Starting phenix.real_space_refine on Sat Sep 12 05:29:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rsh_24670/09_2026/7rsh_24670.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rsh_24670/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7rsh_24670/09_2026/7rsh_24670.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rsh_24670/09_2026/7rsh_24670.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rsh_24670/09_2026/7rsh_24670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rsh_24670/09_2026/7rsh_24670.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rsh_24670/09_2026/7rsh_24670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rsh_24670/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 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: 3.85, per 1000 atoms: 0.28 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: 1.14 Conformation dependent library (CDL) restraints added in 572.2 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: 0.43 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: 2.17 Time building geometry restraints manager: 1.53 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: 18265 3.92 - 7.84: 407 7.84 - 11.76: 48 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 - 24.23: 7889 24.23 - 48.46: 547 48.46 - 72.68: 88 72.68 - 96.91: 16 96.91 - 121.14: 16 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 - 0.053: 1641 0.053 - 0.106: 414 0.106 - 0.158: 85 0.158 - 0.211: 4 0.211 - 0.264: 4 Chirality restraints: 2148 Sorted by residual: chirality pdb=" C2' CMP D 502 " pdb=" C1' CMP D 502 " pdb=" C3' CMP D 502 " pdb=" O2' CMP D 502 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C2' CMP A 501 " pdb=" C1' CMP A 501 " pdb=" C3' CMP A 501 " pdb=" O2' CMP A 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C2' CMP B 501 " pdb=" C1' CMP B 501 " pdb=" C3' CMP B 501 " pdb=" O2' CMP B 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.73e+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: 1.110 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.830 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.010 ------------------------------------------------------------------------------- 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= 0.450 Angle : 1.449 19.594 18762 Z= 0.572 Chirality : 0.048 0.264 2148 Planarity : 0.017 0.357 2248 Dihedral : 16.980 121.140 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 0.00939 / 0.45 (13992) covalent geometry : angle 1.44922 / 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 : 0.411 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: 0.6403 time to fit residues: 128.5270 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 : 0.455 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.183665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.146954 restraints weight = 14797.797| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.86 r_work: 0.3108 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1092 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= 0.133 Angle : 0.717 8.670 18762 Z= 0.323 Chirality : 0.042 0.133 2148 Planarity : 0.006 0.085 2248 Dihedral : 13.218 112.193 2468 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.56 % Allowed : 11.48 % 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: -0.03 (0.22), residues: 1588 helix: 0.66 (0.18), residues: 1016 sheet: -0.33 (0.58), residues: 88 loop : -1.29 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 374 TYR 0.006 0.001 TYR D 175 PHE 0.012 0.001 PHE A 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 0.00312 / 0.13 (13992) covalent geometry : angle 0.71693 / 0.32 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.04261 / 2.74 ( 752) hydrogen bonds : angle 4.47181 / 3.35 ( 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 188 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 0.484 Fit side-chains REVERT: A 203 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8152 (mp) REVERT: A 273 ARG cc_start: 0.8077 (ptt90) cc_final: 0.6842 (ptp90) REVERT: A 330 ARG cc_start: 0.7097 (mtt90) cc_final: 0.6595 (ttm-80) REVERT: A 333 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: A 337 ASP cc_start: 0.8516 (m-30) cc_final: 0.8287 (m-30) REVERT: B 156 MET cc_start: 0.8736 (ttp) cc_final: 0.8520 (ttm) REVERT: B 203 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8153 (mp) REVERT: B 273 ARG cc_start: 0.8085 (ptt90) cc_final: 0.6891 (ptp90) REVERT: B 330 ARG cc_start: 0.7105 (mtt90) cc_final: 0.6811 (ttm-80) REVERT: B 337 ASP cc_start: 0.8524 (m-30) cc_final: 0.8293 (m-30) REVERT: C 156 MET cc_start: 0.8717 (ttp) cc_final: 0.8502 (ttm) REVERT: C 203 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8149 (mp) REVERT: C 273 ARG cc_start: 0.8108 (ptt90) cc_final: 0.6896 (ptp90) REVERT: C 337 ASP cc_start: 0.8552 (m-30) cc_final: 0.8314 (m-30) REVERT: D 203 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8137 (mp) REVERT: D 273 ARG cc_start: 0.8055 (ptt90) cc_final: 0.6786 (ptp90) REVERT: D 333 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: D 337 ASP cc_start: 0.8289 (m-30) cc_final: 0.8052 (m-30) outliers start: 49 outliers final: 6 residues processed: 164 average time/residue: 0.6339 time to fit residues: 113.5784 Evaluate side-chains 140 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 333 GLU 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: 2.9990 chunk 44 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 155 optimal weight: 0.0770 chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 62 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.184292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.147165 restraints weight = 14848.374| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.70 r_work: 0.3118 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1468 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= 0.122 Angle : 0.660 8.467 18762 Z= 0.297 Chirality : 0.041 0.146 2148 Planarity : 0.005 0.066 2248 Dihedral : 12.013 80.487 2464 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.58 % Allowed : 12.35 % Favored : 83.07 % 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: 0.74 (0.23), residues: 1588 helix: 1.21 (0.18), residues: 976 sheet: -0.03 (0.59), residues: 88 loop : -0.69 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 391 TYR 0.006 0.001 TYR B 175 PHE 0.008 0.001 PHE D 64 TRP 0.006 0.001 TRP B 264 HIS 0.002 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (13992) covalent geometry : angle 0.66008 / 0.30 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03864 / 2.49 ( 752) hydrogen bonds : angle 4.18196 / 3.15 ( 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 219 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 156 time to evaluate : 0.480 Fit side-chains REVERT: A 203 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8197 (mp) REVERT: A 273 ARG cc_start: 0.8043 (ptt90) cc_final: 0.6789 (mtm-85) REVERT: A 330 ARG cc_start: 0.7077 (mtt90) cc_final: 0.6523 (ttm-80) REVERT: A 333 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6571 (mp0) REVERT: B 156 MET cc_start: 0.8670 (ttp) cc_final: 0.8467 (ttm) REVERT: B 203 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8193 (mp) REVERT: B 273 ARG cc_start: 0.8040 (ptt90) cc_final: 0.6788 (mtm-85) REVERT: B 330 ARG cc_start: 0.7086 (mtt90) cc_final: 0.6695 (mtm-85) REVERT: C 156 MET cc_start: 0.8655 (ttp) cc_final: 0.8453 (ttm) REVERT: C 203 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8190 (mp) REVERT: C 273 ARG cc_start: 0.8009 (ptt90) cc_final: 0.6747 (mtm-85) REVERT: C 330 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6862 (mtm-85) REVERT: C 333 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7132 (mm-30) REVERT: D 203 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8188 (mp) REVERT: D 273 ARG cc_start: 0.8010 (ptt90) cc_final: 0.6772 (mtm-85) REVERT: D 330 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6856 (mtm-85) REVERT: D 333 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7140 (mm-30) outliers start: 63 outliers final: 15 residues processed: 196 average time/residue: 0.5310 time to fit residues: 114.6085 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 : 0.319 ------------------------------------------------------------------------------- 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 224 LYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 333 GLU 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 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: 0.5980 chunk 108 optimal weight: 0.6980 chunk 138 optimal weight: 0.5980 chunk 111 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 123 optimal weight: 4.9990 chunk 20 optimal weight: 0.0870 chunk 6 optimal weight: 7.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.180459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.143093 restraints weight = 14952.430| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.01 r_work: 0.3127 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13992 Z= 0.109 Angle : 0.654 8.402 18762 Z= 0.288 Chirality : 0.041 0.159 2148 Planarity : 0.005 0.056 2248 Dihedral : 10.982 58.240 2464 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.49 % Allowed : 15.26 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.23), residues: 1588 helix: 1.43 (0.18), residues: 972 sheet: 0.35 (0.62), residues: 88 loop : -0.59 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 391 TYR 0.006 0.001 TYR A 175 PHE 0.008 0.001 PHE D 40 TRP 0.004 0.001 TRP C 264 HIS 0.002 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (13992) covalent geometry : angle 0.65440 / 0.29 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03499 / 2.25 ( 752) hydrogen bonds : angle 4.04136 / 3.06 ( 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 198 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 0.432 Fit side-chains REVERT: A 44 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5484 (mm) REVERT: A 203 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 273 ARG cc_start: 0.7995 (ptt90) cc_final: 0.6767 (mtm-85) REVERT: A 330 ARG cc_start: 0.6967 (mtt90) cc_final: 0.6656 (ttm-80) REVERT: A 369 MET cc_start: 0.7418 (ppp) cc_final: 0.7064 (mpp) REVERT: B 44 LEU cc_start: 0.5954 (OUTLIER) cc_final: 0.5473 (mm) REVERT: B 203 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8262 (mp) REVERT: B 273 ARG cc_start: 0.7998 (ptt90) cc_final: 0.6764 (mtm-85) REVERT: B 330 ARG cc_start: 0.7016 (mtt90) cc_final: 0.6471 (mtm-85) REVERT: C 44 LEU cc_start: 0.5946 (OUTLIER) cc_final: 0.5476 (mm) REVERT: C 203 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8259 (mp) REVERT: C 273 ARG cc_start: 0.7951 (ptt90) cc_final: 0.6726 (mtm-85) REVERT: C 330 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6763 (mtm-85) REVERT: C 333 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7090 (mm-30) REVERT: D 44 LEU cc_start: 0.5958 (OUTLIER) cc_final: 0.5487 (mm) REVERT: D 203 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8257 (mp) REVERT: D 273 ARG cc_start: 0.8015 (ptt90) cc_final: 0.6781 (mtm-85) REVERT: D 330 ARG cc_start: 0.7003 (mtt90) cc_final: 0.6743 (mtm-85) outliers start: 48 outliers final: 11 residues processed: 178 average time/residue: 0.5842 time to fit residues: 113.9431 Evaluate side-chains 164 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 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 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 203 ILE 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 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 346 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 83 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.180369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.142577 restraints weight = 14961.782| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.94 r_work: 0.3082 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13992 Z= 0.150 Angle : 0.671 8.689 18762 Z= 0.303 Chirality : 0.043 0.152 2148 Planarity : 0.005 0.057 2248 Dihedral : 11.272 57.605 2464 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.07 % Allowed : 14.90 % Favored : 81.03 % 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: 0.97 (0.23), residues: 1588 helix: 1.38 (0.18), residues: 972 sheet: 0.29 (0.61), residues: 88 loop : -0.61 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 235 TYR 0.009 0.001 TYR D 170 PHE 0.006 0.001 PHE C 260 TRP 0.007 0.002 TRP B 176 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.15 (13992) covalent geometry : angle 0.67065 / 0.30 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.04124 / 2.65 ( 752) hydrogen bonds : angle 4.04516 / 3.06 ( 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 193 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 0.537 Fit side-chains REVERT: A 44 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5546 (mm) REVERT: A 77 LEU cc_start: 0.2201 (OUTLIER) cc_final: 0.1910 (tt) REVERT: A 273 ARG cc_start: 0.7982 (ptt90) cc_final: 0.6718 (mtm-85) REVERT: A 327 TYR cc_start: 0.8568 (m-10) cc_final: 0.7888 (m-80) REVERT: A 330 ARG cc_start: 0.6977 (mtt90) cc_final: 0.6279 (ttm-80) REVERT: A 333 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6777 (mp0) REVERT: B 44 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5560 (mm) REVERT: B 77 LEU cc_start: 0.2211 (OUTLIER) cc_final: 0.1917 (tt) REVERT: B 273 ARG cc_start: 0.7963 (ptt90) cc_final: 0.6701 (mtm-85) REVERT: B 327 TYR cc_start: 0.8566 (m-10) cc_final: 0.7879 (m-80) REVERT: B 330 ARG cc_start: 0.7067 (mtt90) cc_final: 0.6772 (ttm-80) REVERT: C 44 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5560 (mm) REVERT: C 77 LEU cc_start: 0.2202 (OUTLIER) cc_final: 0.1907 (tt) REVERT: C 273 ARG cc_start: 0.7975 (ptt90) cc_final: 0.6723 (mtm-85) REVERT: C 327 TYR cc_start: 0.8562 (m-10) cc_final: 0.7920 (m-80) REVERT: C 330 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6500 (ttm-80) REVERT: C 333 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: D 44 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5568 (mm) REVERT: D 77 LEU cc_start: 0.2186 (OUTLIER) cc_final: 0.1899 (tt) REVERT: D 273 ARG cc_start: 0.7973 (ptt90) cc_final: 0.6677 (mtm-85) REVERT: D 327 TYR cc_start: 0.8572 (m-10) cc_final: 0.7875 (m-80) REVERT: D 330 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6662 (ttm-80) outliers start: 56 outliers final: 17 residues processed: 178 average time/residue: 0.5253 time to fit residues: 103.7046 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 : 0.471 ------------------------------------------------------------------------------- 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 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 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 225 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 334 MET 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: 0.6980 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 145 optimal weight: 0.0570 chunk 17 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.185829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.148049 restraints weight = 14702.499| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.79 r_work: 0.3117 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1941 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= 0.113 Angle : 0.634 8.546 18762 Z= 0.284 Chirality : 0.041 0.151 2148 Planarity : 0.005 0.056 2248 Dihedral : 10.469 56.583 2464 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.92 % Allowed : 16.57 % Favored : 79.51 % 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: 1.14 (0.23), residues: 1588 helix: 1.54 (0.18), residues: 976 sheet: 0.50 (0.62), residues: 88 loop : -0.65 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 235 TYR 0.006 0.001 TYR D 175 PHE 0.008 0.001 PHE C 40 TRP 0.005 0.001 TRP B 264 HIS 0.002 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (13992) covalent geometry : angle 0.63432 / 0.28 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03620 / 2.33 ( 752) hydrogen bonds : angle 3.97179 / 3.02 ( 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 191 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 137 time to evaluate : 0.513 Fit side-chains REVERT: A 44 LEU cc_start: 0.5969 (OUTLIER) cc_final: 0.5706 (mm) REVERT: A 77 LEU cc_start: 0.1986 (OUTLIER) cc_final: 0.1712 (tt) REVERT: A 203 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8235 (mp) REVERT: A 273 ARG cc_start: 0.8009 (ptt90) cc_final: 0.6790 (mtm-85) REVERT: A 327 TYR cc_start: 0.8531 (m-10) cc_final: 0.7875 (m-80) REVERT: A 330 ARG cc_start: 0.6963 (mtt90) cc_final: 0.6270 (ttm-80) REVERT: A 333 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6773 (mp0) REVERT: B 44 LEU cc_start: 0.5974 (OUTLIER) cc_final: 0.5702 (mm) REVERT: B 77 LEU cc_start: 0.2182 (OUTLIER) cc_final: 0.1900 (tt) REVERT: B 203 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8230 (mp) REVERT: B 273 ARG cc_start: 0.8006 (ptt90) cc_final: 0.6790 (mtm-85) REVERT: B 327 TYR cc_start: 0.8519 (m-10) cc_final: 0.7852 (m-80) REVERT: B 330 ARG cc_start: 0.6990 (mtt90) cc_final: 0.6675 (mtm-85) REVERT: C 44 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5705 (mm) REVERT: C 77 LEU cc_start: 0.2180 (OUTLIER) cc_final: 0.1891 (tt) REVERT: C 203 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8226 (mp) REVERT: C 273 ARG cc_start: 0.7989 (ptt90) cc_final: 0.6779 (mtm-85) REVERT: C 330 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6484 (ttm-80) REVERT: C 333 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6527 (mp0) REVERT: D 44 LEU cc_start: 0.5965 (OUTLIER) cc_final: 0.5698 (mm) REVERT: D 77 LEU cc_start: 0.2049 (OUTLIER) cc_final: 0.1773 (tt) REVERT: D 203 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8230 (mp) REVERT: D 273 ARG cc_start: 0.8013 (ptt90) cc_final: 0.6765 (mtm-85) REVERT: D 327 TYR cc_start: 0.8534 (m-10) cc_final: 0.7858 (m-80) REVERT: D 330 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6596 (ttm-80) outliers start: 54 outliers final: 14 residues processed: 176 average time/residue: 0.5617 time to fit residues: 108.9105 Evaluate side-chains 159 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 230 LEU 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 230 LEU 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 230 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 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 230 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 330 ARG 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: 3.9990 chunk 153 optimal weight: 6.9990 chunk 135 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 0.0470 chunk 9 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.9480 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.184442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.147369 restraints weight = 14807.207| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.91 r_work: 0.3092 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1975 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= 0.132 Angle : 0.654 8.625 18762 Z= 0.292 Chirality : 0.042 0.146 2148 Planarity : 0.005 0.056 2248 Dihedral : 10.504 58.321 2464 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.78 % Allowed : 17.08 % Favored : 79.14 % 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: 1.13 (0.23), residues: 1588 helix: 1.54 (0.18), residues: 976 sheet: 0.45 (0.61), residues: 88 loop : -0.66 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 391 TYR 0.009 0.001 TYR C 170 PHE 0.006 0.001 PHE A 366 TRP 0.005 0.001 TRP C 176 HIS 0.002 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (13992) covalent geometry : angle 0.65368 / 0.29 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03909 / 2.51 ( 752) hydrogen bonds : angle 3.97320 / 3.01 ( 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 182 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 130 time to evaluate : 0.382 Fit side-chains REVERT: A 44 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5946 (mm) REVERT: A 77 LEU cc_start: 0.2023 (OUTLIER) cc_final: 0.1749 (tt) REVERT: A 203 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8160 (mp) REVERT: A 273 ARG cc_start: 0.8046 (ptt90) cc_final: 0.6871 (mtm-85) REVERT: A 327 TYR cc_start: 0.8567 (m-10) cc_final: 0.7964 (m-80) REVERT: A 330 ARG cc_start: 0.7008 (mtt90) cc_final: 0.6318 (ttm-80) REVERT: A 333 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6827 (mp0) REVERT: B 44 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5876 (mm) REVERT: B 77 LEU cc_start: 0.2019 (OUTLIER) cc_final: 0.1747 (tt) REVERT: B 203 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8155 (mp) REVERT: B 273 ARG cc_start: 0.8031 (ptt90) cc_final: 0.6839 (mtm-85) REVERT: B 327 TYR cc_start: 0.8557 (m-10) cc_final: 0.7954 (m-80) REVERT: B 330 ARG cc_start: 0.7007 (mtt90) cc_final: 0.6525 (ttm-80) REVERT: C 44 LEU cc_start: 0.6199 (OUTLIER) cc_final: 0.5939 (mm) REVERT: C 77 LEU cc_start: 0.2019 (OUTLIER) cc_final: 0.1740 (tt) REVERT: C 203 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8153 (mp) REVERT: C 273 ARG cc_start: 0.8029 (ptt90) cc_final: 0.6868 (mtm-85) REVERT: C 330 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6529 (ttm-80) REVERT: C 333 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: D 44 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5939 (mm) REVERT: D 77 LEU cc_start: 0.1975 (OUTLIER) cc_final: 0.1707 (tt) REVERT: D 203 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8156 (mp) REVERT: D 273 ARG cc_start: 0.8039 (ptt90) cc_final: 0.6856 (mtm-85) REVERT: D 330 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6631 (ttm-80) outliers start: 52 outliers final: 10 residues processed: 172 average time/residue: 0.5701 time to fit residues: 108.3266 Evaluate side-chains 152 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 346 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 159 optimal weight: 0.6980 chunk 148 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 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 = 0.4005 r_free = 0.4005 target = 0.185032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.147333 restraints weight = 14725.401| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.96 r_work: 0.3104 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2100 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= 0.119 Angle : 0.639 11.542 18762 Z= 0.285 Chirality : 0.041 0.149 2148 Planarity : 0.004 0.057 2248 Dihedral : 10.175 59.633 2464 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.63 % Allowed : 17.15 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.23), residues: 1588 helix: 1.62 (0.18), residues: 980 sheet: 0.52 (0.62), residues: 88 loop : -0.62 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 81 TYR 0.007 0.001 TYR B 170 PHE 0.007 0.001 PHE C 40 TRP 0.005 0.001 TRP D 264 HIS 0.002 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (13992) covalent geometry : angle 0.63937 / 0.28 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03716 / 2.39 ( 752) hydrogen bonds : angle 3.93876 / 2.99 ( 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 182 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 132 time to evaluate : 0.510 Fit side-chains REVERT: A 44 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.6024 (mm) REVERT: A 77 LEU cc_start: 0.1995 (OUTLIER) cc_final: 0.1740 (tt) REVERT: A 203 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8220 (mp) REVERT: A 273 ARG cc_start: 0.8017 (ptt90) cc_final: 0.6850 (mtm-85) REVERT: A 330 ARG cc_start: 0.7032 (mtt90) cc_final: 0.6288 (ttm-80) REVERT: A 333 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6840 (mp0) REVERT: B 44 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.6022 (mm) REVERT: B 77 LEU cc_start: 0.1996 (OUTLIER) cc_final: 0.1742 (tt) REVERT: B 203 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8211 (mp) REVERT: B 273 ARG cc_start: 0.8007 (ptt90) cc_final: 0.6800 (mtm-85) REVERT: B 327 TYR cc_start: 0.8543 (m-10) cc_final: 0.7930 (m-80) REVERT: B 330 ARG cc_start: 0.6982 (mtt90) cc_final: 0.6508 (ttm-80) REVERT: C 44 LEU cc_start: 0.6251 (OUTLIER) cc_final: 0.6025 (mm) REVERT: C 77 LEU cc_start: 0.2002 (OUTLIER) cc_final: 0.1738 (tt) REVERT: C 203 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8218 (mp) REVERT: C 273 ARG cc_start: 0.7941 (ptt90) cc_final: 0.6742 (mtm-85) REVERT: C 330 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6461 (ttm-80) REVERT: C 333 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: D 44 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.6023 (mm) REVERT: D 77 LEU cc_start: 0.1951 (OUTLIER) cc_final: 0.1702 (tt) REVERT: D 203 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8220 (mp) REVERT: D 273 ARG cc_start: 0.8008 (ptt90) cc_final: 0.6831 (mtm-85) REVERT: D 318 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8173 (tp30) REVERT: D 330 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6612 (ttm-80) outliers start: 50 outliers final: 13 residues processed: 168 average time/residue: 0.6137 time to fit residues: 112.9660 Evaluate side-chains 157 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 230 LEU 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 230 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 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 230 LEU 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 334 MET 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: 0.0370 chunk 153 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.9864 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.184371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.146879 restraints weight = 14784.486| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.05 r_work: 0.3081 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2113 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= 0.135 Angle : 0.671 11.703 18762 Z= 0.297 Chirality : 0.043 0.147 2148 Planarity : 0.005 0.057 2248 Dihedral : 10.255 57.223 2464 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.62 % Allowed : 18.90 % Favored : 78.49 % 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: 1.20 (0.23), residues: 1588 helix: 1.60 (0.18), residues: 980 sheet: 0.47 (0.61), residues: 88 loop : -0.65 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 356 TYR 0.008 0.001 TYR B 170 PHE 0.006 0.001 PHE A 366 TRP 0.005 0.001 TRP C 176 HIS 0.002 0.001 HIS C 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (13992) covalent geometry : angle 0.67146 / 0.30 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03955 / 2.55 ( 752) hydrogen bonds : angle 3.95198 / 3.00 ( 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 168 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.542 Fit side-chains REVERT: A 44 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.6015 (mm) REVERT: A 77 LEU cc_start: 0.2012 (OUTLIER) cc_final: 0.1776 (tt) REVERT: A 203 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8125 (mp) REVERT: A 273 ARG cc_start: 0.7930 (ptt90) cc_final: 0.6881 (mtm-85) REVERT: A 277 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8226 (ttpt) REVERT: A 330 ARG cc_start: 0.7030 (mtt90) cc_final: 0.6279 (ttm-80) REVERT: A 333 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6793 (mp0) REVERT: B 44 LEU cc_start: 0.6251 (OUTLIER) cc_final: 0.6022 (mm) REVERT: B 77 LEU cc_start: 0.2030 (OUTLIER) cc_final: 0.1786 (tt) REVERT: B 203 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8122 (mp) REVERT: B 273 ARG cc_start: 0.7913 (ptt90) cc_final: 0.6837 (mtm-85) REVERT: B 330 ARG cc_start: 0.6974 (mtt90) cc_final: 0.6483 (ttm-80) REVERT: C 44 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.6050 (mm) REVERT: C 77 LEU cc_start: 0.2018 (OUTLIER) cc_final: 0.1774 (tt) REVERT: C 203 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8123 (mp) REVERT: C 273 ARG cc_start: 0.7881 (ptt90) cc_final: 0.6773 (mtm-85) REVERT: C 330 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6651 (ttm-80) REVERT: C 333 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7218 (mm-30) REVERT: D 44 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.6019 (mm) REVERT: D 77 LEU cc_start: 0.1944 (OUTLIER) cc_final: 0.1722 (tt) REVERT: D 203 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8121 (mp) REVERT: D 273 ARG cc_start: 0.7932 (ptt90) cc_final: 0.6852 (mtm-85) REVERT: D 318 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: D 330 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6274 (ttm-80) outliers start: 36 outliers final: 7 residues processed: 157 average time/residue: 0.5479 time to fit residues: 94.8312 Evaluate side-chains 149 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 277 LYS 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 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 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 318 GLU Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 334 MET 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: 6.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 48 optimal weight: 0.0870 chunk 150 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.185920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.148227 restraints weight = 14723.653| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.98 r_work: 0.3111 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2204 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= 0.118 Angle : 0.656 11.272 18762 Z= 0.289 Chirality : 0.042 0.148 2148 Planarity : 0.004 0.057 2248 Dihedral : 9.823 54.638 2464 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.96 % Allowed : 19.84 % Favored : 78.20 % 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: 1.28 (0.23), residues: 1588 helix: 1.68 (0.18), residues: 980 sheet: 0.51 (0.62), residues: 88 loop : -0.67 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 356 TYR 0.006 0.001 TYR D 170 PHE 0.008 0.001 PHE D 40 TRP 0.005 0.001 TRP C 264 HIS 0.002 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (13992) covalent geometry : angle 0.65632 / 0.29 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03692 / 2.38 ( 752) hydrogen bonds : angle 3.91658 / 2.97 ( 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 155 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.376 Fit side-chains REVERT: A 77 LEU cc_start: 0.2050 (OUTLIER) cc_final: 0.1835 (tt) REVERT: A 203 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8216 (mp) REVERT: A 273 ARG cc_start: 0.7924 (ptt90) cc_final: 0.6717 (mtm-85) REVERT: A 330 ARG cc_start: 0.7078 (mtt90) cc_final: 0.6322 (ttm-80) REVERT: A 333 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6790 (mp0) REVERT: B 44 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.6056 (mm) REVERT: B 77 LEU cc_start: 0.2062 (OUTLIER) cc_final: 0.1845 (tt) REVERT: B 203 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8216 (mp) REVERT: B 273 ARG cc_start: 0.7906 (ptt90) cc_final: 0.6694 (mtm-85) REVERT: B 330 ARG cc_start: 0.7021 (mtt90) cc_final: 0.6347 (ttm-80) REVERT: C 44 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.6053 (mm) REVERT: C 77 LEU cc_start: 0.1985 (OUTLIER) cc_final: 0.1741 (tt) REVERT: C 203 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8210 (mp) REVERT: C 273 ARG cc_start: 0.7888 (ptt90) cc_final: 0.6687 (mtm-85) REVERT: C 330 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6417 (ttm-80) REVERT: C 333 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: D 77 LEU cc_start: 0.1878 (OUTLIER) cc_final: 0.1669 (tt) REVERT: D 203 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8217 (mp) REVERT: D 273 ARG cc_start: 0.7984 (ptt90) cc_final: 0.6803 (mtm-85) REVERT: D 330 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6715 (ttm-80) REVERT: D 333 GLU cc_start: 0.7478 (mp0) cc_final: 0.7227 (mm-30) outliers start: 27 outliers final: 7 residues processed: 145 average time/residue: 0.5891 time to fit residues: 93.6572 Evaluate side-chains 146 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 330 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 346 VAL 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 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 114 optimal weight: 0.0000 chunk 111 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.186677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.148238 restraints weight = 14698.130| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.94 r_work: 0.3126 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13992 Z= 0.114 Angle : 0.649 11.113 18762 Z= 0.285 Chirality : 0.042 0.148 2148 Planarity : 0.004 0.056 2248 Dihedral : 9.505 54.232 2464 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.40 % Allowed : 19.33 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.23), residues: 1588 helix: 1.69 (0.18), residues: 984 sheet: 0.59 (0.62), residues: 88 loop : -0.70 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 356 TYR 0.006 0.001 TYR D 175 PHE 0.006 0.001 PHE D 366 TRP 0.004 0.001 TRP C 264 HIS 0.002 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (13992) covalent geometry : angle 0.64947 / 0.29 (18760) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03612 / 2.32 ( 752) hydrogen bonds : angle 3.89721 / 2.96 ( 2184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4776.97 seconds wall clock time: 82 minutes 3.96 seconds (4923.96 seconds total)