Starting phenix.real_space_refine on Fri Jul 3 11:49:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rsh_24670/07_2026/7rsh_24670.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rsh_24670/07_2026/7rsh_24670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rsh_24670/07_2026/7rsh_24670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rsh_24670/07_2026/7rsh_24670.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rsh_24670/07_2026/7rsh_24670.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rsh_24670/07_2026/7rsh_24670.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rsh_24670/07_2026/7rsh_24670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rsh_24670/07_2026/7rsh_24670.map" } resolution = 3.0 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= 0.006 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 8 5.49 5 S 28 5.16 5 C 9244 2.51 5 N 2148 2.21 5 O 2316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 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: 13744 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3191 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 25, 'TRANS': 375} Chain breaks: 1 Chain: "D" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3191 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 25, 'TRANS': 375} Chain breaks: 1 Chain: "A" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'PGW': 14} Classifications: {'RNA': 1, 'undetermined': 14} Modifications used: {'rna3p': 1} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PGW:plan-1': 12, 'PGW:plan-2': 12, 'PGW:plan-3': 8} Unresolved non-hydrogen planarities: 119 Chain: "D" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'PGW': 14} Classifications: {'RNA': 1, 'undetermined': 14} Modifications used: {'rna3p': 1} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PGW:plan-1': 12, 'PGW:plan-2': 12, 'PGW:plan-3': 8} Unresolved non-hydrogen planarities: 119 Restraints were copied for chains: B, C Time building chain proxies: 3.32, per 1000 atoms: 0.24 Number of scatterers: 13744 At special positions: 0 Unit cell: (106.937, 106.937, 123.877, 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 8 15.00 O 2316 8.00 N 2148 7.00 C 9244 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: 1.19 Conformation dependent library (CDL) restraints added in 651.9 milliseconds 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 8 sheets defined 64.8% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 14 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 43 through 63 removed outlier: 4.385A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.617A pdb=" N LEU A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 101 through 106 removed outlier: 4.081A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.940A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.962A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 158 removed outlier: 3.588A pdb=" N LEU A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 223 Processing helix chain 'A' and resid 227 through 246 Processing helix chain 'A' and resid 249 through 268 removed outlier: 3.727A pdb=" N ILE A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) 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: 3.940A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 4.310A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 404 through 417 removed outlier: 3.627A pdb=" N ARG A 417 " --> pdb=" O GLU A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 43 through 63 removed outlier: 4.385A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.617A pdb=" N LEU B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 101 through 106 removed outlier: 4.080A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.940A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.962A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 158 removed outlier: 3.588A pdb=" N LEU B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 223 Processing helix chain 'B' and resid 227 through 246 Processing helix chain 'B' and resid 249 through 268 removed outlier: 3.727A pdb=" N ILE B 257 " --> pdb=" O GLN B 253 " (cutoff:3.500A) 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: 3.940A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 4.310A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 404 through 417 removed outlier: 3.627A pdb=" N ARG B 417 " --> pdb=" O GLU B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 43 through 63 removed outlier: 4.385A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.617A pdb=" N LEU C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 101 through 106 removed outlier: 4.080A pdb=" N LEU C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.941A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.963A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 158 removed outlier: 3.589A pdb=" N LEU C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 223 Processing helix chain 'C' and resid 227 through 246 Processing helix chain 'C' and resid 249 through 268 removed outlier: 3.727A pdb=" N ILE C 257 " --> pdb=" O GLN C 253 " (cutoff:3.500A) 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: 3.940A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 4.311A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 404 through 417 removed outlier: 3.627A pdb=" N ARG C 417 " --> pdb=" O GLU C 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 43 through 63 removed outlier: 4.386A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.618A pdb=" N LEU D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 101 through 106 removed outlier: 4.081A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.940A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 126 removed outlier: 3.962A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 removed outlier: 3.589A pdb=" N LEU D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 223 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 249 through 268 removed outlier: 3.727A pdb=" N ILE D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) 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: 3.940A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 4.310A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 404 through 417 removed outlier: 3.627A pdb=" N ARG D 417 " --> pdb=" O GLU D 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 320 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.961A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 329 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 3.610A 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 320 Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.960A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 329 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 3.610A 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 320 Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.961A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 329 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 3.610A 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 320 Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.960A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 329 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 752 hydrogen bonds defined for protein. 2184 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: 2.49 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1992 1.31 - 1.43: 3463 1.43 - 1.56: 8473 1.56 - 1.68: 16 1.68 - 1.80: 48 Bond restraints: 13992 Sorted by residual: bond pdb=" C10 PGW D 515 " pdb=" C9 PGW D 515 " ideal model delta sigma weight residual 1.333 1.529 -0.196 2.00e-02 2.50e+03 9.63e+01 bond pdb=" C10 PGW A 514 " pdb=" C9 PGW A 514 " ideal model delta sigma weight residual 1.333 1.529 -0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C10 PGW B 514 " pdb=" C9 PGW B 514 " ideal model delta sigma weight residual 1.333 1.529 -0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C10 PGW C 514 " pdb=" C9 PGW C 514 " ideal model delta sigma weight residual 1.333 1.528 -0.195 2.00e-02 2.50e+03 9.54e+01 bond pdb=" C10 PGW B 509 " pdb=" C9 PGW B 509 " ideal model delta sigma weight residual 1.333 1.528 -0.195 2.00e-02 2.50e+03 9.52e+01 ... (remaining 13987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 18281 3.92 - 7.84: 399 7.84 - 11.76: 40 11.76 - 15.68: 4 15.68 - 19.59: 36 Bond angle restraints: 18760 Sorted by residual: angle pdb=" C06 PGW D 511 " pdb=" C10 PGW D 511 " pdb=" C9 PGW D 511 " ideal model delta sigma weight residual 126.92 107.33 19.59 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C06 PGW A 510 " pdb=" C10 PGW A 510 " pdb=" C9 PGW A 510 " ideal model delta sigma weight residual 126.92 107.33 19.59 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C06 PGW B 510 " pdb=" C10 PGW B 510 " pdb=" C9 PGW B 510 " ideal model delta sigma weight residual 126.92 107.33 19.59 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C06 PGW C 510 " pdb=" C10 PGW C 510 " pdb=" C9 PGW C 510 " ideal model delta sigma weight residual 126.92 107.37 19.55 3.00e+00 1.11e-01 4.25e+01 angle pdb=" C06 PGW D 504 " pdb=" C10 PGW D 504 " pdb=" C9 PGW D 504 " ideal model delta sigma weight residual 126.92 108.41 18.51 3.00e+00 1.11e-01 3.81e+01 ... (remaining 18755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.35: 8180 31.35 - 62.69: 324 62.69 - 94.04: 32 94.04 - 125.38: 16 125.38 - 156.73: 4 Dihedral angle restraints: 8556 sinusoidal: 3840 harmonic: 4716 Sorted by residual: dihedral pdb=" C5' CMP B 501 " pdb=" O5' CMP B 501 " pdb=" P CMP B 501 " pdb=" O1P CMP B 501 " ideal model delta sinusoidal sigma weight residual 60.00 168.92 -108.92 1 2.00e+01 2.50e-03 3.18e+01 dihedral pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual 60.00 168.89 -108.89 1 2.00e+01 2.50e-03 3.18e+01 dihedral pdb=" C5' CMP D 502 " pdb=" O5' CMP D 502 " pdb=" P CMP D 502 " pdb=" O1P CMP D 502 " ideal model delta sinusoidal sigma weight residual 60.00 168.86 -108.86 1 2.00e+01 2.50e-03 3.18e+01 ... (remaining 8553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1408 0.041 - 0.081: 519 0.081 - 0.122: 205 0.122 - 0.162: 12 0.162 - 0.203: 4 Chirality restraints: 2148 Sorted by residual: chirality pdb=" C02 PGW C 502 " pdb=" C01 PGW C 502 " pdb=" C03 PGW C 502 " pdb=" O01 PGW C 502 " both_signs ideal model delta sigma weight residual False 2.36 2.56 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C02 PGW D 503 " pdb=" C01 PGW D 503 " pdb=" C03 PGW D 503 " pdb=" O01 PGW D 503 " both_signs ideal model delta sigma weight residual False 2.36 2.56 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C02 PGW B 502 " pdb=" C01 PGW B 502 " pdb=" C03 PGW B 502 " pdb=" O01 PGW B 502 " both_signs ideal model delta sigma weight residual False 2.36 2.56 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2145 not shown) Planarity restraints: 2248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 503 " 0.109 2.00e-02 2.50e+03 3.57e-01 1.27e+03 pdb=" C10 PGW A 503 " 0.136 2.00e-02 2.50e+03 pdb=" C8 PGW A 503 " 0.351 2.00e-02 2.50e+03 pdb=" C9 PGW A 503 " -0.596 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 503 " 0.109 2.00e-02 2.50e+03 3.57e-01 1.27e+03 pdb=" C10 PGW B 503 " 0.136 2.00e-02 2.50e+03 pdb=" C8 PGW B 503 " 0.351 2.00e-02 2.50e+03 pdb=" C9 PGW B 503 " -0.596 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 504 " -0.112 2.00e-02 2.50e+03 3.57e-01 1.27e+03 pdb=" C10 PGW D 504 " -0.132 2.00e-02 2.50e+03 pdb=" C8 PGW D 504 " -0.352 2.00e-02 2.50e+03 pdb=" C9 PGW D 504 " 0.596 2.00e-02 2.50e+03 ... (remaining 2245 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2010 2.76 - 3.29: 12733 3.29 - 3.83: 21149 3.83 - 4.36: 26144 4.36 - 4.90: 44892 Nonbonded interactions: 106928 Sorted by model distance: nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR A 180 " pdb=" OH TYR D 186 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR C 186 " pdb=" OG1 THR D 180 " model vdw 2.249 3.040 nonbonded pdb=" NH2 ARG B 238 " pdb=" OE2 GLU C 278 " model vdw 2.267 3.120 ... (remaining 106923 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 418 or (resid 503 and (name C06 or name C07 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or \ (resid 505 and (name C20 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27)) or (resid 506 and (name C15 or name C22 or name C \ 23 or name C24 or name C25 or name C26 or name C27)) or (resid 507 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27)) or resid 509 thro \ ugh 510 or (resid 512 and (name C15 or name C16 or name C17 or name C18 or name \ C25 or name C26 or name C27)) or (resid 513 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'B' and (resid 10 through 418 or (resid 503 and (name C06 or name C07 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or \ (resid 505 and (name C20 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27)) or (resid 506 and (name C15 or name C22 or name C \ 23 or name C24 or name C25 or name C26 or name C27)) or (resid 507 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27)) or resid 509 thro \ ugh 510 or (resid 512 and (name C15 or name C16 or name C17 or name C18 or name \ C25 or name C26 or name C27)) or (resid 513 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'C' and (resid 10 through 418 or (resid 503 and (name C06 or name C07 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or \ (resid 505 and (name C20 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27)) or (resid 506 and (name C15 or name C22 or name C \ 23 or name C24 or name C25 or name C26 or name C27)) or (resid 507 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27)) or resid 509 thro \ ugh 510 or (resid 512 and (name C15 or name C16 or name C17 or name C18 or name \ C25 or name C26 or name C27)) or (resid 513 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'D' and (resid 10 through 418 or (resid 503 and (name C06 or name C07 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or \ (resid 505 and (name C20 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27)) or (resid 506 and (name C15 or name C22 or name C \ 23 or name C24 or name C25 or name C26 or name C27)) or (resid 507 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27)) or resid 509 thro \ ugh 510 or (resid 512 and (name C15 or name C16 or name C17 or name C18 or name \ C25 or name C26 or name C27)) or resid 513)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.390 Find NCS groups from input model: 0.480 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: 0.010 Load rotamer database and sin/cos tables:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.009 0.196 13992 Z= 0.449 Angle : 1.427 19.594 18762 Z= 0.569 Chirality : 0.047 0.203 2148 Planarity : 0.017 0.357 2248 Dihedral : 17.307 156.726 5504 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.58 % Allowed : 0.07 % Favored : 99.35 % 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: -0.72 (0.22), residues: 1588 helix: 0.10 (0.17), residues: 1004 sheet: -0.50 (0.56), residues: 88 loop : -1.48 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 111 TYR 0.008 0.001 TYR C 170 PHE 0.018 0.002 PHE C 64 TRP 0.017 0.002 TRP B 264 HIS 0.002 0.001 HIS C 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00936 / 0.45 (13992) covalent geometry : angle 1.42751 / 0.57 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.13843 / 8.94 ( 752) hydrogen bonds : angle 5.63293 / 4.19 ( 2184) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 0.487 Fit side-chains REVERT: A 330 ARG cc_start: 0.7096 (mtt90) cc_final: 0.6620 (mtm-85) REVERT: B 330 ARG cc_start: 0.7097 (mtt90) cc_final: 0.6589 (mtm-85) REVERT: C 330 ARG cc_start: 0.7058 (mtt90) cc_final: 0.6605 (mtm-85) REVERT: D 327 TYR cc_start: 0.7900 (m-10) cc_final: 0.7134 (m-80) REVERT: D 330 ARG cc_start: 0.7055 (mtt90) cc_final: 0.6631 (mtm-85) REVERT: D 403 ARG cc_start: 0.7457 (mtt180) cc_final: 0.7056 (mtt180) outliers start: 8 outliers final: 2 residues processed: 184 average time/residue: 0.5231 time to fit residues: 105.1193 Evaluate side-chains 147 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 276 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.183480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.146963 restraints weight = 14811.083| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.83 r_work: 0.3110 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13992 Z= 0.137 Angle : 0.686 8.554 18762 Z= 0.321 Chirality : 0.042 0.134 2148 Planarity : 0.006 0.085 2248 Dihedral : 14.990 153.132 2468 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.78 % Allowed : 11.26 % Favored : 84.96 % 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: -0.06 (0.22), residues: 1588 helix: 0.63 (0.18), residues: 1016 sheet: -0.31 (0.58), residues: 88 loop : -1.31 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 111 TYR 0.006 0.001 TYR D 170 PHE 0.012 0.001 PHE C 64 TRP 0.008 0.001 TRP B 264 HIS 0.003 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (13992) covalent geometry : angle 0.68614 / 0.32 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.04288 / 2.75 ( 752) hydrogen bonds : angle 4.48576 / 3.36 ( 2184) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 140 time to evaluate : 0.359 Fit side-chains REVERT: A 156 MET cc_start: 0.8734 (ttp) cc_final: 0.8524 (ttm) REVERT: A 273 ARG cc_start: 0.8078 (ptt90) cc_final: 0.6836 (ptp90) REVERT: A 330 ARG cc_start: 0.7111 (mtt90) cc_final: 0.6785 (ttm-80) REVERT: A 337 ASP cc_start: 0.8494 (m-30) cc_final: 0.8221 (m-30) REVERT: B 203 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8130 (mp) REVERT: B 273 ARG cc_start: 0.8084 (ptt90) cc_final: 0.6886 (ptp90) REVERT: B 330 ARG cc_start: 0.7114 (mtt90) cc_final: 0.6814 (ttm-80) REVERT: B 337 ASP cc_start: 0.8506 (m-30) cc_final: 0.8222 (m-30) REVERT: C 156 MET cc_start: 0.8739 (ttp) cc_final: 0.8535 (ttm) REVERT: C 273 ARG cc_start: 0.8082 (ptt90) cc_final: 0.6886 (ptp90) REVERT: C 337 ASP cc_start: 0.8502 (m-30) cc_final: 0.8218 (m-30) REVERT: D 273 ARG cc_start: 0.8036 (ptt90) cc_final: 0.6783 (ptp90) REVERT: D 391 ARG cc_start: 0.8644 (ptm-80) cc_final: 0.8109 (ptm-80) outliers start: 52 outliers final: 7 residues processed: 165 average time/residue: 0.5343 time to fit residues: 96.2929 Evaluate side-chains 137 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 244 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 chunk 144 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 45 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.184208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.146970 restraints weight = 14862.765| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.74 r_work: 0.3116 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13992 Z= 0.127 Angle : 0.629 8.169 18762 Z= 0.296 Chirality : 0.041 0.131 2148 Planarity : 0.005 0.066 2248 Dihedral : 13.253 132.424 2464 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 4.65 % Allowed : 12.14 % Favored : 83.21 % 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: 0.73 (0.23), residues: 1588 helix: 1.20 (0.18), residues: 976 sheet: -0.10 (0.58), residues: 88 loop : -0.67 (0.30), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 391 TYR 0.007 0.001 TYR D 175 PHE 0.008 0.001 PHE D 64 TRP 0.006 0.001 TRP C 264 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (13992) covalent geometry : angle 0.62863 / 0.30 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03885 / 2.50 ( 752) hydrogen bonds : angle 4.18793 / 3.16 ( 2184) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 159 time to evaluate : 0.365 Fit side-chains REVERT: A 156 MET cc_start: 0.8661 (ttp) cc_final: 0.8460 (ttm) REVERT: A 203 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8274 (mp) REVERT: A 273 ARG cc_start: 0.8078 (ptt90) cc_final: 0.6845 (mtm-85) REVERT: A 330 ARG cc_start: 0.7070 (mtt90) cc_final: 0.6684 (mtm-85) REVERT: B 203 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8189 (mp) REVERT: B 273 ARG cc_start: 0.8054 (ptt90) cc_final: 0.6791 (mtm-85) REVERT: B 330 ARG cc_start: 0.7087 (mtt90) cc_final: 0.6687 (mtm-85) REVERT: C 156 MET cc_start: 0.8657 (ttp) cc_final: 0.8456 (ttm) REVERT: C 203 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8268 (mp) REVERT: C 273 ARG cc_start: 0.8029 (ptt90) cc_final: 0.6762 (mtm-85) REVERT: C 330 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6871 (mtm-85) REVERT: C 333 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7115 (mm-30) REVERT: D 203 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8266 (mp) REVERT: D 273 ARG cc_start: 0.8054 (ptt90) cc_final: 0.6798 (mtm-85) REVERT: D 330 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6845 (mtm-85) REVERT: D 333 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7070 (mm-30) outliers start: 64 outliers final: 15 residues processed: 199 average time/residue: 0.4995 time to fit residues: 109.4837 Evaluate side-chains 156 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 133 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 0.3980 chunk 123 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.178855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.140951 restraints weight = 14976.440| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.88 r_work: 0.3105 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13992 Z= 0.126 Angle : 0.635 8.076 18762 Z= 0.295 Chirality : 0.042 0.160 2148 Planarity : 0.005 0.055 2248 Dihedral : 12.789 135.131 2464 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.29 % Allowed : 14.53 % Favored : 81.18 % 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: 0.92 (0.23), residues: 1588 helix: 1.35 (0.18), residues: 972 sheet: 0.20 (0.60), residues: 88 loop : -0.61 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 374 TYR 0.007 0.001 TYR C 170 PHE 0.007 0.001 PHE D 40 TRP 0.004 0.001 TRP C 264 HIS 0.002 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (13992) covalent geometry : angle 0.63473 / 0.30 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03795 / 2.44 ( 752) hydrogen bonds : angle 4.10747 / 3.11 ( 2184) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 138 time to evaluate : 0.425 Fit side-chains REVERT: A 156 MET cc_start: 0.8648 (ttp) cc_final: 0.8435 (ttm) REVERT: A 203 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8201 (mp) REVERT: A 273 ARG cc_start: 0.7984 (ptt90) cc_final: 0.6719 (mtm-85) REVERT: A 330 ARG cc_start: 0.6984 (mtt90) cc_final: 0.6465 (mtm-85) REVERT: A 369 MET cc_start: 0.7446 (ppp) cc_final: 0.7039 (mtp) REVERT: B 203 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8153 (mp) REVERT: B 273 ARG cc_start: 0.7962 (ptt90) cc_final: 0.6733 (mtm-85) REVERT: B 330 ARG cc_start: 0.6996 (mtt90) cc_final: 0.6630 (mtm-85) REVERT: C 156 MET cc_start: 0.8637 (ttp) cc_final: 0.8427 (ttm) REVERT: C 203 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8197 (mp) REVERT: C 273 ARG cc_start: 0.7925 (ptt90) cc_final: 0.6691 (mtm-85) REVERT: C 330 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6773 (mtm-85) REVERT: C 333 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7126 (mm-30) REVERT: D 203 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8199 (mp) REVERT: D 273 ARG cc_start: 0.7967 (ptt90) cc_final: 0.6687 (mtm-85) REVERT: D 330 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6764 (mtm-85) REVERT: D 333 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7106 (mm-30) outliers start: 59 outliers final: 16 residues processed: 178 average time/residue: 0.5411 time to fit residues: 105.8109 Evaluate side-chains 159 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 83 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.179671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.140581 restraints weight = 14977.247| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.69 r_work: 0.3290 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13992 Z= 0.124 Angle : 0.617 7.815 18762 Z= 0.289 Chirality : 0.042 0.132 2148 Planarity : 0.005 0.056 2248 Dihedral : 12.261 133.706 2464 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.63 % Allowed : 15.19 % Favored : 81.18 % 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: 1.03 (0.23), residues: 1588 helix: 1.44 (0.18), residues: 972 sheet: 0.37 (0.61), residues: 88 loop : -0.62 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 235 TYR 0.007 0.001 TYR C 170 PHE 0.006 0.001 PHE D 40 TRP 0.005 0.001 TRP C 264 HIS 0.002 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (13992) covalent geometry : angle 0.61734 / 0.29 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03723 / 2.39 ( 752) hydrogen bonds : angle 4.00329 / 3.04 ( 2184) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 0.457 Fit side-chains REVERT: A 44 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5717 (mm) REVERT: A 77 LEU cc_start: 0.2342 (OUTLIER) cc_final: 0.2007 (tt) REVERT: A 203 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8196 (mp) REVERT: A 273 ARG cc_start: 0.8086 (ptt90) cc_final: 0.7045 (mtm-85) REVERT: A 327 TYR cc_start: 0.8490 (m-10) cc_final: 0.7795 (m-80) REVERT: A 330 ARG cc_start: 0.7119 (mtt90) cc_final: 0.6879 (ttm-80) REVERT: B 44 LEU cc_start: 0.6092 (OUTLIER) cc_final: 0.5723 (mm) REVERT: B 77 LEU cc_start: 0.2338 (OUTLIER) cc_final: 0.2020 (tt) REVERT: B 203 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8161 (mp) REVERT: B 273 ARG cc_start: 0.8087 (ptt90) cc_final: 0.7049 (mtm-85) REVERT: B 330 ARG cc_start: 0.7066 (mtt90) cc_final: 0.6561 (mtm-85) REVERT: C 44 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5702 (mm) REVERT: C 77 LEU cc_start: 0.2357 (OUTLIER) cc_final: 0.2025 (tt) REVERT: C 203 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8197 (mp) REVERT: C 273 ARG cc_start: 0.8103 (ptt90) cc_final: 0.7062 (mtm-85) REVERT: C 327 TYR cc_start: 0.8492 (m-10) cc_final: 0.7786 (m-80) REVERT: C 330 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6811 (ttm-80) REVERT: C 333 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: D 44 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5728 (mm) REVERT: D 77 LEU cc_start: 0.2330 (OUTLIER) cc_final: 0.2002 (tt) REVERT: D 203 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8194 (mp) REVERT: D 273 ARG cc_start: 0.8085 (ptt90) cc_final: 0.7032 (mtm-85) REVERT: D 327 TYR cc_start: 0.8490 (m-10) cc_final: 0.7840 (m-80) REVERT: D 330 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6808 (ttm-80) REVERT: D 333 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7133 (mm-30) outliers start: 50 outliers final: 11 residues processed: 174 average time/residue: 0.5221 time to fit residues: 99.9460 Evaluate side-chains 156 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 30 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.181302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.143697 restraints weight = 14781.059| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.95 r_work: 0.3085 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13992 Z= 0.139 Angle : 0.627 7.952 18762 Z= 0.295 Chirality : 0.042 0.131 2148 Planarity : 0.005 0.057 2248 Dihedral : 12.193 133.754 2464 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.49 % Allowed : 17.15 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.23), residues: 1588 helix: 1.47 (0.18), residues: 964 sheet: 0.41 (0.61), residues: 88 loop : -0.75 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 235 TYR 0.008 0.001 TYR C 170 PHE 0.005 0.001 PHE A 366 TRP 0.005 0.001 TRP C 176 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (13992) covalent geometry : angle 0.62692 / 0.30 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03954 / 2.54 ( 752) hydrogen bonds : angle 3.99896 / 3.03 ( 2184) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 0.488 Fit side-chains REVERT: A 44 LEU cc_start: 0.6225 (OUTLIER) cc_final: 0.5971 (mm) REVERT: A 77 LEU cc_start: 0.2203 (OUTLIER) cc_final: 0.1916 (tt) REVERT: A 203 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8195 (mp) REVERT: A 273 ARG cc_start: 0.7992 (ptt90) cc_final: 0.6743 (mtm-85) REVERT: A 327 TYR cc_start: 0.8550 (m-10) cc_final: 0.7935 (m-80) REVERT: A 330 ARG cc_start: 0.7043 (mtt90) cc_final: 0.6574 (ttm-80) REVERT: B 44 LEU cc_start: 0.6225 (OUTLIER) cc_final: 0.5968 (mm) REVERT: B 77 LEU cc_start: 0.2198 (OUTLIER) cc_final: 0.1917 (tt) REVERT: B 203 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8159 (mp) REVERT: B 273 ARG cc_start: 0.7994 (ptt90) cc_final: 0.6750 (mtm-85) REVERT: B 327 TYR cc_start: 0.8563 (m-10) cc_final: 0.7883 (m-80) REVERT: B 330 ARG cc_start: 0.7021 (mtt90) cc_final: 0.6736 (ttm-80) REVERT: C 44 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5971 (mm) REVERT: C 77 LEU cc_start: 0.2206 (OUTLIER) cc_final: 0.1921 (tt) REVERT: C 203 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8194 (mp) REVERT: C 273 ARG cc_start: 0.7983 (ptt90) cc_final: 0.6730 (mtm-85) REVERT: C 327 TYR cc_start: 0.8552 (m-10) cc_final: 0.7919 (m-80) REVERT: C 330 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6523 (ttm-80) REVERT: C 333 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6595 (mp0) REVERT: D 44 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5973 (mm) REVERT: D 77 LEU cc_start: 0.2069 (OUTLIER) cc_final: 0.1784 (tt) REVERT: D 203 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8195 (mp) REVERT: D 273 ARG cc_start: 0.8003 (ptt90) cc_final: 0.6750 (mtm-85) REVERT: D 327 TYR cc_start: 0.8558 (m-10) cc_final: 0.7921 (m-80) REVERT: D 330 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6739 (ttm-80) REVERT: D 333 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6921 (mm-30) outliers start: 48 outliers final: 12 residues processed: 168 average time/residue: 0.5465 time to fit residues: 100.9424 Evaluate side-chains 154 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 5 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.178007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.140150 restraints weight = 14918.058| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.33 r_work: 0.3021 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13992 Z= 0.213 Angle : 0.704 8.902 18762 Z= 0.334 Chirality : 0.046 0.137 2148 Planarity : 0.005 0.059 2248 Dihedral : 13.215 132.498 2464 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.80 % Allowed : 16.50 % Favored : 78.71 % 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: 0.65 (0.22), residues: 1588 helix: 1.23 (0.18), residues: 960 sheet: 0.17 (0.59), residues: 88 loop : -0.91 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 235 TYR 0.011 0.002 TYR B 170 PHE 0.008 0.001 PHE D 260 TRP 0.007 0.002 TRP A 264 HIS 0.003 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.21 (13992) covalent geometry : angle 0.70415 / 0.33 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.04889 / 3.14 ( 752) hydrogen bonds : angle 4.17342 / 3.15 ( 2184) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 136 time to evaluate : 0.530 Fit side-chains REVERT: A 77 LEU cc_start: 0.2016 (OUTLIER) cc_final: 0.1762 (tt) REVERT: A 273 ARG cc_start: 0.7895 (ptt90) cc_final: 0.6786 (mtm-85) REVERT: A 330 ARG cc_start: 0.7136 (mtt90) cc_final: 0.6419 (ttm-80) REVERT: A 389 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8363 (pp) REVERT: B 77 LEU cc_start: 0.2018 (OUTLIER) cc_final: 0.1770 (tt) REVERT: B 273 ARG cc_start: 0.7892 (ptt90) cc_final: 0.6793 (mtm-85) REVERT: B 277 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8250 (ttpt) REVERT: B 318 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7949 (tp30) REVERT: B 327 TYR cc_start: 0.8595 (m-10) cc_final: 0.8048 (m-80) REVERT: B 330 ARG cc_start: 0.7115 (mtt90) cc_final: 0.6772 (mtm-85) REVERT: C 77 LEU cc_start: 0.2022 (OUTLIER) cc_final: 0.1771 (tt) REVERT: C 273 ARG cc_start: 0.7889 (ptt90) cc_final: 0.6785 (mtm-85) REVERT: C 277 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8261 (ttpt) REVERT: C 318 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7917 (tp30) REVERT: C 330 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6441 (ttm-80) REVERT: C 333 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6633 (mp0) REVERT: C 389 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8375 (pp) REVERT: D 77 LEU cc_start: 0.1972 (OUTLIER) cc_final: 0.1723 (tt) REVERT: D 273 ARG cc_start: 0.7889 (ptt90) cc_final: 0.6782 (mtm-85) REVERT: D 318 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7943 (tp30) REVERT: D 330 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6404 (ttm-80) REVERT: D 333 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6498 (mp0) REVERT: D 389 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8366 (pp) outliers start: 66 outliers final: 24 residues processed: 183 average time/residue: 0.5254 time to fit residues: 105.8991 Evaluate side-chains 170 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 34 optimal weight: 0.0470 chunk 124 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 56 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8280 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.183959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.146979 restraints weight = 14749.738| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.94 r_work: 0.3090 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13992 Z= 0.131 Angle : 0.619 8.173 18762 Z= 0.293 Chirality : 0.041 0.130 2148 Planarity : 0.005 0.058 2248 Dihedral : 12.323 133.630 2464 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.56 % Allowed : 18.53 % Favored : 77.91 % 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: 1588 helix: 1.41 (0.18), residues: 980 sheet: 0.30 (0.60), residues: 88 loop : -0.68 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 81 TYR 0.006 0.001 TYR D 175 PHE 0.007 0.001 PHE D 40 TRP 0.007 0.001 TRP C 264 HIS 0.003 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (13992) covalent geometry : angle 0.61938 / 0.29 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03946 / 2.54 ( 752) hydrogen bonds : angle 4.04505 / 3.06 ( 2184) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 0.458 Fit side-chains REVERT: A 44 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5634 (mm) REVERT: A 77 LEU cc_start: 0.1998 (OUTLIER) cc_final: 0.1740 (tt) REVERT: A 203 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8211 (mp) REVERT: A 273 ARG cc_start: 0.7993 (ptt90) cc_final: 0.6822 (mtm-85) REVERT: A 277 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8273 (ttpt) REVERT: A 327 TYR cc_start: 0.8562 (m-10) cc_final: 0.8022 (m-80) REVERT: A 330 ARG cc_start: 0.7088 (mtt90) cc_final: 0.6831 (mtm-85) REVERT: A 333 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: B 44 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5645 (mm) REVERT: B 77 LEU cc_start: 0.2018 (OUTLIER) cc_final: 0.1760 (tt) REVERT: B 203 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8178 (mp) REVERT: B 273 ARG cc_start: 0.7974 (ptt90) cc_final: 0.6746 (mtm-85) REVERT: B 327 TYR cc_start: 0.8597 (m-10) cc_final: 0.7981 (m-80) REVERT: B 330 ARG cc_start: 0.7048 (mtt90) cc_final: 0.6700 (mtm-85) REVERT: C 44 LEU cc_start: 0.5995 (OUTLIER) cc_final: 0.5648 (mm) REVERT: C 77 LEU cc_start: 0.2025 (OUTLIER) cc_final: 0.1761 (tt) REVERT: C 203 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8208 (mp) REVERT: C 273 ARG cc_start: 0.7981 (ptt90) cc_final: 0.6758 (mtm-85) REVERT: C 330 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6458 (ttm-80) REVERT: C 333 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: D 44 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.5648 (mm) REVERT: D 77 LEU cc_start: 0.1975 (OUTLIER) cc_final: 0.1714 (tt) REVERT: D 203 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8211 (mp) REVERT: D 273 ARG cc_start: 0.8001 (ptt90) cc_final: 0.6771 (mtm-85) REVERT: D 330 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6415 (ttm-80) REVERT: D 333 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6653 (mp0) outliers start: 49 outliers final: 12 residues processed: 165 average time/residue: 0.5073 time to fit residues: 92.1561 Evaluate side-chains 162 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 134 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 151 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 60 optimal weight: 0.0370 overall best weight: 0.7860 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.185029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.148006 restraints weight = 14782.566| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.91 r_work: 0.3098 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13992 Z= 0.127 Angle : 0.633 12.005 18762 Z= 0.292 Chirality : 0.042 0.130 2148 Planarity : 0.005 0.057 2248 Dihedral : 11.937 133.447 2464 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.12 % Allowed : 19.69 % Favored : 77.18 % 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: 1.11 (0.23), residues: 1588 helix: 1.55 (0.18), residues: 980 sheet: 0.40 (0.61), residues: 88 loop : -0.72 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 391 TYR 0.007 0.001 TYR C 170 PHE 0.007 0.001 PHE B 366 TRP 0.006 0.001 TRP A 264 HIS 0.002 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (13992) covalent geometry : angle 0.63273 / 0.29 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03836 / 2.47 ( 752) hydrogen bonds : angle 3.97507 / 3.01 ( 2184) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.494 Fit side-chains REVERT: A 44 LEU cc_start: 0.6213 (OUTLIER) cc_final: 0.5965 (mm) REVERT: A 77 LEU cc_start: 0.1968 (OUTLIER) cc_final: 0.1717 (tt) REVERT: A 203 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8226 (mp) REVERT: A 273 ARG cc_start: 0.7959 (ptt90) cc_final: 0.6751 (mtm-85) REVERT: A 330 ARG cc_start: 0.7060 (mtt90) cc_final: 0.6615 (ttm-80) REVERT: A 333 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7182 (mm-30) REVERT: B 44 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5963 (mm) REVERT: B 77 LEU cc_start: 0.2076 (OUTLIER) cc_final: 0.1859 (tt) REVERT: B 203 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8205 (mp) REVERT: B 273 ARG cc_start: 0.7941 (ptt90) cc_final: 0.6726 (mtm-85) REVERT: B 327 TYR cc_start: 0.8578 (m-10) cc_final: 0.7974 (m-80) REVERT: B 330 ARG cc_start: 0.7031 (mtt90) cc_final: 0.6696 (mtm-85) REVERT: C 44 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5971 (mm) REVERT: C 77 LEU cc_start: 0.2087 (OUTLIER) cc_final: 0.1863 (tt) REVERT: C 203 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8223 (mp) REVERT: C 273 ARG cc_start: 0.7960 (ptt90) cc_final: 0.6744 (mtm-85) REVERT: C 330 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6698 (ttm-80) REVERT: C 333 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7256 (mm-30) REVERT: D 44 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5958 (mm) REVERT: D 77 LEU cc_start: 0.1964 (OUTLIER) cc_final: 0.1726 (tt) REVERT: D 203 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8228 (mp) REVERT: D 273 ARG cc_start: 0.7958 (ptt90) cc_final: 0.6745 (mtm-85) REVERT: D 330 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6474 (ttm-80) REVERT: D 333 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6676 (mp0) outliers start: 43 outliers final: 11 residues processed: 163 average time/residue: 0.5372 time to fit residues: 96.0330 Evaluate side-chains 158 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 75 optimal weight: 0.0040 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.182698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.145022 restraints weight = 14773.100| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.96 r_work: 0.3103 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13992 Z= 0.124 Angle : 0.629 11.605 18762 Z= 0.291 Chirality : 0.042 0.128 2148 Planarity : 0.004 0.058 2248 Dihedral : 11.679 133.445 2464 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.62 % Allowed : 20.28 % Favored : 77.11 % 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: 1.19 (0.23), residues: 1588 helix: 1.62 (0.18), residues: 980 sheet: 0.47 (0.61), residues: 88 loop : -0.71 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 391 TYR 0.007 0.001 TYR A 170 PHE 0.008 0.001 PHE D 40 TRP 0.005 0.001 TRP C 264 HIS 0.002 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (13992) covalent geometry : angle 0.62863 / 0.29 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03782 / 2.44 ( 752) hydrogen bonds : angle 3.94924 / 2.99 ( 2184) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.492 Fit side-chains REVERT: A 44 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.6000 (mm) REVERT: A 77 LEU cc_start: 0.2052 (OUTLIER) cc_final: 0.1832 (tt) REVERT: A 203 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8220 (mp) REVERT: A 273 ARG cc_start: 0.7885 (ptt90) cc_final: 0.6673 (mtm-85) REVERT: A 277 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8224 (ttpt) REVERT: A 330 ARG cc_start: 0.7010 (mtt90) cc_final: 0.6562 (ttm-80) REVERT: A 333 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6967 (mm-30) REVERT: B 44 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5999 (mm) REVERT: B 203 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8181 (mp) REVERT: B 273 ARG cc_start: 0.7890 (ptt90) cc_final: 0.6658 (mtm-85) REVERT: B 330 ARG cc_start: 0.7002 (mtt90) cc_final: 0.6458 (ttm-80) REVERT: C 44 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.6039 (mm) REVERT: C 203 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8215 (mp) REVERT: C 273 ARG cc_start: 0.7897 (ptt90) cc_final: 0.6664 (mtm-85) REVERT: C 330 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6422 (ttm-80) REVERT: C 333 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: D 44 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.6003 (mm) REVERT: D 203 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8217 (mp) REVERT: D 273 ARG cc_start: 0.7910 (ptt90) cc_final: 0.6678 (mtm-85) REVERT: D 330 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6438 (ttm-80) REVERT: D 333 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6634 (mp0) outliers start: 36 outliers final: 10 residues processed: 154 average time/residue: 0.5791 time to fit residues: 97.5769 Evaluate side-chains 159 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 114 optimal weight: 0.0060 chunk 111 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.187484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.150402 restraints weight = 14575.814| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.84 r_work: 0.3117 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13992 Z= 0.125 Angle : 0.642 11.369 18762 Z= 0.292 Chirality : 0.041 0.129 2148 Planarity : 0.004 0.057 2248 Dihedral : 11.496 133.206 2464 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.25 % Allowed : 20.35 % Favored : 77.40 % 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: 1.24 (0.23), residues: 1588 helix: 1.64 (0.18), residues: 984 sheet: 0.44 (0.61), residues: 88 loop : -0.66 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 391 TYR 0.007 0.001 TYR D 170 PHE 0.008 0.001 PHE B 366 TRP 0.005 0.001 TRP C 264 HIS 0.002 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (13992) covalent geometry : angle 0.64180 / 0.29 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03762 / 2.42 ( 752) hydrogen bonds : angle 3.92767 / 2.98 ( 2184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4373.43 seconds wall clock time: 75 minutes 14.93 seconds (4514.93 seconds total)