Starting phenix.real_space_refine on Fri Jul 3 10:09:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tkt_25981/07_2026/7tkt_25981.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tkt_25981/07_2026/7tkt_25981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7tkt_25981/07_2026/7tkt_25981.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tkt_25981/07_2026/7tkt_25981.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tkt_25981/07_2026/7tkt_25981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tkt_25981/07_2026/7tkt_25981.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tkt_25981/07_2026/7tkt_25981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tkt_25981/07_2026/7tkt_25981.map" } resolution = 3.6 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= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 28 5.16 5 C 8844 2.51 5 N 2080 2.21 5 O 2288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13252 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3103 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 23, 'TRANS': 366} Chain breaks: 1 Chain: "D" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3103 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 23, 'TRANS': 366} Chain breaks: 1 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 210 Unusual residues: {'PGW': 13} Classifications: {'RNA': 1, 'undetermined': 13} Modifications used: {'rna3p': 1} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 552 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-3': 10, 'PGW:plan-1': 11, 'PGW:plan-2': 11} Unresolved non-hydrogen planarities: 104 Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 210 Unusual residues: {'PGW': 13} Classifications: {'RNA': 1, 'undetermined': 13} Modifications used: {'rna3p': 1} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 552 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-1': 11, 'PGW:plan-2': 11, 'PGW:plan-3': 10} Unresolved non-hydrogen planarities: 104 Restraints were copied for chains: B, C Time building chain proxies: 3.61, per 1000 atoms: 0.27 Number of scatterers: 13252 At special positions: 0 Unit cell: (105.226, 105.226, 122.763, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 12 15.00 O 2288 8.00 N 2080 7.00 C 8844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 153 " distance=0.00 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 387 " distance=0.00 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 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 512.0 milliseconds 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 63.3% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 12 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.009A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 removed outlier: 4.113A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 107 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.775A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 158 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 224 Processing helix chain 'A' and resid 227 through 246 removed outlier: 3.555A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 306 through 315 removed outlier: 4.108A pdb=" N ILE A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.855A pdb=" N LEU A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 416 " --> pdb=" O GLN A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 81 through 89 removed outlier: 4.009A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 removed outlier: 4.113A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 107 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 110 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.775A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 158 Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 224 Processing helix chain 'B' and resid 227 through 246 removed outlier: 3.555A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 268 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 306 through 315 removed outlier: 4.109A pdb=" N ILE B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 404 through 416 removed outlier: 3.855A pdb=" N LEU B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B 416 " --> pdb=" O GLN B 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 81 through 89 removed outlier: 4.010A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 removed outlier: 4.113A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 107 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER C 108 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 110 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.775A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 158 Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 224 Processing helix chain 'C' and resid 227 through 246 removed outlier: 3.555A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 268 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 306 through 315 removed outlier: 4.107A pdb=" N ILE C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 404 through 416 removed outlier: 3.855A pdb=" N LEU C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL C 416 " --> pdb=" O GLN C 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 44 through 56 Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 81 through 89 removed outlier: 4.009A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 112 removed outlier: 4.113A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 107 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D 110 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 126 removed outlier: 3.776A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.555A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 268 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 306 through 315 removed outlier: 4.107A pdb=" N ILE D 310 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 404 through 416 removed outlier: 3.855A pdb=" N LEU D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL D 416 " --> pdb=" O GLN D 412 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.747A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.747A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.747A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 319 Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.747A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 2088 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: 1.95 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3845 1.34 - 1.45: 1694 1.45 - 1.57: 7881 1.57 - 1.69: 16 1.69 - 1.81: 56 Bond restraints: 13492 Sorted by residual: bond pdb=" C10 PGW B 513 " pdb=" C9 PGW B 513 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.33e+01 bond pdb=" C10 PGW D 502 " pdb=" C9 PGW D 502 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C10 PGW B 510 " pdb=" C9 PGW B 510 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C10 PGW C 510 " pdb=" C9 PGW C 510 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C10 PGW A 510 " pdb=" C9 PGW A 510 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 ... (remaining 13487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.21: 17753 4.21 - 8.43: 379 8.43 - 12.64: 8 12.64 - 16.86: 0 16.86 - 21.07: 16 Bond angle restraints: 18156 Sorted by residual: angle pdb=" C10 PGW B 513 " pdb=" C9 PGW B 513 " pdb=" C8 PGW B 513 " ideal model delta sigma weight residual 127.02 105.95 21.07 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW D 505 " pdb=" C9 PGW D 505 " pdb=" C8 PGW D 505 " ideal model delta sigma weight residual 127.02 105.96 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW C 513 " pdb=" C9 PGW C 513 " pdb=" C8 PGW C 513 " ideal model delta sigma weight residual 127.02 105.96 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW A 513 " pdb=" C9 PGW A 513 " pdb=" C8 PGW A 513 " ideal model delta sigma weight residual 127.02 105.96 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW C 510 " pdb=" C9 PGW C 510 " pdb=" C8 PGW C 510 " ideal model delta sigma weight residual 127.02 106.26 20.76 3.00e+00 1.11e-01 4.79e+01 ... (remaining 18151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 7924 34.68 - 69.36: 188 69.36 - 104.04: 36 104.04 - 138.71: 12 138.71 - 173.39: 16 Dihedral angle restraints: 8176 sinusoidal: 3588 harmonic: 4588 Sorted by residual: dihedral pdb=" C3' CMP C 501 " pdb=" O3' CMP C 501 " pdb=" P CMP C 501 " pdb=" O1P CMP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 100.95 -160.95 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C3' CMP D 507 " pdb=" O3' CMP D 507 " pdb=" P CMP D 507 " pdb=" O1P CMP D 507 " ideal model delta sinusoidal sigma weight residual -60.00 100.94 -160.94 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C3' CMP A 501 " pdb=" O3' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 100.94 -160.94 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 8173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1311 0.034 - 0.069: 547 0.069 - 0.103: 191 0.103 - 0.137: 39 0.137 - 0.171: 12 Chirality restraints: 2100 Sorted by residual: chirality pdb=" C02 PGW C 503 " pdb=" C01 PGW C 503 " pdb=" C03 PGW C 503 " pdb=" O01 PGW C 503 " both_signs ideal model delta sigma weight residual False 2.36 2.53 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" C02 PGW D 509 " pdb=" C01 PGW D 509 " pdb=" C03 PGW D 509 " pdb=" O01 PGW D 509 " both_signs ideal model delta sigma weight residual False 2.36 2.53 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA GLN D 412 " pdb=" N GLN D 412 " pdb=" C GLN D 412 " pdb=" CB GLN D 412 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 2097 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 513 " -0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C10 PGW B 513 " 0.161 2.00e-02 2.50e+03 pdb=" C8 PGW B 513 " -0.158 2.00e-02 2.50e+03 pdb=" C9 PGW B 513 " 0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 505 " 0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C10 PGW D 505 " -0.161 2.00e-02 2.50e+03 pdb=" C8 PGW D 505 " 0.158 2.00e-02 2.50e+03 pdb=" C9 PGW D 505 " -0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW C 513 " 0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C10 PGW C 513 " -0.161 2.00e-02 2.50e+03 pdb=" C8 PGW C 513 " 0.158 2.00e-02 2.50e+03 pdb=" C9 PGW C 513 " -0.156 2.00e-02 2.50e+03 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1950 2.76 - 3.29: 12129 3.29 - 3.83: 21391 3.83 - 4.36: 22528 4.36 - 4.90: 40837 Nonbonded interactions: 98835 Sorted by model distance: nonbonded pdb=" OG1 THR A 180 " pdb=" OH TYR D 186 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR C 186 " pdb=" OG1 THR D 180 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR B 262 " pdb=" OD2 ASP B 388 " model vdw 2.264 3.040 ... (remaining 98830 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or \ name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513 \ through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 \ )))) selection = (chain 'B' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or \ name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513 \ through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 \ )))) selection = (chain 'C' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or \ name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513 \ through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 \ )))) selection = (chain 'D' and (resid 10 through 416 or resid 502 or (resid 504 through 505 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 508 \ and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resi \ d 509 and (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28)) or resid 510 through 511 or resid 513 through 514)) } 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 group one per residue 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.650 Find NCS groups from input model: 0.330 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.007 0.171 13492 Z= 0.327 Angle : 1.264 21.069 18158 Z= 0.478 Chirality : 0.044 0.171 2100 Planarity : 0.008 0.159 2172 Dihedral : 18.716 173.393 5212 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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 are not related in a simple way. whole: 0.63 (0.22), residues: 1544 helix: 1.56 (0.18), residues: 936 sheet: 0.59 (0.57), residues: 84 loop : -1.78 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 311 TYR 0.009 0.001 TYR B 26 PHE 0.005 0.001 PHE D 386 TRP 0.005 0.001 TRP B 264 HIS 0.002 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.33 (13492) covalent geometry : angle 1.26412 / 0.48 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.12057 / 8.10 ( 728) hydrogen bonds : angle 5.41712 / 3.91 ( 2088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.335 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1070 time to fit residues: 24.2715 Evaluate side-chains 125 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0070 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN B 217 ASN C 217 ASN D 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.159091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.125705 restraints weight = 20966.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125874 restraints weight = 16238.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126493 restraints weight = 14231.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.126690 restraints weight = 12612.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.127595 restraints weight = 11865.444| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13492 Z= 0.119 Angle : 0.612 9.101 18158 Z= 0.285 Chirality : 0.041 0.132 2100 Planarity : 0.004 0.042 2172 Dihedral : 17.706 163.362 2268 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.30 % Allowed : 7.24 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.23), residues: 1544 helix: 1.93 (0.18), residues: 928 sheet: -0.69 (0.41), residues: 156 loop : -1.95 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 111 TYR 0.014 0.001 TYR C 26 PHE 0.012 0.001 PHE B 40 TRP 0.006 0.001 TRP C 176 HIS 0.002 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (13492) covalent geometry : angle 0.61227 / 0.29 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03640 / 2.42 ( 728) hydrogen bonds : angle 4.13574 / 2.94 ( 2088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 0.473 Fit side-chains REVERT: A 82 LEU cc_start: 0.7427 (tt) cc_final: 0.6698 (mp) REVERT: B 57 ASP cc_start: 0.5507 (t0) cc_final: 0.5153 (p0) REVERT: B 82 LEU cc_start: 0.7409 (tt) cc_final: 0.6696 (mp) REVERT: C 82 LEU cc_start: 0.7414 (tt) cc_final: 0.6702 (mp) REVERT: D 82 LEU cc_start: 0.7411 (tt) cc_final: 0.6698 (mp) REVERT: D 369 MET cc_start: 0.7601 (tpp) cc_final: 0.7389 (tpt) outliers start: 4 outliers final: 0 residues processed: 138 average time/residue: 0.0943 time to fit residues: 20.0508 Evaluate side-chains 126 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 105 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.155545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.122787 restraints weight = 21337.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122983 restraints weight = 16470.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124434 restraints weight = 13103.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125026 restraints weight = 11369.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.124880 restraints weight = 10585.831| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13492 Z= 0.154 Angle : 0.618 9.012 18158 Z= 0.291 Chirality : 0.041 0.133 2100 Planarity : 0.004 0.039 2172 Dihedral : 16.856 162.805 2268 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.52 % Allowed : 13.28 % Favored : 86.19 % 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 are not related in a simple way. whole: 0.94 (0.23), residues: 1544 helix: 1.95 (0.18), residues: 928 sheet: -0.61 (0.44), residues: 132 loop : -1.72 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 377 TYR 0.012 0.001 TYR D 26 PHE 0.029 0.002 PHE C 40 TRP 0.009 0.001 TRP B 176 HIS 0.003 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (13492) covalent geometry : angle 0.61802 / 0.29 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03787 / 2.51 ( 728) hydrogen bonds : angle 3.93806 / 2.78 ( 2088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.480 Fit side-chains REVERT: A 82 LEU cc_start: 0.7434 (tt) cc_final: 0.6696 (mp) REVERT: B 82 LEU cc_start: 0.7431 (tt) cc_final: 0.6691 (mp) REVERT: C 82 LEU cc_start: 0.7425 (tt) cc_final: 0.6705 (mp) REVERT: D 82 LEU cc_start: 0.7425 (tt) cc_final: 0.6705 (mp) REVERT: D 369 MET cc_start: 0.7734 (tpp) cc_final: 0.7516 (tpt) outliers start: 7 outliers final: 0 residues processed: 134 average time/residue: 0.0987 time to fit residues: 20.4716 Evaluate side-chains 118 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 65 optimal weight: 0.0060 chunk 75 optimal weight: 0.8980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.156982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122913 restraints weight = 21407.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122724 restraints weight = 17307.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123131 restraints weight = 14597.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.123527 restraints weight = 13545.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124153 restraints weight = 12496.742| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13492 Z= 0.119 Angle : 0.592 9.156 18158 Z= 0.277 Chirality : 0.041 0.136 2100 Planarity : 0.004 0.037 2172 Dihedral : 16.128 163.204 2268 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.30 % Allowed : 15.97 % Favored : 83.73 % 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 are not related in a simple way. whole: 0.99 (0.23), residues: 1544 helix: 1.98 (0.18), residues: 928 sheet: -0.48 (0.45), residues: 128 loop : -1.71 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 111 TYR 0.007 0.001 TYR C 26 PHE 0.027 0.001 PHE B 40 TRP 0.008 0.001 TRP C 176 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (13492) covalent geometry : angle 0.59238 / 0.28 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03326 / 2.21 ( 728) hydrogen bonds : angle 3.77015 / 2.65 ( 2088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7419 (tt) cc_final: 0.6728 (mp) REVERT: B 82 LEU cc_start: 0.7406 (tt) cc_final: 0.6730 (mp) REVERT: C 82 LEU cc_start: 0.7418 (tt) cc_final: 0.6715 (mp) REVERT: D 82 LEU cc_start: 0.7423 (tt) cc_final: 0.6720 (mp) outliers start: 4 outliers final: 0 residues processed: 130 average time/residue: 0.1074 time to fit residues: 20.7297 Evaluate side-chains 121 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 121 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 87 optimal weight: 0.0470 chunk 96 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.157747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.124635 restraints weight = 21343.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.124607 restraints weight = 16964.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124948 restraints weight = 13335.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.125188 restraints weight = 12807.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.126637 restraints weight = 11901.257| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13492 Z= 0.114 Angle : 0.596 10.155 18158 Z= 0.276 Chirality : 0.041 0.141 2100 Planarity : 0.004 0.035 2172 Dihedral : 15.738 163.494 2268 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.37 % Allowed : 17.91 % Favored : 81.72 % 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 are not related in a simple way. whole: 0.99 (0.23), residues: 1544 helix: 1.98 (0.18), residues: 928 sheet: -0.51 (0.45), residues: 128 loop : -1.70 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 111 TYR 0.005 0.001 TYR A 128 PHE 0.028 0.001 PHE A 40 TRP 0.007 0.001 TRP D 176 HIS 0.002 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (13492) covalent geometry : angle 0.59567 / 0.28 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03204 / 2.13 ( 728) hydrogen bonds : angle 3.68834 / 2.58 ( 2088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7399 (tt) cc_final: 0.6751 (mp) REVERT: A 96 PHE cc_start: 0.7355 (m-80) cc_final: 0.7147 (m-10) REVERT: A 369 MET cc_start: 0.7804 (tpp) cc_final: 0.7569 (tpt) REVERT: B 82 LEU cc_start: 0.7408 (tt) cc_final: 0.6722 (mp) REVERT: C 82 LEU cc_start: 0.7414 (tt) cc_final: 0.6719 (mp) REVERT: C 369 MET cc_start: 0.7808 (tpp) cc_final: 0.7577 (tpt) REVERT: D 82 LEU cc_start: 0.7424 (tt) cc_final: 0.6710 (mp) outliers start: 5 outliers final: 0 residues processed: 134 average time/residue: 0.0949 time to fit residues: 19.5121 Evaluate side-chains 121 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 21 optimal weight: 0.7980 chunk 126 optimal weight: 8.9990 chunk 7 optimal weight: 0.3980 chunk 64 optimal weight: 0.0670 chunk 17 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.158184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121102 restraints weight = 21604.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124101 restraints weight = 13992.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126009 restraints weight = 10772.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.127180 restraints weight = 9300.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127503 restraints weight = 8509.083| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13492 Z= 0.110 Angle : 0.596 9.371 18158 Z= 0.277 Chirality : 0.041 0.134 2100 Planarity : 0.004 0.035 2172 Dihedral : 15.384 163.920 2268 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.30 % Allowed : 19.48 % Favored : 80.22 % 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 are not related in a simple way. whole: 1.02 (0.23), residues: 1544 helix: 2.02 (0.18), residues: 928 sheet: -0.50 (0.46), residues: 128 loop : -1.72 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 111 TYR 0.004 0.001 TYR A 128 PHE 0.027 0.001 PHE A 40 TRP 0.006 0.001 TRP D 176 HIS 0.001 0.000 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (13492) covalent geometry : angle 0.59578 / 0.28 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03084 / 2.04 ( 728) hydrogen bonds : angle 3.62869 / 2.54 ( 2088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7356 (tt) cc_final: 0.6751 (mp) REVERT: A 369 MET cc_start: 0.7831 (tpp) cc_final: 0.7600 (tpt) REVERT: B 82 LEU cc_start: 0.7355 (tt) cc_final: 0.6732 (mp) REVERT: C 82 LEU cc_start: 0.7445 (tt) cc_final: 0.6804 (mp) REVERT: C 369 MET cc_start: 0.7832 (tpp) cc_final: 0.7612 (tpt) REVERT: D 82 LEU cc_start: 0.7448 (tt) cc_final: 0.6805 (mp) outliers start: 4 outliers final: 0 residues processed: 125 average time/residue: 0.0851 time to fit residues: 16.4059 Evaluate side-chains 112 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 106 optimal weight: 0.2980 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.157169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120773 restraints weight = 21556.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122449 restraints weight = 17201.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.123433 restraints weight = 11920.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.124028 restraints weight = 10686.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124215 restraints weight = 10458.028| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13492 Z= 0.121 Angle : 0.606 9.961 18158 Z= 0.282 Chirality : 0.041 0.135 2100 Planarity : 0.004 0.034 2172 Dihedral : 15.179 163.514 2268 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 20.07 % Favored : 79.93 % 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 are not related in a simple way. whole: 1.03 (0.23), residues: 1544 helix: 2.03 (0.18), residues: 928 sheet: -0.51 (0.46), residues: 128 loop : -1.73 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 374 TYR 0.006 0.001 TYR B 175 PHE 0.028 0.001 PHE A 40 TRP 0.007 0.001 TRP C 176 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (13492) covalent geometry : angle 0.60581 / 0.28 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03166 / 2.09 ( 728) hydrogen bonds : angle 3.61714 / 2.53 ( 2088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7473 (tt) cc_final: 0.6854 (mp) REVERT: A 334 MET cc_start: 0.6790 (tmm) cc_final: 0.6463 (tmm) REVERT: A 369 MET cc_start: 0.7791 (tpp) cc_final: 0.7562 (tpt) REVERT: B 82 LEU cc_start: 0.7478 (tt) cc_final: 0.6829 (mp) REVERT: B 334 MET cc_start: 0.6782 (tmm) cc_final: 0.6417 (tmm) REVERT: C 82 LEU cc_start: 0.7468 (tt) cc_final: 0.6818 (mp) REVERT: C 334 MET cc_start: 0.6788 (tmm) cc_final: 0.6463 (tmm) REVERT: C 369 MET cc_start: 0.7811 (tpp) cc_final: 0.7584 (tpt) REVERT: D 82 LEU cc_start: 0.7467 (tt) cc_final: 0.6814 (mp) REVERT: D 334 MET cc_start: 0.6782 (tmm) cc_final: 0.6461 (tmm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0931 time to fit residues: 18.8885 Evaluate side-chains 121 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 33 optimal weight: 0.0020 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 chunk 119 optimal weight: 0.0370 chunk 125 optimal weight: 0.7980 overall best weight: 0.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.158701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.121575 restraints weight = 21357.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.124629 restraints weight = 13761.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126568 restraints weight = 10591.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127281 restraints weight = 9087.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128305 restraints weight = 8434.074| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13492 Z= 0.109 Angle : 0.596 9.346 18158 Z= 0.277 Chirality : 0.041 0.138 2100 Planarity : 0.004 0.035 2172 Dihedral : 14.822 163.975 2268 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.52 % Allowed : 20.30 % Favored : 79.18 % 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 are not related in a simple way. whole: 1.10 (0.23), residues: 1544 helix: 2.04 (0.18), residues: 924 sheet: -0.35 (0.55), residues: 92 loop : -1.52 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 374 TYR 0.005 0.001 TYR A 170 PHE 0.027 0.001 PHE A 40 TRP 0.006 0.001 TRP A 176 HIS 0.001 0.000 HIS D 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (13492) covalent geometry : angle 0.59617 / 0.28 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03030 / 2.02 ( 728) hydrogen bonds : angle 3.57475 / 2.49 ( 2088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.7417 (t80) cc_final: 0.7217 (t80) REVERT: A 82 LEU cc_start: 0.7441 (tt) cc_final: 0.6853 (mp) REVERT: A 369 MET cc_start: 0.7732 (tpp) cc_final: 0.7510 (tpt) REVERT: B 25 TYR cc_start: 0.7415 (t80) cc_final: 0.7206 (t80) REVERT: B 82 LEU cc_start: 0.7455 (tt) cc_final: 0.6816 (mp) REVERT: B 234 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7611 (tm-30) REVERT: C 82 LEU cc_start: 0.7452 (tt) cc_final: 0.6805 (mp) REVERT: C 369 MET cc_start: 0.7736 (tpp) cc_final: 0.7512 (tpt) REVERT: D 82 LEU cc_start: 0.7446 (tt) cc_final: 0.6806 (mp) outliers start: 7 outliers final: 0 residues processed: 131 average time/residue: 0.1054 time to fit residues: 21.2141 Evaluate side-chains 120 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 84 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.156162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119425 restraints weight = 21554.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.121300 restraints weight = 15987.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121352 restraints weight = 11774.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.121959 restraints weight = 11556.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122191 restraints weight = 10565.581| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13492 Z= 0.138 Angle : 0.649 10.526 18158 Z= 0.303 Chirality : 0.042 0.212 2100 Planarity : 0.004 0.034 2172 Dihedral : 14.742 163.442 2268 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.67 % Allowed : 20.60 % Favored : 78.73 % 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 are not related in a simple way. whole: 1.04 (0.23), residues: 1544 helix: 1.95 (0.18), residues: 924 sheet: -0.39 (0.55), residues: 92 loop : -1.46 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 374 TYR 0.007 0.001 TYR D 327 PHE 0.029 0.001 PHE A 40 TRP 0.008 0.001 TRP A 176 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (13492) covalent geometry : angle 0.64921 / 0.30 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03393 / 2.26 ( 728) hydrogen bonds : angle 3.67936 / 2.57 ( 2088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7463 (tt) cc_final: 0.6875 (mp) REVERT: A 369 MET cc_start: 0.7761 (tpp) cc_final: 0.7540 (tpt) REVERT: B 82 LEU cc_start: 0.7461 (tt) cc_final: 0.6851 (mp) REVERT: C 82 LEU cc_start: 0.7449 (tt) cc_final: 0.6862 (mp) REVERT: C 369 MET cc_start: 0.7780 (tpp) cc_final: 0.7558 (tpt) REVERT: D 82 LEU cc_start: 0.7448 (tt) cc_final: 0.6860 (mp) outliers start: 9 outliers final: 2 residues processed: 135 average time/residue: 0.1017 time to fit residues: 21.0843 Evaluate side-chains 130 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 48 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 0.0010 chunk 52 optimal weight: 7.9990 chunk 25 optimal weight: 0.0670 chunk 57 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.157652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120385 restraints weight = 21541.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.123442 restraints weight = 13925.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.125405 restraints weight = 10691.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126421 restraints weight = 9192.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.127263 restraints weight = 8443.020| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13492 Z= 0.120 Angle : 0.679 13.829 18158 Z= 0.309 Chirality : 0.043 0.254 2100 Planarity : 0.004 0.034 2172 Dihedral : 14.550 163.756 2268 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.22 % Allowed : 21.12 % Favored : 78.66 % 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 are not related in a simple way. whole: 1.08 (0.23), residues: 1544 helix: 1.96 (0.18), residues: 924 sheet: -0.26 (0.56), residues: 92 loop : -1.43 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 374 TYR 0.005 0.001 TYR C 128 PHE 0.031 0.001 PHE A 40 TRP 0.007 0.001 TRP B 176 HIS 0.001 0.000 HIS C 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (13492) covalent geometry : angle 0.67870 / 0.31 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03270 / 2.18 ( 728) hydrogen bonds : angle 3.66417 / 2.56 ( 2088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.7409 (t80) cc_final: 0.7202 (t80) REVERT: A 82 LEU cc_start: 0.7427 (tt) cc_final: 0.6752 (mp) REVERT: A 369 MET cc_start: 0.7707 (tpp) cc_final: 0.7464 (tpt) REVERT: B 25 TYR cc_start: 0.7416 (t80) cc_final: 0.7203 (t80) REVERT: B 82 LEU cc_start: 0.7481 (tt) cc_final: 0.6812 (mp) REVERT: B 234 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 82 LEU cc_start: 0.7463 (tt) cc_final: 0.6781 (mp) REVERT: C 369 MET cc_start: 0.7714 (tpp) cc_final: 0.7472 (tpt) REVERT: D 82 LEU cc_start: 0.7463 (tt) cc_final: 0.6781 (mp) outliers start: 3 outliers final: 2 residues processed: 130 average time/residue: 0.0991 time to fit residues: 19.9225 Evaluate side-chains 125 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 0.0270 chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 110 optimal weight: 0.0070 chunk 134 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.0470 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.160114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.123524 restraints weight = 21404.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126614 restraints weight = 13789.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128632 restraints weight = 10575.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.129628 restraints weight = 9043.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.130492 restraints weight = 8310.438| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13492 Z= 0.113 Angle : 0.661 14.608 18158 Z= 0.301 Chirality : 0.043 0.232 2100 Planarity : 0.004 0.034 2172 Dihedral : 14.153 163.855 2268 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.30 % Allowed : 22.01 % Favored : 77.69 % 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 are not related in a simple way. whole: 1.11 (0.23), residues: 1544 helix: 1.97 (0.18), residues: 924 sheet: -0.18 (0.56), residues: 92 loop : -1.39 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 374 TYR 0.007 0.001 TYR A 327 PHE 0.034 0.001 PHE A 40 TRP 0.006 0.001 TRP B 155 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (13492) covalent geometry : angle 0.66105 / 0.30 (18156) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.02994 / 1.98 ( 728) hydrogen bonds : angle 3.59773 / 2.51 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1792.58 seconds wall clock time: 31 minutes 48.42 seconds (1908.42 seconds total)