Starting phenix.real_space_refine on Sat Aug 23 17:20:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tkt_25981/08_2025/7tkt_25981.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tkt_25981/08_2025/7tkt_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tkt_25981/08_2025/7tkt_25981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tkt_25981/08_2025/7tkt_25981.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tkt_25981/08_2025/7tkt_25981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tkt_25981/08_2025/7tkt_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-2.0-5787/lib/python3.9/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: 475 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: 475 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: 2.79, per 1000 atoms: 0.21 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: 0.74 Conformation dependent library (CDL) restraints added in 388.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.27 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: 2.07 Time building geometry restraints manager: 1.05 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: 7976 34.68 - 69.36: 208 69.36 - 104.04: 52 104.04 - 138.71: 12 138.71 - 173.39: 32 Dihedral angle restraints: 8280 sinusoidal: 3692 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 8277 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: 0.03 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: 1.090 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.600 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 21.053 173.393 5316 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 aren 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 covalent geometry : bond 0.00659 (13492) covalent geometry : angle 1.26412 (18156) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.12057 ( 728) hydrogen bonds : angle 5.41712 ( 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 : 0.308 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.0985 time to fit residues: 22.2467 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 : 0.379 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3999 r_free = 0.3999 target = 0.158893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.125972 restraints weight = 21003.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126501 restraints weight = 15994.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.126620 restraints weight = 12932.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.127385 restraints weight = 12406.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127781 restraints weight = 11221.051| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.0992 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= 0.124 Angle : 0.615 9.030 18158 Z= 0.286 Chirality : 0.041 0.139 2100 Planarity : 0.004 0.042 2172 Dihedral : 21.067 163.491 2372 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.67 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 aren not related in a simple way. whole: 0.84 (0.23), residues: 1544 helix: 1.94 (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 0.002 0.000 ARG A 382 TYR 0.013 0.001 TYR B 25 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 covalent geometry : bond 0.00264 (13492) covalent geometry : angle 0.61548 (18156) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03607 ( 728) hydrogen bonds : angle 4.11342 ( 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 136 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.478 Fit side-chains REVERT: A 82 LEU cc_start: 0.7423 (tt) cc_final: 0.6686 (mp) REVERT: B 57 ASP cc_start: 0.5469 (t0) cc_final: 0.5164 (p0) REVERT: B 82 LEU cc_start: 0.7405 (tt) cc_final: 0.6686 (mp) REVERT: C 82 LEU cc_start: 0.7413 (tt) cc_final: 0.6689 (mp) REVERT: D 82 LEU cc_start: 0.7420 (tt) cc_final: 0.6678 (mp) REVERT: D 369 MET cc_start: 0.7610 (tpp) cc_final: 0.7400 (tpt) outliers start: 4 outliers final: 0 residues processed: 136 average time/residue: 0.0890 time to fit residues: 18.6558 Evaluate side-chains 123 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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: 2.9990 chunk 121 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.155867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121354 restraints weight = 21554.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121297 restraints weight = 16698.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122797 restraints weight = 13011.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123265 restraints weight = 11318.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123588 restraints weight = 10322.824| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13492 Z= 0.145 Angle : 0.616 8.986 18158 Z= 0.289 Chirality : 0.041 0.132 2100 Planarity : 0.004 0.038 2172 Dihedral : 18.719 162.862 2372 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.60 % Allowed : 13.13 % Favored : 86.27 % 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: 0.95 (0.23), residues: 1544 helix: 1.96 (0.18), residues: 928 sheet: -0.64 (0.44), residues: 132 loop : -1.71 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 377 TYR 0.009 0.001 TYR D 26 PHE 0.032 0.001 PHE D 40 TRP 0.009 0.001 TRP A 176 HIS 0.003 0.001 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00340 (13492) covalent geometry : angle 0.61626 (18156) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03701 ( 728) hydrogen bonds : angle 3.88937 ( 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 138 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.519 Fit side-chains REVERT: A 82 LEU cc_start: 0.7411 (tt) cc_final: 0.6724 (mp) REVERT: B 82 LEU cc_start: 0.7398 (tt) cc_final: 0.6731 (mp) REVERT: C 82 LEU cc_start: 0.7401 (tt) cc_final: 0.6732 (mp) REVERT: D 82 LEU cc_start: 0.7401 (tt) cc_final: 0.6730 (mp) REVERT: D 369 MET cc_start: 0.7808 (tpp) cc_final: 0.7602 (tpt) outliers start: 8 outliers final: 0 residues processed: 134 average time/residue: 0.1089 time to fit residues: 22.4189 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 : 0.500 ------------------------------------------------------------------------------- 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: 2.9990 chunk 71 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 61 optimal weight: 0.2980 chunk 86 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.157127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.122844 restraints weight = 21380.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122780 restraints weight = 17270.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123469 restraints weight = 14672.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.123665 restraints weight = 13216.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124663 restraints weight = 12342.276| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13492 Z= 0.119 Angle : 0.593 8.796 18158 Z= 0.277 Chirality : 0.041 0.136 2100 Planarity : 0.004 0.037 2172 Dihedral : 17.312 163.164 2372 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.07 % Allowed : 16.12 % Favored : 83.81 % 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: 0.98 (0.23), residues: 1544 helix: 1.98 (0.18), residues: 928 sheet: -0.54 (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 D 111 TYR 0.008 0.001 TYR C 26 PHE 0.025 0.001 PHE B 40 TRP 0.008 0.001 TRP D 176 HIS 0.002 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00270 (13492) covalent geometry : angle 0.59336 (18156) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03344 ( 728) hydrogen bonds : angle 3.76568 ( 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 129 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.538 Fit side-chains REVERT: A 82 LEU cc_start: 0.7411 (tt) cc_final: 0.6724 (mp) REVERT: A 369 MET cc_start: 0.7807 (tpp) cc_final: 0.7584 (tpt) REVERT: B 82 LEU cc_start: 0.7405 (tt) cc_final: 0.6722 (mp) REVERT: B 369 MET cc_start: 0.7781 (tpp) cc_final: 0.7554 (tpt) REVERT: C 82 LEU cc_start: 0.7417 (tt) cc_final: 0.6718 (mp) REVERT: D 82 LEU cc_start: 0.7418 (tt) cc_final: 0.6719 (mp) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.1301 time to fit residues: 24.5003 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 : 0.505 ------------------------------------------------------------------------------- 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: 4.9990 chunk 101 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.157324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.124453 restraints weight = 21363.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.124171 restraints weight = 16477.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.125055 restraints weight = 12925.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.125465 restraints weight = 12154.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125914 restraints weight = 11084.470| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13492 Z= 0.116 Angle : 0.595 10.149 18158 Z= 0.277 Chirality : 0.041 0.135 2100 Planarity : 0.004 0.035 2172 Dihedral : 16.729 163.558 2372 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.52 % Allowed : 17.61 % Favored : 81.87 % 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: 0.97 (0.23), residues: 1544 helix: 1.98 (0.18), residues: 928 sheet: -0.53 (0.45), residues: 128 loop : -1.74 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 111 TYR 0.008 0.001 TYR A 26 PHE 0.028 0.001 PHE A 40 TRP 0.007 0.001 TRP B 176 HIS 0.002 0.000 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00263 (13492) covalent geometry : angle 0.59476 (18156) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03232 ( 728) hydrogen bonds : angle 3.68824 ( 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 139 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7411 (tt) cc_final: 0.6761 (mp) REVERT: A 369 MET cc_start: 0.7818 (tpp) cc_final: 0.7606 (tpt) REVERT: B 82 LEU cc_start: 0.7417 (tt) cc_final: 0.6715 (mp) REVERT: B 369 MET cc_start: 0.7820 (tpp) cc_final: 0.7610 (tpt) REVERT: C 82 LEU cc_start: 0.7414 (tt) cc_final: 0.6717 (mp) REVERT: D 82 LEU cc_start: 0.7418 (tt) cc_final: 0.6717 (mp) outliers start: 7 outliers final: 0 residues processed: 139 average time/residue: 0.1097 time to fit residues: 23.5904 Evaluate side-chains 122 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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: 0.8980 chunk 126 optimal weight: 7.9990 chunk 7 optimal weight: 0.0000 chunk 64 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 146 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.158381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.126226 restraints weight = 21236.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125665 restraints weight = 17537.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125887 restraints weight = 14673.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.126822 restraints weight = 13454.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127147 restraints weight = 11715.360| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13492 Z= 0.108 Angle : 0.598 9.081 18158 Z= 0.277 Chirality : 0.041 0.140 2100 Planarity : 0.004 0.035 2172 Dihedral : 16.373 163.952 2372 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.07 % Allowed : 20.00 % 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 aren not related in a simple way. whole: 0.96 (0.23), residues: 1544 helix: 1.98 (0.18), residues: 928 sheet: -0.52 (0.46), residues: 128 loop : -1.77 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 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 C 99 Details of bonding type rmsd covalent geometry : bond 0.00240 (13492) covalent geometry : angle 0.59813 (18156) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03049 ( 728) hydrogen bonds : angle 3.63125 ( 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 128 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7478 (tt) cc_final: 0.6819 (mp) REVERT: B 82 LEU cc_start: 0.7410 (tt) cc_final: 0.6712 (mp) REVERT: B 334 MET cc_start: 0.6915 (tmm) cc_final: 0.6647 (tmm) REVERT: C 82 LEU cc_start: 0.7469 (tt) cc_final: 0.6777 (mp) REVERT: D 82 LEU cc_start: 0.7471 (tt) cc_final: 0.6777 (mp) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.1087 time to fit residues: 21.5480 Evaluate side-chains 119 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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: 0.0270 chunk 155 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.157310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122149 restraints weight = 21188.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123171 restraints weight = 14698.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.123919 restraints weight = 13341.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124314 restraints weight = 11299.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.124525 restraints weight = 11471.834| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1869 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= 0.120 Angle : 0.609 9.635 18158 Z= 0.282 Chirality : 0.042 0.194 2100 Planarity : 0.004 0.034 2172 Dihedral : 16.238 163.657 2372 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 21.12 % Favored : 78.88 % 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: 1.08 (0.23), residues: 1544 helix: 2.01 (0.18), residues: 928 sheet: -0.46 (0.54), residues: 92 loop : -1.51 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 111 TYR 0.006 0.001 TYR C 175 PHE 0.025 0.001 PHE A 40 TRP 0.007 0.001 TRP D 176 HIS 0.002 0.000 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00277 (13492) covalent geometry : angle 0.60861 (18156) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03184 ( 728) hydrogen bonds : angle 3.61279 ( 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 130 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 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: 0.7463 (tt) cc_final: 0.6850 (mp) REVERT: A 334 MET cc_start: 0.6846 (tmm) cc_final: 0.6517 (tmm) REVERT: B 82 LEU cc_start: 0.7475 (tt) cc_final: 0.6819 (mp) REVERT: B 234 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7673 (tm-30) REVERT: C 82 LEU cc_start: 0.7470 (tt) cc_final: 0.6814 (mp) REVERT: C 334 MET cc_start: 0.6829 (tmm) cc_final: 0.6495 (tmm) REVERT: D 82 LEU cc_start: 0.7475 (tt) cc_final: 0.6815 (mp) REVERT: D 334 MET cc_start: 0.6818 (tmm) cc_final: 0.6484 (tmm) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1091 time to fit residues: 21.8598 Evaluate side-chains 124 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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: 0.9990 chunk 139 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.151257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.114237 restraints weight = 21481.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116250 restraints weight = 15832.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116126 restraints weight = 11457.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116883 restraints weight = 11702.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.116964 restraints weight = 10555.739| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13492 Z= 0.225 Angle : 0.688 10.011 18158 Z= 0.330 Chirality : 0.045 0.181 2100 Planarity : 0.004 0.034 2172 Dihedral : 16.722 162.539 2372 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.04 % Allowed : 20.37 % Favored : 78.58 % 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: 0.76 (0.23), residues: 1544 helix: 1.86 (0.18), residues: 924 sheet: -0.60 (0.46), residues: 128 loop : -1.92 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 382 TYR 0.012 0.001 TYR D 175 PHE 0.019 0.002 PHE A 40 TRP 0.013 0.001 TRP A 176 HIS 0.005 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00547 (13492) covalent geometry : angle 0.68780 (18156) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04342 ( 728) hydrogen bonds : angle 3.96241 ( 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 151 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7475 (tt) cc_final: 0.6839 (mp) REVERT: B 82 LEU cc_start: 0.7475 (tt) cc_final: 0.6860 (mp) REVERT: B 334 MET cc_start: 0.6945 (tmm) cc_final: 0.6420 (tmm) REVERT: C 82 LEU cc_start: 0.7475 (tt) cc_final: 0.6859 (mp) REVERT: D 82 LEU cc_start: 0.7475 (tt) cc_final: 0.6857 (mp) outliers start: 14 outliers final: 0 residues processed: 151 average time/residue: 0.1100 time to fit residues: 25.2988 Evaluate side-chains 130 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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: 0.0770 chunk 123 optimal weight: 0.0060 chunk 50 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 2 optimal weight: 0.0970 chunk 152 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 overall best weight: 0.3952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN B 412 GLN C 412 GLN D 412 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.156327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121285 restraints weight = 21315.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122443 restraints weight = 16040.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122703 restraints weight = 11945.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123133 restraints weight = 11499.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.123461 restraints weight = 10790.419| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13492 Z= 0.122 Angle : 0.651 13.653 18158 Z= 0.305 Chirality : 0.043 0.231 2100 Planarity : 0.004 0.037 2172 Dihedral : 16.223 163.944 2372 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.90 % Allowed : 21.94 % Favored : 77.16 % 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: 0.88 (0.23), residues: 1544 helix: 1.93 (0.18), residues: 924 sheet: -0.62 (0.45), residues: 128 loop : -1.77 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 111 TYR 0.006 0.001 TYR A 128 PHE 0.027 0.002 PHE A 40 TRP 0.007 0.001 TRP A 176 HIS 0.002 0.000 HIS D 292 Details of bonding type rmsd covalent geometry : bond 0.00271 (13492) covalent geometry : angle 0.65153 (18156) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03382 ( 728) hydrogen bonds : angle 3.75612 ( 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 151 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7457 (tt) cc_final: 0.6822 (mp) REVERT: A 234 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7670 (tm-30) REVERT: B 82 LEU cc_start: 0.7450 (tt) cc_final: 0.6847 (mp) REVERT: B 234 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7674 (tm-30) REVERT: B 334 MET cc_start: 0.6582 (tmm) cc_final: 0.6334 (tmm) REVERT: C 82 LEU cc_start: 0.7447 (tt) cc_final: 0.6838 (mp) REVERT: C 234 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7674 (tm-30) REVERT: D 82 LEU cc_start: 0.7445 (tt) cc_final: 0.6837 (mp) REVERT: D 234 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7667 (tm-30) outliers start: 12 outliers final: 3 residues processed: 148 average time/residue: 0.1019 time to fit residues: 23.1024 Evaluate side-chains 137 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 LEU 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: 0.7980 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 0.0470 chunk 52 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 142 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.156688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.119633 restraints weight = 21376.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122689 restraints weight = 13721.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124683 restraints weight = 10540.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125539 restraints weight = 9071.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.126372 restraints weight = 8374.889| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13492 Z= 0.125 Angle : 0.684 13.112 18158 Z= 0.315 Chirality : 0.043 0.241 2100 Planarity : 0.004 0.036 2172 Dihedral : 16.047 163.755 2372 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.52 % Allowed : 22.39 % Favored : 77.09 % 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: 0.94 (0.23), residues: 1544 helix: 1.95 (0.18), residues: 924 sheet: -0.56 (0.46), residues: 128 loop : -1.70 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 111 TYR 0.005 0.001 TYR A 128 PHE 0.030 0.002 PHE A 40 TRP 0.006 0.001 TRP A 176 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00286 (13492) covalent geometry : angle 0.68381 (18156) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03320 ( 728) hydrogen bonds : angle 3.71433 ( 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 142 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7401 (tt) cc_final: 0.6758 (mp) REVERT: A 153 CYS cc_start: 0.8881 (m) cc_final: 0.8484 (m) REVERT: B 82 LEU cc_start: 0.7411 (tt) cc_final: 0.6774 (mp) REVERT: B 234 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 334 MET cc_start: 0.6663 (tmm) cc_final: 0.6441 (tmm) REVERT: C 82 LEU cc_start: 0.7413 (tt) cc_final: 0.6746 (mp) REVERT: D 82 LEU cc_start: 0.7421 (tt) cc_final: 0.6748 (mp) outliers start: 7 outliers final: 0 residues processed: 139 average time/residue: 0.1096 time to fit residues: 23.6265 Evaluate side-chains 131 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.0980 chunk 87 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.0270 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.153503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.121002 restraints weight = 21076.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120590 restraints weight = 23400.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120876 restraints weight = 20832.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.121771 restraints weight = 18617.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.121734 restraints weight = 16424.108| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13492 Z= 0.122 Angle : 0.682 13.092 18158 Z= 0.313 Chirality : 0.043 0.231 2100 Planarity : 0.004 0.035 2172 Dihedral : 15.906 163.717 2372 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.07 % Allowed : 23.28 % Favored : 76.64 % 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: 1.07 (0.23), residues: 1544 helix: 1.96 (0.18), residues: 924 sheet: -0.39 (0.56), residues: 92 loop : -1.42 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 111 TYR 0.005 0.001 TYR C 327 PHE 0.032 0.002 PHE C 40 TRP 0.006 0.001 TRP A 176 HIS 0.001 0.000 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00278 (13492) covalent geometry : angle 0.68196 (18156) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03224 ( 728) hydrogen bonds : angle 3.65997 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1877.82 seconds wall clock time: 33 minutes 31.45 seconds (2011.45 seconds total)