Starting phenix.real_space_refine on Wed May 14 13:09:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhh_38351/05_2025/8xhh_38351.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhh_38351/05_2025/8xhh_38351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xhh_38351/05_2025/8xhh_38351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhh_38351/05_2025/8xhh_38351.map" model { file = "/net/cci-nas-00/data/ceres_data/8xhh_38351/05_2025/8xhh_38351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhh_38351/05_2025/8xhh_38351.cif" } resolution = 2.38 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= 0.001 sd= 0.026 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 72 5.16 5 C 7413 2.51 5 N 2019 2.21 5 O 2337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11841 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 3891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3891 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 19, 'TRANS': 470} Chain breaks: 1 Chain: "A" Number of atoms: 3891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3891 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 19, 'TRANS': 470} Chain breaks: 1 Chain: "B" Number of atoms: 3891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3891 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 19, 'TRANS': 470} Chain breaks: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.03, per 1000 atoms: 0.68 Number of scatterers: 11841 At special positions: 0 Unit cell: (87.55, 87.55, 150.45, 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 72 16.00 O 2337 8.00 N 2019 7.00 C 7413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 467 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS A 467 " distance=2.03 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 467 " distance=2.04 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 72 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " 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 701 " - " ASN A 484 " " NAG A 702 " - " ASN A 169 " " NAG A 703 " - " ASN A 290 " " NAG A 704 " - " ASN A 28 " " NAG A 705 " - " ASN A 16 " " NAG B 601 " - " ASN B 484 " " NAG B 602 " - " ASN B 28 " " NAG B 603 " - " ASN B 169 " " NAG C 601 " - " ASN C 169 " " NAG C 602 " - " ASN C 28 " " NAG C 603 " - " ASN C 290 " " NAG C 604 " - " ASN C 484 " Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.6 seconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2694 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 32 sheets defined 28.4% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 69 through 76 removed outlier: 3.912A pdb=" N ASP C 73 " --> pdb=" O PRO C 70 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG C 74 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 76 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.607A pdb=" N TRP C 127 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 368 through 388 Processing helix chain 'C' and resid 404 through 457 removed outlier: 3.609A pdb=" N GLU C 435 " --> pdb=" O LEU C 431 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 492 through 502 removed outlier: 3.872A pdb=" N ASN C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.983A pdb=" N TRP A 127 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 367 through 388 Processing helix chain 'A' and resid 404 through 457 Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 488 through 502 removed outlier: 3.890A pdb=" N TYR A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLU A 495 " --> pdb=" O LYS A 491 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 69 through 76 removed outlier: 4.056A pdb=" N ASP B 73 " --> pdb=" O PRO B 70 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG B 74 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.845A pdb=" N TRP B 127 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 367 through 388 removed outlier: 3.754A pdb=" N THR B 371 " --> pdb=" O ASP B 367 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 457 removed outlier: 3.688A pdb=" N GLU B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 488 through 502 removed outlier: 4.051A pdb=" N TYR B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU B 494 " --> pdb=" O PRO B 490 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLU B 495 " --> pdb=" O LYS B 491 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN B 501 " --> pdb=" O LYS B 497 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 362 through 364 Processing sheet with id=AA2, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.309A pdb=" N GLU C 19 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 49 removed outlier: 5.924A pdb=" N LEU C 46 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N CYS C 278 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.685A pdb=" N LEU C 55 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE C 84 " --> pdb=" O MET C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 100 removed outlier: 5.350A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS C 115 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG C 263 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL C 113 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 99 through 100 removed outlier: 7.773A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.594A pdb=" N ALA C 138 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N GLU C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'C' and resid 282 through 283 removed outlier: 3.774A pdb=" N GLY C 304 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 394 " --> pdb=" O GLY C 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 364 Processing sheet with id=AB4, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.207A pdb=" N GLU A 19 " --> pdb=" O VAL A 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AB6, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AB7, first strand: chain 'A' and resid 46 through 49 removed outlier: 5.902A pdb=" N LEU A 46 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N CYS A 278 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.625A pdb=" N LEU A 55 " --> pdb=" O MET A 85 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A 84 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.477A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N HIS A 115 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARG A 263 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL A 113 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 98 through 100 removed outlier: 7.954A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.754A pdb=" N ALA A 138 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N GLU A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'A' and resid 287 through 289 removed outlier: 4.146A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 362 through 364 removed outlier: 3.600A pdb=" N GLY B 11 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 8 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 468 " --> pdb=" O ILE B 8 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AC7, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AC8, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AC9, first strand: chain 'B' and resid 55 through 56 removed outlier: 6.680A pdb=" N LEU B 55 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 84 " --> pdb=" O MET B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.424A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS B 115 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG B 263 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 113 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 98 through 100 removed outlier: 7.955A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 136 through 141 removed outlier: 4.947A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AD5, first strand: chain 'B' and resid 282 through 283 507 hydrogen bonds defined for protein. 1395 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: 4.91 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3906 1.35 - 1.47: 2909 1.47 - 1.59: 5176 1.59 - 1.71: 0 1.71 - 1.84: 108 Bond restraints: 12099 Sorted by residual: bond pdb=" CG PRO C 294 " pdb=" CD PRO C 294 " ideal model delta sigma weight residual 1.503 1.389 0.114 3.40e-02 8.65e+02 1.13e+01 bond pdb=" C1 NAG A 704 " pdb=" O5 NAG A 704 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.04e+00 bond pdb=" CB PRO C 294 " pdb=" CG PRO C 294 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.01e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.03e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.89e+00 ... (remaining 12094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 16203 2.26 - 4.51: 142 4.51 - 6.77: 17 6.77 - 9.02: 1 9.02 - 11.28: 5 Bond angle restraints: 16368 Sorted by residual: angle pdb=" N PRO C 294 " pdb=" CD PRO C 294 " pdb=" CG PRO C 294 " ideal model delta sigma weight residual 103.20 92.84 10.36 1.50e+00 4.44e-01 4.77e+01 angle pdb=" CA PRO C 294 " pdb=" N PRO C 294 " pdb=" CD PRO C 294 " ideal model delta sigma weight residual 112.00 102.71 9.29 1.40e+00 5.10e-01 4.40e+01 angle pdb=" CA CYS B 467 " pdb=" CB CYS B 467 " pdb=" SG CYS B 467 " ideal model delta sigma weight residual 114.40 123.56 -9.16 2.30e+00 1.89e-01 1.59e+01 angle pdb=" N CYS B 467 " pdb=" CA CYS B 467 " pdb=" C CYS B 467 " ideal model delta sigma weight residual 109.18 114.82 -5.64 1.42e+00 4.96e-01 1.57e+01 angle pdb=" CA GLU C 387 " pdb=" CB GLU C 387 " pdb=" CG GLU C 387 " ideal model delta sigma weight residual 114.10 120.46 -6.36 2.00e+00 2.50e-01 1.01e+01 ... (remaining 16363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6170 17.95 - 35.90: 862 35.90 - 53.84: 293 53.84 - 71.79: 80 71.79 - 89.74: 17 Dihedral angle restraints: 7422 sinusoidal: 3207 harmonic: 4215 Sorted by residual: dihedral pdb=" CA CYS B 47 " pdb=" C CYS B 47 " pdb=" N LYS B 48 " pdb=" CA LYS B 48 " ideal model delta harmonic sigma weight residual 180.00 -154.37 -25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CB CYS B 9 " pdb=" SG CYS B 9 " pdb=" SG CYS B 467 " pdb=" CB CYS B 467 " ideal model delta sinusoidal sigma weight residual 93.00 52.85 40.15 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CA CYS B 467 " pdb=" C CYS B 467 " pdb=" N PHE B 468 " pdb=" CA PHE B 468 " ideal model delta harmonic sigma weight residual -180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 7419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1312 0.040 - 0.079: 327 0.079 - 0.119: 135 0.119 - 0.158: 16 0.158 - 0.198: 1 Chirality restraints: 1791 Sorted by residual: chirality pdb=" CA CYS B 467 " pdb=" N CYS B 467 " pdb=" C CYS B 467 " pdb=" CB CYS B 467 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" CA ILE B 10 " pdb=" N ILE B 10 " pdb=" C ILE B 10 " pdb=" CB ILE B 10 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA GLU A 433 " pdb=" N GLU A 433 " pdb=" C GLU A 433 " pdb=" CB GLU A 433 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1788 not shown) Planarity restraints: 2127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 387 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" CD GLU C 387 " -0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU C 387 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU C 387 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 324 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C VAL C 324 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL C 324 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO C 325 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 387 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C GLU C 387 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU C 387 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS C 388 " -0.009 2.00e-02 2.50e+03 ... (remaining 2124 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 709 2.73 - 3.27: 10401 3.27 - 3.82: 18836 3.82 - 4.36: 22661 4.36 - 4.90: 40357 Nonbonded interactions: 92964 Sorted by model distance: nonbonded pdb=" O TYR C 492 " pdb=" OG SER C 496 " model vdw 2.190 3.040 nonbonded pdb=" O THR C 23 " pdb=" NH1 ARG C 27 " model vdw 2.216 3.120 nonbonded pdb=" OG1 THR C 284 " pdb=" O GLY C 287 " model vdw 2.252 3.040 nonbonded pdb=" O TYR A 492 " pdb=" OG SER A 496 " model vdw 2.280 3.040 nonbonded pdb=" OG1 THR B 284 " pdb=" O GLY B 287 " model vdw 2.282 3.040 ... (remaining 92959 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' and (resid 6 through 502 or resid 701 through 703)) selection = chain 'B' selection = (chain 'C' and (resid 6 through 502 or resid 601 through 603)) } 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: 2.550 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.190 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 12129 Z= 0.144 Angle : 0.552 11.279 16440 Z= 0.285 Chirality : 0.041 0.198 1791 Planarity : 0.004 0.041 2115 Dihedral : 18.977 89.740 4674 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.55 % Allowed : 27.08 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1458 helix: 2.20 (0.27), residues: 381 sheet: 0.85 (0.32), residues: 294 loop : -1.41 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 422 HIS 0.005 0.001 HIS A 472 PHE 0.018 0.001 PHE C 440 TYR 0.008 0.001 TYR B 103 ARG 0.010 0.000 ARG C 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 12) link_NAG-ASN : angle 1.74081 ( 36) hydrogen bonds : bond 0.18131 ( 471) hydrogen bonds : angle 6.87104 ( 1395) SS BOND : bond 0.00368 ( 18) SS BOND : angle 1.37928 ( 36) covalent geometry : bond 0.00328 (12099) covalent geometry : angle 0.54375 (16368) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 346 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 436 ARG cc_start: 0.7147 (mtt180) cc_final: 0.6894 (mtt180) REVERT: C 458 ASP cc_start: 0.7181 (t0) cc_final: 0.6918 (t0) REVERT: A 405 ARG cc_start: 0.7979 (mmp80) cc_final: 0.7766 (mmp-170) outliers start: 59 outliers final: 52 residues processed: 398 average time/residue: 1.3651 time to fit residues: 580.8165 Evaluate side-chains 379 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 327 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 0.0050 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 175 GLN C 360 GLN A 210 ASN A 224 ASN A 277 ASN A 283 GLN A 455 GLN A 472 HIS B 13 HIS B 160 ASN B 224 ASN B 283 GLN B 356 HIS B 402 ASN ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.118989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.108166 restraints weight = 15427.776| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.71 r_work: 0.3447 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12129 Z= 0.215 Angle : 0.550 8.702 16440 Z= 0.294 Chirality : 0.044 0.181 1791 Planarity : 0.004 0.037 2115 Dihedral : 9.302 83.460 1921 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.71 % Allowed : 25.54 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1458 helix: 2.33 (0.27), residues: 381 sheet: 0.52 (0.30), residues: 327 loop : -1.36 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 81 HIS 0.006 0.001 HIS A 296 PHE 0.020 0.002 PHE C 440 TYR 0.014 0.002 TYR C 12 ARG 0.007 0.001 ARG C 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 12) link_NAG-ASN : angle 1.77243 ( 36) hydrogen bonds : bond 0.06276 ( 471) hydrogen bonds : angle 5.10710 ( 1395) SS BOND : bond 0.00306 ( 18) SS BOND : angle 1.28958 ( 36) covalent geometry : bond 0.00519 (12099) covalent geometry : angle 0.54111 (16368) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 343 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 436 ARG cc_start: 0.7597 (mtt180) cc_final: 0.7294 (mtt180) REVERT: C 458 ASP cc_start: 0.7522 (t0) cc_final: 0.7201 (t0) REVERT: C 495 GLU cc_start: 0.7782 (tp30) cc_final: 0.7398 (tp30) REVERT: B 80 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7466 (tt0) REVERT: B 262 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8105 (ttmt) REVERT: B 491 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8509 (ttpp) outliers start: 61 outliers final: 42 residues processed: 383 average time/residue: 1.3954 time to fit residues: 571.4602 Evaluate side-chains 381 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 337 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 498 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 48 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 81 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 175 GLN C 191 GLN A 196 GLN A 210 ASN A 224 ASN A 283 GLN A 472 HIS B 13 HIS B 160 ASN B 224 ASN B 283 GLN B 356 HIS B 472 HIS B 480 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.119549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108246 restraints weight = 15475.653| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.76 r_work: 0.3445 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12129 Z= 0.182 Angle : 0.513 6.612 16440 Z= 0.276 Chirality : 0.043 0.142 1791 Planarity : 0.004 0.040 2115 Dihedral : 7.809 80.446 1876 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.40 % Allowed : 25.54 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1458 helix: 2.42 (0.27), residues: 381 sheet: 0.55 (0.30), residues: 327 loop : -1.34 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 81 HIS 0.006 0.001 HIS B 472 PHE 0.022 0.002 PHE C 440 TYR 0.012 0.002 TYR C 12 ARG 0.009 0.001 ARG C 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 12) link_NAG-ASN : angle 1.51358 ( 36) hydrogen bonds : bond 0.05872 ( 471) hydrogen bonds : angle 4.81635 ( 1395) SS BOND : bond 0.00300 ( 18) SS BOND : angle 1.15794 ( 36) covalent geometry : bond 0.00436 (12099) covalent geometry : angle 0.50636 (16368) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 337 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 GLN cc_start: 0.6017 (OUTLIER) cc_final: 0.5554 (mp10) REVERT: C 458 ASP cc_start: 0.7534 (t0) cc_final: 0.7202 (t0) REVERT: C 495 GLU cc_start: 0.7769 (tp30) cc_final: 0.7320 (tp30) REVERT: A 159 SER cc_start: 0.8100 (t) cc_final: 0.7875 (t) REVERT: A 372 GLN cc_start: 0.7638 (tp40) cc_final: 0.7384 (tp-100) REVERT: B 80 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7459 (tt0) REVERT: B 94 LEU cc_start: 0.9137 (mt) cc_final: 0.8900 (mp) REVERT: B 118 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8687 (mtpt) REVERT: B 491 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8525 (ttpp) outliers start: 57 outliers final: 34 residues processed: 373 average time/residue: 1.4345 time to fit residues: 572.4146 Evaluate side-chains 358 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 321 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 2 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 141 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 175 GLN A 196 GLN A 210 ASN A 224 ASN A 360 GLN A 472 HIS A 499 ASN B 13 HIS B 160 ASN B 224 ASN B 480 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.119827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.108562 restraints weight = 15428.122| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.75 r_work: 0.3453 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12129 Z= 0.143 Angle : 0.500 8.293 16440 Z= 0.267 Chirality : 0.042 0.155 1791 Planarity : 0.004 0.037 2115 Dihedral : 7.186 77.997 1861 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.01 % Allowed : 26.00 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1458 helix: 2.53 (0.27), residues: 381 sheet: 0.61 (0.30), residues: 327 loop : -1.31 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 422 HIS 0.006 0.001 HIS B 356 PHE 0.016 0.001 PHE C 440 TYR 0.011 0.001 TYR C 12 ARG 0.008 0.000 ARG C 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 12) link_NAG-ASN : angle 1.51283 ( 36) hydrogen bonds : bond 0.05495 ( 471) hydrogen bonds : angle 4.67864 ( 1395) SS BOND : bond 0.00347 ( 18) SS BOND : angle 1.20618 ( 36) covalent geometry : bond 0.00338 (12099) covalent geometry : angle 0.49276 (16368) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 334 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 GLN cc_start: 0.6021 (OUTLIER) cc_final: 0.5572 (mp10) REVERT: C 405 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7601 (mmp80) REVERT: C 458 ASP cc_start: 0.7534 (t0) cc_final: 0.7198 (t0) REVERT: C 495 GLU cc_start: 0.7744 (tp30) cc_final: 0.7336 (tp30) REVERT: A 372 GLN cc_start: 0.7570 (tp40) cc_final: 0.7364 (tp-100) REVERT: B 94 LEU cc_start: 0.9121 (mt) cc_final: 0.8903 (mp) REVERT: B 491 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8487 (ttpp) outliers start: 52 outliers final: 35 residues processed: 366 average time/residue: 1.3951 time to fit residues: 546.2437 Evaluate side-chains 358 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 321 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 84 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 175 GLN C 191 GLN A 196 GLN A 210 ASN A 224 ASN B 13 HIS B 160 ASN B 224 ASN B 283 GLN B 480 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.117879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.106930 restraints weight = 15374.403| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.65 r_work: 0.3430 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 12129 Z= 0.322 Angle : 0.603 8.219 16440 Z= 0.322 Chirality : 0.047 0.174 1791 Planarity : 0.004 0.039 2115 Dihedral : 6.964 75.114 1859 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.94 % Allowed : 25.46 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.22), residues: 1458 helix: 2.30 (0.27), residues: 381 sheet: 0.67 (0.30), residues: 321 loop : -1.44 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 81 HIS 0.010 0.002 HIS A 296 PHE 0.028 0.002 PHE C 440 TYR 0.017 0.002 TYR C 12 ARG 0.008 0.001 ARG B 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 12) link_NAG-ASN : angle 1.78904 ( 36) hydrogen bonds : bond 0.06637 ( 471) hydrogen bonds : angle 4.88993 ( 1395) SS BOND : bond 0.00415 ( 18) SS BOND : angle 1.56552 ( 36) covalent geometry : bond 0.00787 (12099) covalent geometry : angle 0.59396 (16368) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 337 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 GLN cc_start: 0.6008 (OUTLIER) cc_final: 0.5562 (mp10) REVERT: C 458 ASP cc_start: 0.7458 (t0) cc_final: 0.7085 (t0) REVERT: A 159 SER cc_start: 0.8157 (OUTLIER) cc_final: 0.7906 (t) REVERT: A 372 GLN cc_start: 0.7676 (tp40) cc_final: 0.7470 (tp-100) REVERT: B 491 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8528 (ttpp) outliers start: 64 outliers final: 43 residues processed: 373 average time/residue: 1.3895 time to fit residues: 554.2957 Evaluate side-chains 382 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 336 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 498 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 175 GLN C 390 ASN A 196 GLN A 210 ASN A 224 ASN A 360 GLN B 7 GLN B 13 HIS B 160 ASN B 224 ASN B 283 GLN B 299 HIS B 480 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.119209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.107892 restraints weight = 15534.248| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.76 r_work: 0.3440 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12129 Z= 0.181 Angle : 0.534 8.181 16440 Z= 0.286 Chirality : 0.043 0.170 1791 Planarity : 0.004 0.037 2115 Dihedral : 6.436 73.453 1853 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.09 % Allowed : 26.39 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1458 helix: 2.39 (0.27), residues: 381 sheet: 0.58 (0.30), residues: 327 loop : -1.40 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 81 HIS 0.007 0.001 HIS B 356 PHE 0.018 0.002 PHE C 440 TYR 0.021 0.002 TYR C 489 ARG 0.007 0.000 ARG C 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 12) link_NAG-ASN : angle 1.64445 ( 36) hydrogen bonds : bond 0.05797 ( 471) hydrogen bonds : angle 4.72215 ( 1395) SS BOND : bond 0.00419 ( 18) SS BOND : angle 1.19659 ( 36) covalent geometry : bond 0.00436 (12099) covalent geometry : angle 0.52680 (16368) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 325 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 GLN cc_start: 0.5999 (OUTLIER) cc_final: 0.5588 (mp10) REVERT: C 458 ASP cc_start: 0.7531 (t0) cc_final: 0.7174 (t0) REVERT: C 495 GLU cc_start: 0.7858 (tp30) cc_final: 0.7585 (tp30) REVERT: B 94 LEU cc_start: 0.9137 (mt) cc_final: 0.8921 (mp) REVERT: B 479 MET cc_start: 0.8173 (mmt) cc_final: 0.7918 (mmt) REVERT: B 491 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8510 (ttpp) outliers start: 53 outliers final: 40 residues processed: 357 average time/residue: 1.4634 time to fit residues: 559.5023 Evaluate side-chains 353 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 311 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 99 optimal weight: 0.0980 chunk 64 optimal weight: 0.0370 chunk 136 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 175 GLN C 191 GLN A 210 ASN A 224 ASN B 13 HIS B 160 ASN B 224 ASN B 480 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.120688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.109308 restraints weight = 15632.858| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.78 r_work: 0.3461 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12129 Z= 0.114 Angle : 0.491 6.718 16440 Z= 0.262 Chirality : 0.041 0.131 1791 Planarity : 0.004 0.039 2115 Dihedral : 5.987 72.444 1852 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.70 % Allowed : 27.47 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1458 helix: 2.59 (0.27), residues: 381 sheet: 0.68 (0.30), residues: 327 loop : -1.30 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 422 HIS 0.006 0.001 HIS B 356 PHE 0.016 0.001 PHE C 440 TYR 0.021 0.001 TYR C 489 ARG 0.009 0.000 ARG C 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 12) link_NAG-ASN : angle 1.59552 ( 36) hydrogen bonds : bond 0.05042 ( 471) hydrogen bonds : angle 4.51884 ( 1395) SS BOND : bond 0.00333 ( 18) SS BOND : angle 1.21614 ( 36) covalent geometry : bond 0.00262 (12099) covalent geometry : angle 0.48278 (16368) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 323 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 392 GLN cc_start: 0.6043 (OUTLIER) cc_final: 0.5666 (mp10) REVERT: C 405 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7612 (mmp80) REVERT: C 458 ASP cc_start: 0.7498 (t0) cc_final: 0.7122 (t0) REVERT: C 495 GLU cc_start: 0.7841 (tp30) cc_final: 0.7541 (tp30) REVERT: B 94 LEU cc_start: 0.9119 (mt) cc_final: 0.8882 (mp) REVERT: B 436 ARG cc_start: 0.7660 (mpt180) cc_final: 0.7450 (mpt180) REVERT: B 458 ASP cc_start: 0.7840 (t0) cc_final: 0.7619 (t0) outliers start: 48 outliers final: 35 residues processed: 349 average time/residue: 1.3963 time to fit residues: 521.3258 Evaluate side-chains 351 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 314 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 175 GLN A 210 ASN A 224 ASN A 455 GLN B 13 HIS B 160 ASN B 224 ASN B 480 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.120223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108880 restraints weight = 15523.325| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.77 r_work: 0.3456 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12129 Z= 0.145 Angle : 0.521 6.880 16440 Z= 0.278 Chirality : 0.042 0.131 1791 Planarity : 0.004 0.042 2115 Dihedral : 5.757 71.656 1847 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.47 % Allowed : 28.24 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1458 helix: 2.59 (0.27), residues: 381 sheet: 0.70 (0.30), residues: 327 loop : -1.32 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 422 HIS 0.005 0.001 HIS B 356 PHE 0.016 0.001 PHE C 440 TYR 0.022 0.001 TYR C 489 ARG 0.010 0.001 ARG C 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 12) link_NAG-ASN : angle 1.64426 ( 36) hydrogen bonds : bond 0.05258 ( 471) hydrogen bonds : angle 4.51411 ( 1395) SS BOND : bond 0.00352 ( 18) SS BOND : angle 1.31888 ( 36) covalent geometry : bond 0.00345 (12099) covalent geometry : angle 0.51241 (16368) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 320 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 GLN cc_start: 0.6076 (OUTLIER) cc_final: 0.5700 (mp10) REVERT: C 405 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7624 (mmp80) REVERT: C 458 ASP cc_start: 0.7516 (t0) cc_final: 0.7131 (t0) REVERT: B 94 LEU cc_start: 0.9121 (mt) cc_final: 0.8900 (mp) REVERT: B 436 ARG cc_start: 0.7653 (mpt180) cc_final: 0.7415 (mpt180) REVERT: B 458 ASP cc_start: 0.7862 (t0) cc_final: 0.7646 (t0) outliers start: 45 outliers final: 39 residues processed: 345 average time/residue: 1.4009 time to fit residues: 517.1539 Evaluate side-chains 358 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 317 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 498 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 105 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 175 GLN C 191 GLN A 210 ASN A 224 ASN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS B 160 ASN B 224 ASN B 480 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.119715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.108413 restraints weight = 15586.387| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.77 r_work: 0.3451 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12129 Z= 0.164 Angle : 0.539 7.146 16440 Z= 0.288 Chirality : 0.042 0.135 1791 Planarity : 0.004 0.043 2115 Dihedral : 5.535 71.365 1845 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.47 % Allowed : 28.09 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.22), residues: 1458 helix: 2.56 (0.27), residues: 381 sheet: 0.69 (0.30), residues: 327 loop : -1.33 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 81 HIS 0.006 0.001 HIS B 356 PHE 0.018 0.001 PHE C 440 TYR 0.023 0.002 TYR C 489 ARG 0.010 0.001 ARG C 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 12) link_NAG-ASN : angle 1.64509 ( 36) hydrogen bonds : bond 0.05404 ( 471) hydrogen bonds : angle 4.55459 ( 1395) SS BOND : bond 0.00352 ( 18) SS BOND : angle 1.24758 ( 36) covalent geometry : bond 0.00394 (12099) covalent geometry : angle 0.53118 (16368) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 319 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 MET cc_start: 0.8441 (mmm) cc_final: 0.7769 (mmm) REVERT: C 392 GLN cc_start: 0.6085 (OUTLIER) cc_final: 0.5710 (mp10) REVERT: C 405 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7644 (mmp80) REVERT: C 458 ASP cc_start: 0.7516 (t0) cc_final: 0.7114 (t0) REVERT: C 495 GLU cc_start: 0.7801 (tp30) cc_final: 0.7460 (tp30) REVERT: B 94 LEU cc_start: 0.9119 (mt) cc_final: 0.8906 (mp) REVERT: B 497 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7471 (tmtm) outliers start: 45 outliers final: 40 residues processed: 343 average time/residue: 1.4395 time to fit residues: 527.9404 Evaluate side-chains 357 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 314 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 498 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 125 optimal weight: 0.1980 chunk 97 optimal weight: 5.9990 chunk 4 optimal weight: 0.2980 chunk 134 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 175 GLN A 210 ASN A 224 ASN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS B 160 ASN B 224 ASN B 480 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.119530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.108774 restraints weight = 15567.321| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.72 r_work: 0.3466 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12129 Z= 0.130 Angle : 0.525 6.834 16440 Z= 0.281 Chirality : 0.042 0.188 1791 Planarity : 0.004 0.042 2115 Dihedral : 5.442 71.243 1845 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.32 % Allowed : 28.24 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1458 helix: 2.58 (0.27), residues: 381 sheet: 0.72 (0.30), residues: 327 loop : -1.31 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 422 HIS 0.006 0.001 HIS B 356 PHE 0.017 0.001 PHE C 440 TYR 0.022 0.001 TYR C 489 ARG 0.009 0.001 ARG C 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 12) link_NAG-ASN : angle 1.62815 ( 36) hydrogen bonds : bond 0.05144 ( 471) hydrogen bonds : angle 4.51759 ( 1395) SS BOND : bond 0.00325 ( 18) SS BOND : angle 1.12584 ( 36) covalent geometry : bond 0.00305 (12099) covalent geometry : angle 0.51824 (16368) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 318 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 MET cc_start: 0.8419 (mmm) cc_final: 0.7767 (mmm) REVERT: C 392 GLN cc_start: 0.6083 (OUTLIER) cc_final: 0.5699 (mp10) REVERT: C 405 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7636 (mmp80) REVERT: C 458 ASP cc_start: 0.7534 (t0) cc_final: 0.7133 (t0) REVERT: C 495 GLU cc_start: 0.7815 (tp30) cc_final: 0.7453 (tp30) REVERT: B 94 LEU cc_start: 0.9111 (mt) cc_final: 0.8877 (mp) REVERT: B 405 ARG cc_start: 0.7994 (mmp80) cc_final: 0.7762 (mmp-170) REVERT: B 497 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7541 (tmtm) outliers start: 43 outliers final: 36 residues processed: 340 average time/residue: 1.4117 time to fit residues: 512.9323 Evaluate side-chains 351 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 312 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 498 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 97 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 100 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 175 GLN C 191 GLN A 210 ASN A 224 ASN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS B 160 ASN B 224 ASN B 480 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.118525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107240 restraints weight = 15436.989| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.74 r_work: 0.3432 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12129 Z= 0.260 Angle : 0.607 8.115 16440 Z= 0.325 Chirality : 0.046 0.173 1791 Planarity : 0.004 0.043 2115 Dihedral : 5.621 71.093 1844 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.40 % Allowed : 28.09 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1458 helix: 2.33 (0.27), residues: 381 sheet: 0.63 (0.30), residues: 327 loop : -1.41 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 81 HIS 0.009 0.001 HIS B 356 PHE 0.025 0.002 PHE C 440 TYR 0.026 0.002 TYR C 489 ARG 0.010 0.001 ARG C 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 12) link_NAG-ASN : angle 1.72020 ( 36) hydrogen bonds : bond 0.06200 ( 471) hydrogen bonds : angle 4.76119 ( 1395) SS BOND : bond 0.00438 ( 18) SS BOND : angle 1.57308 ( 36) covalent geometry : bond 0.00634 (12099) covalent geometry : angle 0.59812 (16368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11538.59 seconds wall clock time: 198 minutes 34.62 seconds (11914.62 seconds total)