.541 7.529 14823 Z= 0.282 Chirality : 0.041 0.153 1635 Planarity : 0.004 0.075 1920 Dihedral : 5.482 50.391 1584 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.32 % Allowed : 12.75 % 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: -0.26 (0.23), residues: 1332 helix: 0.48 (0.25), residues: 489 sheet: -0.33 (0.30), residues: 273 loop : -0.52 (0.26), 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 0.011 0.001 TYR A 457 ARG 0.017 0.001 ARG C 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 96 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 1.172 Fit side-chains REVERT: A 134 LYS cc_start: 0.7646 (tppt) cc_final: 0.6949 (tmmt) REVERT: A 137 GLU cc_start: 0.6919 (tp30) cc_final: 0.6539 (tp30) REVERT: A 280 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8117 (ttp-110) REVERT: C 124 GLU cc_start: 0.7022 (pt0) cc_final: 0.6187 (pm20) REVERT: C 318 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7809 (mm) REVERT: B 137 GLU cc_start: 0.6850 (tp30) cc_final: 0.6462 (tp30) REVERT: B 391 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8240 (tttm) outliers start: 15 outliers final: 8 residues processed: 93 average time/residue: 1.5822 time to fit residues: 156.9268 Evaluate side-chains 89 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 361 VAL Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 56 optimal weight: 0.0980 chunk 12 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.143543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.113713 restraints weight = 14040.548| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.57 r_work: 0.3311 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10935 Z= 0.196 Angle : 0.538 9.149 14823 Z= 0.280 Chirality : 0.041 0.132 1635 Planarity : 0.004 0.055 1920 Dihedral : 5.434 50.593 1584 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.32 % Allowed : 12.84 % Favored : 85.84 % 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: -0.15 (0.23), residues: 1332 helix: 0.59 (0.25), residues: 489 sheet: -0.30 (0.30), residues: 273 loop : -0.47 (0.26), 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 0.010 0.001 PHE B 93 TYR 0.011 0.001 TYR A 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 98 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 1.208 Fit side-chains REVERT: A 134 LYS cc_start: 0.7627 (tppt) cc_final: 0.6973 (tmmt) REVERT: A 137 GLU cc_start: 0.6880 (tp30) cc_final: 0.6491 (tp30) REVERT: A 280 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8122 (ttp-110) REVERT: C 124 GLU cc_start: 0.6848 (pt0) cc_final: 0.6248 (pm20) REVERT: C 318 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7797 (mm) REVERT: B 137 GLU cc_start: 0.6817 (tp30) cc_final: 0.6388 (tp30) REVERT: B 391 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8241 (tttm) outliers start: 15 outliers final: 10 residues processed: 95 average time/residue: 1.5820 time to fit residues: 160.9178 Evaluate side-chains 93 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 361 VAL Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.9037 > 50: distance: 13 - 37: 34.443 distance: 16 - 34: 29.764 distance: 32 - 34: 29.101 distance: 34 - 35: 21.059 distance: 35 - 36: 39.440 distance: 35 - 38: 24.556 distance: 36 - 37: 34.174 distance: 36 - 41: 22.892 distance: 38 - 39: 26.287 distance: 38 - 40: 19.847 distance: 41 - 42: 13.605 distance: 42 - 43: 25.478 distance: 42 - 45: 44.759 distance: 43 - 44: 22.396 distance: 43 - 46: 56.446 distance: 46 - 47: 34.025 distance: 46 - 52: 41.436 distance: 47 - 48: 43.961 distance: 47 - 50: 23.319 distance: 48 - 49: 39.162 distance: 48 - 53: 13.322 distance: 50 - 51: 7.982 distance: 51 - 52: 57.421 distance: 53 - 54: 15.227 distance: 54 - 55: 21.102 distance: 55 - 56: 29.239 distance: 55 - 57: 31.612 distance: 57 - 58: 20.297 distance: 58 - 59: 20.757 distance: 58 - 61: 20.573 distance: 59 - 60: 41.269 distance: 59 - 68: 23.363 distance: 60 - 191: 23.988 distance: 61 - 62: 15.185 distance: 62 - 63: 4.274 distance: 62 - 64: 3.518 distance: 63 - 65: 3.442 distance: 64 - 66: 6.354 distance: 65 - 67: 4.507 distance: 66 - 67: 3.025 distance: 68 - 69: 10.607 distance: 68 - 157: 9.618 distance: 69 - 70: 21.162 distance: 69 - 72: 17.582 distance: 70 - 71: 15.097 distance: 70 - 77: 28.471 distance: 71 - 154: 23.595 distance: 72 - 73: 20.658 distance: 73 - 74: 16.761 distance: 74 - 75: 7.091 distance: 74 - 76: 11.097 distance: 77 - 78: 21.616 distance: 77 - 194: 18.615 distance: 78 - 79: 17.479 distance: 78 - 81: 5.140 distance: 79 - 80: 13.919 distance: 79 - 84: 15.721 distance: 80 - 206: 19.202 distance: 81 - 82: 25.939 distance: 81 - 83: 19.119 distance: 84 - 85: 33.079 distance: 84 - 143: 11.742 distance: 85 - 86: 39.983 distance: 85 - 88: 40.833 distance: 86 - 87: 21.964 distance: 86 - 95: 34.916 distance: 87 - 140: 31.937 distance: 88 - 89: 39.586 distance: 89 - 90: 27.147 distance: 89 - 91: 26.946 distance: 90 - 92: 10.957 distance: 91 - 93: 15.023 distance: 92 - 94: 4.828 distance: 93 - 94: 4.954 distance: 95 - 96: 18.821 distance: 95 - 209: 17.146 distance: 96 - 97: 17.470 distance: 96 - 99: 23.079 distance: 97 - 98: 33.152 distance: 97 - 102: 23.583 distance: 98 - 221: 27.744 distance: 99 - 100: 52.016 distance: 99 - 101: 45.551 distance: 102 - 103: 12.667 distance: 102 - 128: 21.491 distance: 103 - 104: 39.096 distance: 103 - 106: 30.259 distance: 104 - 105: 42.899 distance: 104 - 108: 26.461 distance: 105 - 125: 35.982 distance: 106 - 107: 49.142