Starting phenix.real_space_refine on Wed Sep 17 22:28:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhh_38351/09_2025/8xhh_38351.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhh_38351/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xhh_38351/09_2025/8xhh_38351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhh_38351/09_2025/8xhh_38351.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xhh_38351/09_2025/8xhh_38351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhh_38351/09_2025/8xhh_38351.map" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.79, per 1000 atoms: 0.24 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: 0.93 Conformation dependent library (CDL) restraints added in 552.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.48 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: 2.40 Time building geometry restraints manager: 1.27 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 703) selection = chain 'B' selection = (chain 'C' and resid 6 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.010 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.870 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.000 ARG C 453 TYR 0.008 0.001 TYR B 103 PHE 0.018 0.001 PHE C 440 TRP 0.010 0.001 TRP A 422 HIS 0.005 0.001 HIS A 472 Details of bonding type rmsd covalent geometry : bond 0.00328 (12099) covalent geometry : angle 0.54375 (16368) SS BOND : bond 0.00368 ( 18) SS BOND : angle 1.37928 ( 36) hydrogen bonds : bond 0.18131 ( 471) hydrogen bonds : angle 6.87104 ( 1395) link_NAG-ASN : bond 0.00289 ( 12) link_NAG-ASN : angle 1.74081 ( 36) *********************** 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 : 0.323 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: 0.6545 time to fit residues: 277.6689 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 : 0.293 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 356 HIS 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 B 480 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.120215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.109211 restraints weight = 15457.443| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.73 r_work: 0.3466 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12129 Z= 0.138 Angle : 0.506 7.809 16440 Z= 0.271 Chirality : 0.042 0.165 1791 Planarity : 0.004 0.040 2115 Dihedral : 9.142 83.212 1921 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.63 % Allowed : 25.54 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.22), residues: 1458 helix: 2.47 (0.27), residues: 381 sheet: 0.55 (0.30), residues: 327 loop : -1.29 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 453 TYR 0.011 0.001 TYR C 12 PHE 0.016 0.001 PHE C 440 TRP 0.008 0.001 TRP C 422 HIS 0.005 0.001 HIS B 472 Details of bonding type rmsd covalent geometry : bond 0.00321 (12099) covalent geometry : angle 0.49733 (16368) SS BOND : bond 0.00371 ( 18) SS BOND : angle 1.07762 ( 36) hydrogen bonds : bond 0.05590 ( 471) hydrogen bonds : angle 5.02748 ( 1395) link_NAG-ASN : bond 0.00305 ( 12) link_NAG-ASN : angle 1.75906 ( 36) *********************** 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 406 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 346 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 436 ARG cc_start: 0.7559 (mtt180) cc_final: 0.7268 (mtt180) REVERT: C 458 ASP cc_start: 0.7552 (t0) cc_final: 0.7237 (t0) REVERT: C 495 GLU cc_start: 0.7761 (tp30) cc_final: 0.7343 (tp30) REVERT: A 372 GLN cc_start: 0.7618 (tp40) cc_final: 0.7304 (tp-100) REVERT: B 80 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7360 (tt0) REVERT: B 262 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8064 (ttmt) REVERT: B 477 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7080 (tp30) REVERT: B 491 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8508 (ttpp) outliers start: 60 outliers final: 40 residues processed: 384 average time/residue: 0.6524 time to fit residues: 267.5015 Evaluate side-chains 370 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 328 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 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 387 GLU Chi-restraints excluded: chain A residue 390 ASN 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 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 21 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 13 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- 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 455 GLN A 472 HIS B 13 HIS B 160 ASN B 224 ASN B 283 GLN B 356 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 = 0.3713 r_free = 0.3713 target = 0.119714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.108573 restraints weight = 15492.926| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.69 r_work: 0.3450 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12129 Z= 0.189 Angle : 0.517 6.781 16440 Z= 0.277 Chirality : 0.043 0.140 1791 Planarity : 0.004 0.039 2115 Dihedral : 7.898 80.503 1872 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.40 % Allowed : 25.39 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.22), residues: 1458 helix: 2.48 (0.27), residues: 381 sheet: 0.59 (0.30), residues: 327 loop : -1.31 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 453 TYR 0.013 0.002 TYR C 12 PHE 0.019 0.002 PHE C 440 TRP 0.008 0.001 TRP B 81 HIS 0.006 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00454 (12099) covalent geometry : angle 0.50967 (16368) SS BOND : bond 0.00298 ( 18) SS BOND : angle 1.14682 ( 36) hydrogen bonds : bond 0.05903 ( 471) hydrogen bonds : angle 4.82733 ( 1395) link_NAG-ASN : bond 0.00230 ( 12) link_NAG-ASN : angle 1.55711 ( 36) *********************** 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 391 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 334 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 GLN cc_start: 0.6032 (OUTLIER) cc_final: 0.5575 (mp10) REVERT: C 458 ASP cc_start: 0.7568 (t0) cc_final: 0.7226 (t0) REVERT: C 495 GLU cc_start: 0.7763 (tp30) cc_final: 0.7337 (tp30) REVERT: A 159 SER cc_start: 0.8141 (t) cc_final: 0.7828 (t) REVERT: A 369 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6906 (tm-30) REVERT: A 372 GLN cc_start: 0.7609 (tp40) cc_final: 0.7407 (tp-100) REVERT: B 94 LEU cc_start: 0.9132 (mt) cc_final: 0.8891 (mp) REVERT: B 477 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7073 (tp30) REVERT: B 491 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8479 (ttpp) outliers start: 57 outliers final: 33 residues processed: 371 average time/residue: 0.6499 time to fit residues: 257.2928 Evaluate side-chains 366 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 331 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 392 GLN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 431 LEU 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 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 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 378 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 41 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 499 ASN B 13 HIS B 160 ASN B 224 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.118920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.107601 restraints weight = 15539.985| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.75 r_work: 0.3436 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12129 Z= 0.220 Angle : 0.538 7.702 16440 Z= 0.289 Chirality : 0.044 0.166 1791 Planarity : 0.004 0.035 2115 Dihedral : 7.198 77.705 1858 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.55 % Allowed : 24.92 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.22), residues: 1458 helix: 2.43 (0.27), residues: 381 sheet: 0.59 (0.30), residues: 327 loop : -1.35 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 74 TYR 0.014 0.002 TYR C 12 PHE 0.022 0.002 PHE C 440 TRP 0.009 0.001 TRP B 81 HIS 0.007 0.001 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00533 (12099) covalent geometry : angle 0.53110 (16368) SS BOND : bond 0.00354 ( 18) SS BOND : angle 1.14231 ( 36) hydrogen bonds : bond 0.06054 ( 471) hydrogen bonds : angle 4.78974 ( 1395) link_NAG-ASN : bond 0.00201 ( 12) link_NAG-ASN : angle 1.59967 ( 36) *********************** 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 392 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 333 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 GLN cc_start: 0.6003 (OUTLIER) cc_final: 0.5567 (mp10) REVERT: C 458 ASP cc_start: 0.7501 (t0) cc_final: 0.7158 (t0) REVERT: C 495 GLU cc_start: 0.7783 (tp30) cc_final: 0.7424 (tp30) REVERT: A 369 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6911 (tm-30) REVERT: A 372 GLN cc_start: 0.7672 (tp40) cc_final: 0.7454 (tp-100) REVERT: B 94 LEU cc_start: 0.9136 (mt) cc_final: 0.8920 (mp) REVERT: B 477 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7056 (tp30) REVERT: B 491 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8523 (ttpp) outliers start: 59 outliers final: 40 residues processed: 370 average time/residue: 0.6396 time to fit residues: 252.7396 Evaluate side-chains 367 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 325 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 321 LEU 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 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 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 389 MET 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 188 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 64 optimal weight: 0.0770 chunk 8 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 C 390 ASN A 196 GLN A 210 ASN A 224 ASN A 360 GLN B 13 HIS B 160 ASN B 224 ASN B 283 GLN B 480 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.119966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108643 restraints weight = 15472.561| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.76 r_work: 0.3452 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12129 Z= 0.138 Angle : 0.500 8.570 16440 Z= 0.267 Chirality : 0.041 0.135 1791 Planarity : 0.004 0.043 2115 Dihedral : 6.530 75.360 1852 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.32 % Allowed : 25.46 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.22), residues: 1458 helix: 2.55 (0.27), residues: 381 sheet: 0.67 (0.30), residues: 327 loop : -1.32 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 453 TYR 0.010 0.001 TYR C 12 PHE 0.020 0.001 PHE C 440 TRP 0.008 0.001 TRP C 422 HIS 0.006 0.001 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00324 (12099) covalent geometry : angle 0.49220 (16368) SS BOND : bond 0.00324 ( 18) SS BOND : angle 1.12912 ( 36) hydrogen bonds : bond 0.05439 ( 471) hydrogen bonds : angle 4.62375 ( 1395) link_NAG-ASN : bond 0.00205 ( 12) link_NAG-ASN : angle 1.63890 ( 36) *********************** 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 374 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 318 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 GLN cc_start: 0.6004 (OUTLIER) cc_final: 0.5572 (mp10) REVERT: C 458 ASP cc_start: 0.7553 (t0) cc_final: 0.7194 (t0) REVERT: C 495 GLU cc_start: 0.7779 (tp30) cc_final: 0.7419 (tp30) REVERT: A 369 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6827 (tm-30) REVERT: B 94 LEU cc_start: 0.9128 (mt) cc_final: 0.8898 (mp) REVERT: B 491 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8457 (ttpp) outliers start: 56 outliers final: 37 residues processed: 351 average time/residue: 0.6274 time to fit residues: 235.4015 Evaluate side-chains 356 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 317 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 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 433 GLU 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 174 GLU Chi-restraints excluded: chain A residue 281 LYS 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 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 188 GLU 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 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 428 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 144 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 B 13 HIS B 160 ASN B 224 ASN B 283 GLN B 480 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.118855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.107887 restraints weight = 15561.716| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.74 r_work: 0.3443 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12129 Z= 0.195 Angle : 0.531 7.889 16440 Z= 0.283 Chirality : 0.043 0.160 1791 Planarity : 0.004 0.041 2115 Dihedral : 6.312 73.949 1850 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.94 % Allowed : 26.70 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.22), residues: 1458 helix: 2.54 (0.27), residues: 381 sheet: 0.65 (0.30), residues: 327 loop : -1.35 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 453 TYR 0.013 0.002 TYR C 12 PHE 0.022 0.002 PHE C 440 TRP 0.009 0.001 TRP B 81 HIS 0.006 0.001 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00470 (12099) covalent geometry : angle 0.52362 (16368) SS BOND : bond 0.00404 ( 18) SS BOND : angle 1.15595 ( 36) hydrogen bonds : bond 0.05750 ( 471) hydrogen bonds : angle 4.65852 ( 1395) link_NAG-ASN : bond 0.00213 ( 12) link_NAG-ASN : angle 1.65951 ( 36) *********************** 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 371 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 320 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 GLN cc_start: 0.6024 (OUTLIER) cc_final: 0.5619 (mp10) REVERT: C 458 ASP cc_start: 0.7560 (t0) cc_final: 0.7199 (t0) REVERT: C 495 GLU cc_start: 0.7846 (tp30) cc_final: 0.7471 (tp30) REVERT: A 369 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6786 (tm-30) REVERT: B 94 LEU cc_start: 0.9128 (mt) cc_final: 0.8909 (mp) REVERT: B 491 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8513 (ttpp) outliers start: 51 outliers final: 39 residues processed: 352 average time/residue: 0.6441 time to fit residues: 242.1321 Evaluate side-chains 357 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 316 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 392 GLN Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 431 LEU 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 174 GLU Chi-restraints excluded: chain A residue 198 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 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 188 GLU 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 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 491 LYS Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 498 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 76 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 B 13 HIS B 160 ASN B 224 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.119237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108213 restraints weight = 15388.491| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.67 r_work: 0.3450 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12129 Z= 0.198 Angle : 0.543 7.881 16440 Z= 0.290 Chirality : 0.043 0.149 1791 Planarity : 0.004 0.044 2115 Dihedral : 6.088 73.615 1850 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.17 % Allowed : 27.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.22), residues: 1458 helix: 2.47 (0.27), residues: 381 sheet: 0.66 (0.30), residues: 327 loop : -1.36 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 74 TYR 0.013 0.002 TYR C 12 PHE 0.022 0.002 PHE C 440 TRP 0.010 0.001 TRP B 81 HIS 0.007 0.001 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00480 (12099) covalent geometry : angle 0.53475 (16368) SS BOND : bond 0.00379 ( 18) SS BOND : angle 1.29524 ( 36) hydrogen bonds : bond 0.05797 ( 471) hydrogen bonds : angle 4.67301 ( 1395) link_NAG-ASN : bond 0.00244 ( 12) link_NAG-ASN : angle 1.64564 ( 36) *********************** 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 374 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 320 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 GLN cc_start: 0.6031 (OUTLIER) cc_final: 0.5650 (mp10) REVERT: C 458 ASP cc_start: 0.7526 (t0) cc_final: 0.7128 (t0) REVERT: C 495 GLU cc_start: 0.7806 (tp30) cc_final: 0.7453 (tp30) REVERT: A 369 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6810 (tm-30) REVERT: B 94 LEU cc_start: 0.9132 (mt) cc_final: 0.8905 (mp) REVERT: B 436 ARG cc_start: 0.7697 (mpt180) cc_final: 0.7444 (mpt180) REVERT: B 458 ASP cc_start: 0.7837 (t0) cc_final: 0.7597 (t0) REVERT: B 491 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8475 (ttpp) outliers start: 54 outliers final: 40 residues processed: 351 average time/residue: 0.6694 time to fit residues: 251.0602 Evaluate side-chains 361 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 319 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 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 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 174 GLU Chi-restraints excluded: chain A residue 198 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 442 ASP 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 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU 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 491 LYS 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 86 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 116 optimal weight: 0.0670 chunk 110 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 355 HIS B 480 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.119722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.108742 restraints weight = 15603.991| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.76 r_work: 0.3456 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12129 Z= 0.139 Angle : 0.514 7.092 16440 Z= 0.274 Chirality : 0.042 0.130 1791 Planarity : 0.004 0.041 2115 Dihedral : 5.767 73.478 1848 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.47 % Allowed : 27.85 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.22), residues: 1458 helix: 2.53 (0.27), residues: 381 sheet: 0.72 (0.30), residues: 327 loop : -1.29 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 74 TYR 0.020 0.001 TYR C 489 PHE 0.018 0.001 PHE C 440 TRP 0.009 0.001 TRP B 81 HIS 0.006 0.001 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00328 (12099) covalent geometry : angle 0.50615 (16368) SS BOND : bond 0.00364 ( 18) SS BOND : angle 1.29129 ( 36) hydrogen bonds : bond 0.05309 ( 471) hydrogen bonds : angle 4.57101 ( 1395) link_NAG-ASN : bond 0.00261 ( 12) link_NAG-ASN : angle 1.61072 ( 36) *********************** 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 371 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 326 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 GLN cc_start: 0.6070 (OUTLIER) cc_final: 0.5690 (mp10) REVERT: C 405 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7617 (mmp80) REVERT: C 458 ASP cc_start: 0.7532 (t0) cc_final: 0.7141 (t0) REVERT: C 495 GLU cc_start: 0.7822 (tp30) cc_final: 0.7474 (tp30) REVERT: A 369 GLU cc_start: 0.7046 (tm-30) cc_final: 0.6757 (tm-30) REVERT: B 436 ARG cc_start: 0.7624 (mpt180) cc_final: 0.7403 (mpt180) REVERT: B 458 ASP cc_start: 0.7855 (t0) cc_final: 0.7636 (t0) outliers start: 45 outliers final: 35 residues processed: 350 average time/residue: 0.6583 time to fit residues: 245.7979 Evaluate side-chains 359 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 322 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 349 ASP 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 454 MET 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 198 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 281 LYS 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 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 278 CYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 4 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 B 13 HIS B 160 ASN B 224 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.119306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.108343 restraints weight = 15420.232| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.74 r_work: 0.3451 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12129 Z= 0.171 Angle : 0.532 7.215 16440 Z= 0.283 Chirality : 0.042 0.138 1791 Planarity : 0.004 0.044 2115 Dihedral : 5.693 73.124 1847 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.63 % Allowed : 27.78 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.22), residues: 1458 helix: 2.49 (0.27), residues: 381 sheet: 0.71 (0.30), residues: 327 loop : -1.31 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 74 TYR 0.011 0.002 TYR C 12 PHE 0.020 0.002 PHE C 440 TRP 0.009 0.001 TRP B 81 HIS 0.007 0.001 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00411 (12099) covalent geometry : angle 0.52446 (16368) SS BOND : bond 0.00361 ( 18) SS BOND : angle 1.28001 ( 36) hydrogen bonds : bond 0.05504 ( 471) hydrogen bonds : angle 4.59113 ( 1395) link_NAG-ASN : bond 0.00228 ( 12) link_NAG-ASN : angle 1.64397 ( 36) *********************** 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 371 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 324 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 392 GLN cc_start: 0.6091 (OUTLIER) cc_final: 0.5713 (mp10) REVERT: C 405 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7628 (mmp80) REVERT: C 458 ASP cc_start: 0.7523 (t0) cc_final: 0.7130 (t0) REVERT: C 495 GLU cc_start: 0.7845 (tp30) cc_final: 0.7559 (tp30) REVERT: A 369 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6769 (tm-30) REVERT: B 272 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7783 (mm-30) REVERT: B 458 ASP cc_start: 0.7855 (t0) cc_final: 0.7635 (t0) REVERT: B 497 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7523 (tmtm) outliers start: 47 outliers final: 37 residues processed: 350 average time/residue: 0.6604 time to fit residues: 246.6293 Evaluate side-chains 359 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 318 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 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 454 MET 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 198 VAL 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 390 ASN 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 213 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 317 LEU 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 117 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 130 optimal weight: 0.0040 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.119745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108739 restraints weight = 15673.731| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.77 r_work: 0.3454 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12129 Z= 0.143 Angle : 0.521 6.921 16440 Z= 0.277 Chirality : 0.042 0.159 1791 Planarity : 0.004 0.042 2115 Dihedral : 5.482 72.821 1845 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.24 % Allowed : 27.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.22), residues: 1458 helix: 2.50 (0.27), residues: 381 sheet: 0.58 (0.30), residues: 333 loop : -1.25 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 74 TYR 0.010 0.001 TYR C 12 PHE 0.019 0.001 PHE C 440 TRP 0.008 0.001 TRP C 422 HIS 0.008 0.001 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00340 (12099) covalent geometry : angle 0.51386 (16368) SS BOND : bond 0.00335 ( 18) SS BOND : angle 1.20038 ( 36) hydrogen bonds : bond 0.05316 ( 471) hydrogen bonds : angle 4.54857 ( 1395) link_NAG-ASN : bond 0.00232 ( 12) link_NAG-ASN : angle 1.62778 ( 36) ********************** 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 365 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 323 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 GLN cc_start: 0.6094 (OUTLIER) cc_final: 0.5700 (mp10) REVERT: C 405 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7609 (mmp80) REVERT: C 458 ASP cc_start: 0.7547 (t0) cc_final: 0.7147 (t0) REVERT: C 495 GLU cc_start: 0.7845 (tp30) cc_final: 0.7569 (tp30) REVERT: B 436 ARG cc_start: 0.7630 (mpt180) cc_final: 0.7399 (mpt180) REVERT: B 497 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7549 (tmtm) outliers start: 42 outliers final: 36 residues processed: 347 average time/residue: 0.6567 time to fit residues: 243.3067 Evaluate side-chains 360 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 321 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 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 454 MET Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 198 VAL 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 390 ASN 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 213 SER Chi-restraints excluded: chain B residue 228 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 317 LEU 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 38 optimal weight: 0.4980 chunk 30 optimal weight: 0.0070 chunk 64 optimal weight: 0.0270 chunk 20 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- 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 B 13 HIS B 160 ASN B 224 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.119268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.108335 restraints weight = 15655.987| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.75 r_work: 0.3451 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12129 Z= 0.167 Angle : 0.539 7.080 16440 Z= 0.287 Chirality : 0.043 0.161 1791 Planarity : 0.004 0.043 2115 Dihedral : 5.433 72.552 1844 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.55 % Allowed : 28.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.22), residues: 1458 helix: 2.47 (0.27), residues: 381 sheet: 0.73 (0.30), residues: 327 loop : -1.31 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 74 TYR 0.011 0.002 TYR C 12 PHE 0.021 0.002 PHE C 440 TRP 0.008 0.001 TRP B 81 HIS 0.014 0.001 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00401 (12099) covalent geometry : angle 0.53144 (16368) SS BOND : bond 0.00353 ( 18) SS BOND : angle 1.27716 ( 36) hydrogen bonds : bond 0.05491 ( 471) hydrogen bonds : angle 4.58018 ( 1395) link_NAG-ASN : bond 0.00227 ( 12) link_NAG-ASN : angle 1.64082 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5574.80 seconds wall clock time: 95 minutes 24.88 seconds (5724.88 seconds total)