Starting phenix.real_space_refine on Wed Mar 4 13:36:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rsh_24670/03_2026/7rsh_24670.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rsh_24670/03_2026/7rsh_24670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rsh_24670/03_2026/7rsh_24670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rsh_24670/03_2026/7rsh_24670.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rsh_24670/03_2026/7rsh_24670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rsh_24670/03_2026/7rsh_24670.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 28 5.16 5 C 9244 2.51 5 N 2148 2.21 5 O 2316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13744 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3191 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 25, 'TRANS': 375} Chain breaks: 1 Chain: "D" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3191 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 25, 'TRANS': 375} Chain breaks: 1 Chain: "A" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'PGW': 14} Classifications: {'RNA': 1, 'undetermined': 14} Modifications used: {'rna3p': 1} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PGW:plan-1': 12, 'PGW:plan-2': 12, 'PGW:plan-3': 8} Unresolved non-hydrogen planarities: 119 Chain: "D" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'PGW': 14} Classifications: {'RNA': 1, 'undetermined': 14} Modifications used: {'rna3p': 1} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 494 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: 3.57, per 1000 atoms: 0.26 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: 0.95 Conformation dependent library (CDL) restraints added in 635.8 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: 0.39 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: 2.15 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1992 1.31 - 1.43: 3463 1.43 - 1.56: 8473 1.56 - 1.68: 16 1.68 - 1.80: 48 Bond restraints: 13992 Sorted by residual: bond pdb=" C10 PGW D 515 " pdb=" C9 PGW D 515 " ideal model delta sigma weight residual 1.333 1.529 -0.196 2.00e-02 2.50e+03 9.63e+01 bond pdb=" C10 PGW A 514 " pdb=" C9 PGW A 514 " ideal model delta sigma weight residual 1.333 1.529 -0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C10 PGW B 514 " pdb=" C9 PGW B 514 " ideal model delta sigma weight residual 1.333 1.529 -0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C10 PGW C 514 " pdb=" C9 PGW C 514 " ideal model delta sigma weight residual 1.333 1.528 -0.195 2.00e-02 2.50e+03 9.54e+01 bond pdb=" C10 PGW B 509 " pdb=" C9 PGW B 509 " ideal model delta sigma weight residual 1.333 1.528 -0.195 2.00e-02 2.50e+03 9.52e+01 ... (remaining 13987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 18281 3.92 - 7.84: 399 7.84 - 11.76: 40 11.76 - 15.68: 4 15.68 - 19.59: 36 Bond angle restraints: 18760 Sorted by residual: angle pdb=" C06 PGW D 511 " pdb=" C10 PGW D 511 " pdb=" C9 PGW D 511 " ideal model delta sigma weight residual 126.92 107.33 19.59 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C06 PGW A 510 " pdb=" C10 PGW A 510 " pdb=" C9 PGW A 510 " ideal model delta sigma weight residual 126.92 107.33 19.59 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C06 PGW B 510 " pdb=" C10 PGW B 510 " pdb=" C9 PGW B 510 " ideal model delta sigma weight residual 126.92 107.33 19.59 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C06 PGW C 510 " pdb=" C10 PGW C 510 " pdb=" C9 PGW C 510 " ideal model delta sigma weight residual 126.92 107.37 19.55 3.00e+00 1.11e-01 4.25e+01 angle pdb=" C06 PGW D 504 " pdb=" C10 PGW D 504 " pdb=" C9 PGW D 504 " ideal model delta sigma weight residual 126.92 108.41 18.51 3.00e+00 1.11e-01 3.81e+01 ... (remaining 18755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 8272 33.70 - 67.40: 292 67.40 - 101.10: 20 101.10 - 134.80: 20 134.80 - 168.50: 12 Dihedral angle restraints: 8616 sinusoidal: 3900 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 8613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1408 0.041 - 0.081: 519 0.081 - 0.122: 205 0.122 - 0.162: 12 0.162 - 0.203: 4 Chirality restraints: 2148 Sorted by residual: chirality pdb=" C02 PGW C 502 " pdb=" C01 PGW C 502 " pdb=" C03 PGW C 502 " pdb=" O01 PGW C 502 " both_signs ideal model delta sigma weight residual False 2.36 2.56 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C02 PGW D 503 " pdb=" C01 PGW D 503 " pdb=" C03 PGW D 503 " pdb=" O01 PGW D 503 " both_signs ideal model delta sigma weight residual False 2.36 2.56 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C02 PGW B 502 " pdb=" C01 PGW B 502 " pdb=" C03 PGW B 502 " pdb=" O01 PGW B 502 " both_signs ideal model delta sigma weight residual False 2.36 2.56 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2145 not shown) Planarity restraints: 2248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 503 " 0.109 2.00e-02 2.50e+03 3.57e-01 1.27e+03 pdb=" C10 PGW A 503 " 0.136 2.00e-02 2.50e+03 pdb=" C8 PGW A 503 " 0.351 2.00e-02 2.50e+03 pdb=" C9 PGW A 503 " -0.596 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 503 " 0.109 2.00e-02 2.50e+03 3.57e-01 1.27e+03 pdb=" C10 PGW B 503 " 0.136 2.00e-02 2.50e+03 pdb=" C8 PGW B 503 " 0.351 2.00e-02 2.50e+03 pdb=" C9 PGW B 503 " -0.596 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 504 " -0.112 2.00e-02 2.50e+03 3.57e-01 1.27e+03 pdb=" C10 PGW D 504 " -0.132 2.00e-02 2.50e+03 pdb=" C8 PGW D 504 " -0.352 2.00e-02 2.50e+03 pdb=" C9 PGW D 504 " 0.596 2.00e-02 2.50e+03 ... (remaining 2245 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2010 2.76 - 3.29: 12733 3.29 - 3.83: 21149 3.83 - 4.36: 26144 4.36 - 4.90: 44892 Nonbonded interactions: 106928 Sorted by model distance: nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR A 180 " pdb=" OH TYR D 186 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR C 186 " pdb=" OG1 THR D 180 " model vdw 2.249 3.040 nonbonded pdb=" NH2 ARG B 238 " pdb=" OE2 GLU C 278 " model vdw 2.267 3.120 ... (remaining 106923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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: 0.010 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.480 Find NCS groups from input model: 0.350 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: 0.010 Load rotamer database and sin/cos tables:8.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.196 13992 Z= 0.449 Angle : 1.427 19.594 18762 Z= 0.569 Chirality : 0.047 0.203 2148 Planarity : 0.017 0.357 2248 Dihedral : 19.070 168.500 5564 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 covalent geometry : bond 0.00936 (13992) covalent geometry : angle 1.42751 (18760) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.13843 ( 752) hydrogen bonds : angle 5.63293 ( 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 : 0.540 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: 0.6329 time to fit residues: 126.4557 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 : 0.494 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.183719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.147340 restraints weight = 14809.244| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.79 r_work: 0.3156 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13992 Z= 0.136 Angle : 0.683 8.583 18762 Z= 0.319 Chirality : 0.042 0.130 2148 Planarity : 0.006 0.085 2248 Dihedral : 18.194 159.719 2528 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.09 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 111 TYR 0.006 0.001 TYR D 175 PHE 0.012 0.001 PHE B 64 TRP 0.007 0.001 TRP B 264 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00312 (13992) covalent geometry : angle 0.68328 (18760) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04190 ( 752) hydrogen bonds : angle 4.45797 ( 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 : 0.395 Fit side-chains REVERT: A 203 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 273 ARG cc_start: 0.8179 (ptt90) cc_final: 0.7030 (ptp90) REVERT: A 330 ARG cc_start: 0.7169 (mtt90) cc_final: 0.6678 (ttm-80) REVERT: A 333 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: A 337 ASP cc_start: 0.8497 (m-30) cc_final: 0.8275 (m-30) REVERT: B 203 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8187 (mp) REVERT: B 273 ARG cc_start: 0.8222 (ptt90) cc_final: 0.7092 (ptp90) REVERT: B 330 ARG cc_start: 0.7177 (mtt90) cc_final: 0.6880 (ttm-80) REVERT: B 337 ASP cc_start: 0.8504 (m-30) cc_final: 0.8282 (m-30) REVERT: C 203 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8182 (mp) REVERT: C 273 ARG cc_start: 0.8208 (ptt90) cc_final: 0.7089 (ptp90) REVERT: C 337 ASP cc_start: 0.8538 (m-30) cc_final: 0.8307 (m-30) REVERT: D 203 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8169 (mp) REVERT: D 273 ARG cc_start: 0.8155 (ptt90) cc_final: 0.6968 (ptp90) REVERT: D 333 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7331 (mp0) outliers start: 49 outliers final: 6 residues processed: 165 average time/residue: 0.6381 time to fit residues: 114.5193 Evaluate side-chains 142 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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: 3.9990 chunk 44 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 155 optimal weight: 0.0970 chunk 108 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.182990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.145490 restraints weight = 14899.578| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.71 r_work: 0.3105 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1405 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= 0.138 Angle : 0.645 8.060 18762 Z= 0.304 Chirality : 0.041 0.129 2148 Planarity : 0.005 0.066 2248 Dihedral : 17.209 158.885 2524 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.43 % Allowed : 12.79 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.23), residues: 1588 helix: 1.12 (0.18), residues: 976 sheet: -0.05 (0.59), residues: 88 loop : -0.70 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 391 TYR 0.007 0.001 TYR C 170 PHE 0.007 0.001 PHE C 64 TRP 0.006 0.001 TRP C 264 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00330 (13992) covalent geometry : angle 0.64473 (18760) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04100 ( 752) hydrogen bonds : angle 4.24434 ( 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 200 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 139 time to evaluate : 0.571 Fit side-chains REVERT: A 203 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 273 ARG cc_start: 0.8076 (ptt90) cc_final: 0.6821 (ptp90) REVERT: A 330 ARG cc_start: 0.7098 (mtt90) cc_final: 0.6571 (ttm-80) REVERT: A 333 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: B 203 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8187 (mp) REVERT: B 273 ARG cc_start: 0.8078 (ptt90) cc_final: 0.6818 (ptp90) REVERT: B 330 ARG cc_start: 0.7106 (mtt90) cc_final: 0.6708 (mtm-85) REVERT: C 203 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8186 (mp) REVERT: C 273 ARG cc_start: 0.8045 (ptt90) cc_final: 0.6823 (ptp90) REVERT: C 330 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6736 (ttm-80) REVERT: D 203 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8145 (mp) REVERT: D 273 ARG cc_start: 0.8057 (ptt90) cc_final: 0.6788 (ptp90) REVERT: D 333 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7142 (mp0) outliers start: 61 outliers final: 15 residues processed: 183 average time/residue: 0.5418 time to fit residues: 109.0161 Evaluate side-chains 151 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 108 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.0870 chunk 123 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.179135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.140394 restraints weight = 14968.668| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.83 r_work: 0.3271 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13992 Z= 0.123 Angle : 0.626 7.983 18762 Z= 0.291 Chirality : 0.041 0.165 2148 Planarity : 0.005 0.055 2248 Dihedral : 16.375 157.723 2524 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.71 % Allowed : 14.39 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.23), residues: 1588 helix: 1.38 (0.18), residues: 972 sheet: 0.23 (0.61), residues: 88 loop : -0.67 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 235 TYR 0.006 0.001 TYR A 175 PHE 0.008 0.001 PHE D 40 TRP 0.005 0.001 TRP D 264 HIS 0.002 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00277 (13992) covalent geometry : angle 0.62620 (18760) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03701 ( 752) hydrogen bonds : angle 4.09460 ( 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 208 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.490 Fit side-chains REVERT: A 203 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8210 (mp) REVERT: A 273 ARG cc_start: 0.8108 (ptt90) cc_final: 0.7065 (mtm-85) REVERT: A 330 ARG cc_start: 0.7069 (mtt90) cc_final: 0.6575 (ttm-80) REVERT: A 333 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: B 203 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8202 (mp) REVERT: B 273 ARG cc_start: 0.8109 (ptt90) cc_final: 0.7059 (mtm-85) REVERT: B 330 ARG cc_start: 0.7063 (mtt90) cc_final: 0.6724 (mtm-85) REVERT: C 203 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8208 (mp) REVERT: C 273 ARG cc_start: 0.8092 (ptt90) cc_final: 0.7029 (mtm-85) REVERT: C 330 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6659 (ttm-80) REVERT: D 77 LEU cc_start: 0.2310 (OUTLIER) cc_final: 0.1997 (tt) REVERT: D 203 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8209 (mp) REVERT: D 273 ARG cc_start: 0.8105 (ptt90) cc_final: 0.7050 (mtm-85) REVERT: D 330 ARG cc_start: 0.7072 (mtt90) cc_final: 0.6817 (mtm-85) outliers start: 51 outliers final: 14 residues processed: 190 average time/residue: 0.5823 time to fit residues: 121.0852 Evaluate side-chains 166 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 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 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 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: 0.6980 chunk 149 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.181621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144287 restraints weight = 14952.484| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.90 r_work: 0.3101 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1808 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= 0.125 Angle : 0.616 7.990 18762 Z= 0.289 Chirality : 0.041 0.130 2148 Planarity : 0.005 0.055 2248 Dihedral : 16.080 155.760 2524 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.85 % Allowed : 14.90 % 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: 1.45 (0.18), residues: 972 sheet: 0.42 (0.62), residues: 88 loop : -0.64 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 235 TYR 0.007 0.001 TYR A 170 PHE 0.006 0.001 PHE D 366 TRP 0.004 0.001 TRP C 264 HIS 0.002 0.001 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00292 (13992) covalent geometry : angle 0.61597 (18760) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03776 ( 752) hydrogen bonds : angle 4.00853 ( 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 190 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 0.473 Fit side-chains REVERT: A 44 LEU cc_start: 0.6126 (OUTLIER) cc_final: 0.5545 (mm) REVERT: A 77 LEU cc_start: 0.2158 (OUTLIER) cc_final: 0.1869 (tt) REVERT: A 203 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8154 (mp) REVERT: A 273 ARG cc_start: 0.7948 (ptt90) cc_final: 0.6708 (mtm-85) REVERT: A 327 TYR cc_start: 0.8541 (m-10) cc_final: 0.7820 (m-80) REVERT: A 330 ARG cc_start: 0.6997 (mtt90) cc_final: 0.6465 (ttm-80) REVERT: A 333 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6537 (mp0) REVERT: A 369 MET cc_start: 0.7436 (ppp) cc_final: 0.7007 (mpp) REVERT: B 44 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5544 (mm) REVERT: B 77 LEU cc_start: 0.2160 (OUTLIER) cc_final: 0.1871 (tt) REVERT: B 203 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8153 (mp) REVERT: B 273 ARG cc_start: 0.7957 (ptt90) cc_final: 0.6712 (mtm-85) REVERT: B 327 TYR cc_start: 0.8581 (m-10) cc_final: 0.7838 (m-80) REVERT: B 330 ARG cc_start: 0.7005 (mtt90) cc_final: 0.6481 (mtm-85) REVERT: C 44 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5554 (mm) REVERT: C 77 LEU cc_start: 0.2178 (OUTLIER) cc_final: 0.1880 (tt) REVERT: C 203 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8153 (mp) REVERT: C 273 ARG cc_start: 0.7967 (ptt90) cc_final: 0.6721 (mtm-85) REVERT: C 327 TYR cc_start: 0.8532 (m-10) cc_final: 0.7798 (m-80) REVERT: C 330 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6812 (mtm-85) REVERT: C 333 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6981 (mm-30) REVERT: D 44 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5555 (mm) REVERT: D 77 LEU cc_start: 0.2025 (OUTLIER) cc_final: 0.1753 (tt) REVERT: D 203 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8155 (mp) REVERT: D 273 ARG cc_start: 0.7976 (ptt90) cc_final: 0.6692 (mtm-85) REVERT: D 327 TYR cc_start: 0.8553 (m-10) cc_final: 0.7877 (m-80) REVERT: D 330 ARG cc_start: 0.7006 (mtt90) cc_final: 0.6713 (ttm-80) outliers start: 53 outliers final: 12 residues processed: 178 average time/residue: 0.5625 time to fit residues: 109.8186 Evaluate side-chains 157 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 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 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 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: 0.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.183576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.146322 restraints weight = 14733.136| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.72 r_work: 0.3100 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13992 Z= 0.148 Angle : 0.634 8.067 18762 Z= 0.299 Chirality : 0.042 0.132 2148 Planarity : 0.005 0.055 2248 Dihedral : 16.168 154.074 2524 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.71 % Allowed : 17.44 % Favored : 78.85 % 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: 1.01 (0.23), residues: 1588 helix: 1.44 (0.18), residues: 972 sheet: 0.37 (0.61), residues: 88 loop : -0.68 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 235 TYR 0.008 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 149 Details of bonding type rmsd covalent geometry : bond 0.00363 (13992) covalent geometry : angle 0.63392 (18760) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04064 ( 752) hydrogen bonds : angle 4.03110 ( 2184) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 130 time to evaluate : 0.316 Fit side-chains REVERT: A 44 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5604 (mm) REVERT: A 77 LEU cc_start: 0.2275 (OUTLIER) cc_final: 0.1967 (tt) REVERT: A 203 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8155 (mp) REVERT: A 273 ARG cc_start: 0.8011 (ptt90) cc_final: 0.6803 (mtm-85) REVERT: A 327 TYR cc_start: 0.8556 (m-10) cc_final: 0.7920 (m-80) REVERT: A 330 ARG cc_start: 0.7019 (mtt90) cc_final: 0.6448 (ttm-80) REVERT: A 333 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6640 (mp0) REVERT: B 44 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5613 (mm) REVERT: B 77 LEU cc_start: 0.2277 (OUTLIER) cc_final: 0.1968 (tt) REVERT: B 203 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8157 (mp) REVERT: B 273 ARG cc_start: 0.7997 (ptt90) cc_final: 0.6791 (mtm-85) REVERT: B 327 TYR cc_start: 0.8556 (m-10) cc_final: 0.7922 (m-80) REVERT: B 330 ARG cc_start: 0.7069 (mtt90) cc_final: 0.6786 (ttm-80) REVERT: C 44 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5614 (mm) REVERT: C 77 LEU cc_start: 0.2274 (OUTLIER) cc_final: 0.1964 (tt) REVERT: C 203 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8152 (mp) REVERT: C 273 ARG cc_start: 0.8003 (ptt90) cc_final: 0.6788 (mtm-85) REVERT: C 330 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6735 (ttm-80) REVERT: D 44 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5606 (mm) REVERT: D 77 LEU cc_start: 0.2029 (OUTLIER) cc_final: 0.1750 (tt) REVERT: D 203 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8151 (mp) REVERT: D 273 ARG cc_start: 0.8033 (ptt90) cc_final: 0.6808 (mtm-85) REVERT: D 330 ARG cc_start: 0.7026 (mtt90) cc_final: 0.6656 (ttm-80) outliers start: 51 outliers final: 10 residues processed: 168 average time/residue: 0.6026 time to fit residues: 110.2600 Evaluate side-chains 153 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 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 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 346 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 5 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.183603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.146484 restraints weight = 14824.899| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.93 r_work: 0.3112 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1962 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= 0.142 Angle : 0.635 8.043 18762 Z= 0.298 Chirality : 0.042 0.129 2148 Planarity : 0.005 0.055 2248 Dihedral : 15.773 152.219 2524 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.92 % Allowed : 17.30 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.23), residues: 1588 helix: 1.46 (0.18), residues: 976 sheet: 0.43 (0.61), residues: 88 loop : -0.68 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 235 TYR 0.007 0.001 TYR B 170 PHE 0.006 0.001 PHE B 366 TRP 0.006 0.001 TRP A 264 HIS 0.002 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00347 (13992) covalent geometry : angle 0.63505 (18760) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03995 ( 752) hydrogen bonds : angle 4.01844 ( 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 183 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 129 time to evaluate : 0.471 Fit side-chains REVERT: A 44 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5679 (mm) REVERT: A 77 LEU cc_start: 0.2004 (OUTLIER) cc_final: 0.1736 (tt) REVERT: A 203 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8192 (mp) REVERT: A 273 ARG cc_start: 0.7988 (ptt90) cc_final: 0.6795 (mtm-85) REVERT: A 327 TYR cc_start: 0.8575 (m-10) cc_final: 0.8001 (m-80) REVERT: A 330 ARG cc_start: 0.7020 (mtt90) cc_final: 0.6453 (ttm-80) REVERT: A 333 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: B 44 LEU cc_start: 0.6116 (OUTLIER) cc_final: 0.5669 (mm) REVERT: B 77 LEU cc_start: 0.1996 (OUTLIER) cc_final: 0.1730 (tt) REVERT: B 203 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8191 (mp) REVERT: B 273 ARG cc_start: 0.7974 (ptt90) cc_final: 0.6779 (mtm-85) REVERT: B 327 TYR cc_start: 0.8582 (m-10) cc_final: 0.8016 (m-80) REVERT: B 330 ARG cc_start: 0.7017 (mtt90) cc_final: 0.6541 (ttm-80) REVERT: C 44 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5700 (mm) REVERT: C 77 LEU cc_start: 0.2106 (OUTLIER) cc_final: 0.1831 (tt) REVERT: C 203 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8187 (mp) REVERT: C 273 ARG cc_start: 0.8010 (ptt90) cc_final: 0.6818 (mtm-85) REVERT: C 330 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6465 (ttm-80) REVERT: D 44 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5697 (mm) REVERT: D 77 LEU cc_start: 0.1960 (OUTLIER) cc_final: 0.1706 (tt) REVERT: D 203 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8192 (mp) REVERT: D 273 ARG cc_start: 0.8019 (ptt90) cc_final: 0.6817 (mtm-85) REVERT: D 330 ARG cc_start: 0.6979 (mtt90) cc_final: 0.6648 (ttm-80) outliers start: 54 outliers final: 13 residues processed: 168 average time/residue: 0.5704 time to fit residues: 104.7996 Evaluate side-chains 153 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 ASP 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 B residue 393 ASP 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 346 VAL Chi-restraints excluded: chain C residue 393 ASP 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 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: 0.9990 chunk 159 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.179834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.140110 restraints weight = 14764.521| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.99 r_work: 0.3207 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13992 Z= 0.164 Angle : 0.643 8.448 18762 Z= 0.305 Chirality : 0.043 0.132 2148 Planarity : 0.005 0.056 2248 Dihedral : 15.856 150.960 2524 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.34 % Allowed : 18.53 % Favored : 78.12 % 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: 0.96 (0.23), residues: 1588 helix: 1.41 (0.18), residues: 976 sheet: 0.29 (0.60), residues: 88 loop : -0.72 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 330 TYR 0.008 0.001 TYR B 170 PHE 0.006 0.001 PHE B 366 TRP 0.006 0.002 TRP B 264 HIS 0.003 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00408 (13992) covalent geometry : angle 0.64263 (18760) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04285 ( 752) hydrogen bonds : angle 4.04627 ( 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 177 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 0.387 Fit side-chains REVERT: A 44 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5681 (mm) REVERT: A 77 LEU cc_start: 0.2025 (OUTLIER) cc_final: 0.1775 (tt) REVERT: A 273 ARG cc_start: 0.7984 (ptt90) cc_final: 0.6889 (mtm-85) REVERT: A 327 TYR cc_start: 0.8584 (m-10) cc_final: 0.8055 (m-80) REVERT: A 330 ARG cc_start: 0.7058 (mtt90) cc_final: 0.6508 (ttm-80) REVERT: A 333 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: B 44 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5691 (mm) REVERT: B 77 LEU cc_start: 0.2126 (OUTLIER) cc_final: 0.1875 (tt) REVERT: B 273 ARG cc_start: 0.7987 (ptt90) cc_final: 0.6902 (mtm-85) REVERT: B 327 TYR cc_start: 0.8590 (m-10) cc_final: 0.8067 (m-80) REVERT: B 330 ARG cc_start: 0.7097 (mtt90) cc_final: 0.6594 (ttm-80) REVERT: C 44 LEU cc_start: 0.6192 (OUTLIER) cc_final: 0.5692 (mm) REVERT: C 77 LEU cc_start: 0.2134 (OUTLIER) cc_final: 0.1876 (tt) REVERT: C 273 ARG cc_start: 0.8076 (ptt90) cc_final: 0.7025 (mtm-85) REVERT: C 330 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6817 (ttm-80) REVERT: C 333 GLU cc_start: 0.7419 (mp0) cc_final: 0.7126 (mm-30) REVERT: D 44 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5707 (mm) REVERT: D 77 LEU cc_start: 0.1967 (OUTLIER) cc_final: 0.1739 (tt) REVERT: D 273 ARG cc_start: 0.8064 (ptt90) cc_final: 0.7013 (mtm-85) REVERT: D 330 ARG cc_start: 0.7044 (mtt90) cc_final: 0.6523 (ttm-80) REVERT: D 333 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7026 (mp0) outliers start: 46 outliers final: 17 residues processed: 167 average time/residue: 0.5488 time to fit residues: 100.4786 Evaluate side-chains 153 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 ASP 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 B residue 393 ASP 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 346 VAL Chi-restraints excluded: chain C residue 393 ASP 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 346 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 134 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 151 optimal weight: 0.0870 chunk 81 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.186304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.148993 restraints weight = 14769.790| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.99 r_work: 0.3114 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13992 Z= 0.114 Angle : 0.617 11.051 18762 Z= 0.285 Chirality : 0.040 0.128 2148 Planarity : 0.004 0.054 2248 Dihedral : 15.190 149.344 2524 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.98 % Allowed : 19.77 % Favored : 77.25 % 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: 1.21 (0.23), residues: 1588 helix: 1.62 (0.18), residues: 980 sheet: 0.50 (0.62), residues: 88 loop : -0.69 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 391 TYR 0.006 0.001 TYR B 175 PHE 0.008 0.001 PHE B 40 TRP 0.006 0.001 TRP C 264 HIS 0.002 0.000 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00255 (13992) covalent geometry : angle 0.61713 (18760) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03561 ( 752) hydrogen bonds : angle 3.95536 ( 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 171 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.387 Fit side-chains REVERT: A 44 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5882 (mm) REVERT: A 77 LEU cc_start: 0.2056 (OUTLIER) cc_final: 0.1806 (tt) REVERT: A 203 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8220 (mp) REVERT: A 273 ARG cc_start: 0.7832 (ptt90) cc_final: 0.6714 (mtm-85) REVERT: A 330 ARG cc_start: 0.6953 (mtt90) cc_final: 0.6343 (ttm-80) REVERT: A 333 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: B 44 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5890 (mm) REVERT: B 77 LEU cc_start: 0.2056 (OUTLIER) cc_final: 0.1807 (tt) REVERT: B 203 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8220 (mp) REVERT: B 273 ARG cc_start: 0.7848 (ptt90) cc_final: 0.6730 (mtm-85) REVERT: B 330 ARG cc_start: 0.7046 (mtt90) cc_final: 0.6486 (ttm-80) REVERT: C 44 LEU cc_start: 0.6243 (OUTLIER) cc_final: 0.5889 (mm) REVERT: C 77 LEU cc_start: 0.2065 (OUTLIER) cc_final: 0.1806 (tt) REVERT: C 203 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8212 (mp) REVERT: C 273 ARG cc_start: 0.7946 (ptt90) cc_final: 0.6853 (mtm-85) REVERT: C 330 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6687 (ttm-80) REVERT: C 333 GLU cc_start: 0.7247 (mp0) cc_final: 0.6921 (mm-30) REVERT: D 44 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5923 (mm) REVERT: D 77 LEU cc_start: 0.1960 (OUTLIER) cc_final: 0.1742 (tt) REVERT: D 203 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8222 (mp) REVERT: D 273 ARG cc_start: 0.7910 (ptt90) cc_final: 0.6781 (mtm-85) REVERT: D 333 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6834 (mp0) outliers start: 41 outliers final: 10 residues processed: 158 average time/residue: 0.5896 time to fit residues: 101.6854 Evaluate side-chains 154 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 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 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 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 75 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 150 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.187847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.151088 restraints weight = 14560.311| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.83 r_work: 0.3124 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13992 Z= 0.125 Angle : 0.633 11.760 18762 Z= 0.292 Chirality : 0.042 0.128 2148 Planarity : 0.004 0.055 2248 Dihedral : 15.099 147.698 2524 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.18 % Allowed : 20.57 % Favored : 77.25 % 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: 1.22 (0.23), residues: 1588 helix: 1.64 (0.18), residues: 980 sheet: 0.48 (0.62), residues: 88 loop : -0.69 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 391 TYR 0.007 0.001 TYR B 170 PHE 0.006 0.001 PHE D 40 TRP 0.004 0.001 TRP C 264 HIS 0.002 0.001 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.00292 (13992) covalent geometry : angle 0.63330 (18760) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03779 ( 752) hydrogen bonds : angle 3.93251 ( 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 159 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.459 Fit side-chains REVERT: A 44 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.6044 (mm) REVERT: A 77 LEU cc_start: 0.2056 (OUTLIER) cc_final: 0.1838 (tt) REVERT: A 203 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8149 (mp) REVERT: A 273 ARG cc_start: 0.7848 (ptt90) cc_final: 0.6647 (mtm-85) REVERT: A 327 TYR cc_start: 0.8520 (m-10) cc_final: 0.7959 (m-80) REVERT: A 330 ARG cc_start: 0.6956 (mtt90) cc_final: 0.6297 (ttm-80) REVERT: A 333 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6572 (mp0) REVERT: B 44 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.6015 (mm) REVERT: B 77 LEU cc_start: 0.2052 (OUTLIER) cc_final: 0.1837 (tt) REVERT: B 203 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8155 (mp) REVERT: B 273 ARG cc_start: 0.7823 (ptt90) cc_final: 0.6625 (mtm-85) REVERT: B 330 ARG cc_start: 0.7000 (mtt90) cc_final: 0.6471 (ttm-80) REVERT: C 44 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.6050 (mm) REVERT: C 77 LEU cc_start: 0.1968 (OUTLIER) cc_final: 0.1730 (tt) REVERT: C 203 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8143 (mp) REVERT: C 273 ARG cc_start: 0.7902 (ptt90) cc_final: 0.6648 (mtm-85) REVERT: C 330 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6719 (ttm-80) REVERT: C 333 GLU cc_start: 0.7387 (mp0) cc_final: 0.7087 (mm-30) REVERT: D 44 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.6016 (mm) REVERT: D 203 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8159 (mp) REVERT: D 273 ARG cc_start: 0.7895 (ptt90) cc_final: 0.6674 (mtm-85) REVERT: D 318 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8097 (tp30) REVERT: D 333 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6815 (mp0) outliers start: 30 outliers final: 7 residues processed: 149 average time/residue: 0.5993 time to fit residues: 97.2135 Evaluate side-chains 148 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 ASP 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 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 318 GLU Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 57 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.182383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144229 restraints weight = 14767.017| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.12 r_work: 0.3094 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2198 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= 0.129 Angle : 0.636 11.255 18762 Z= 0.293 Chirality : 0.042 0.129 2148 Planarity : 0.004 0.055 2248 Dihedral : 15.043 145.707 2524 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.25 % Allowed : 20.57 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.23), residues: 1588 helix: 1.65 (0.18), residues: 980 sheet: 0.47 (0.61), residues: 88 loop : -0.70 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 235 TYR 0.007 0.001 TYR D 170 PHE 0.006 0.001 PHE B 40 TRP 0.005 0.001 TRP B 264 HIS 0.002 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00305 (13992) covalent geometry : angle 0.63579 (18760) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03818 ( 752) hydrogen bonds : angle 3.92944 ( 2184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4403.92 seconds wall clock time: 75 minutes 39.14 seconds (4539.14 seconds total)