Starting phenix.real_space_refine on Thu Jul 2 03:09:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j9b_61257/07_2026/9j9b_61257.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j9b_61257/07_2026/9j9b_61257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j9b_61257/07_2026/9j9b_61257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j9b_61257/07_2026/9j9b_61257.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j9b_61257/07_2026/9j9b_61257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j9b_61257/07_2026/9j9b_61257.map" } resolution = 3.83 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= 0.003 sd= 0.042 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 2 5.49 5 S 31 5.16 5 C 3840 2.51 5 N 1041 2.21 5 O 1133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6047 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 985 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 614 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "C" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2094 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 479 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 901 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 837 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 74 Classifications: {'peptide': 15} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 14} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 63 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Time building chain proxies: 1.58, per 1000 atoms: 0.26 Number of scatterers: 6047 At special positions: 0 Unit cell: (94.05, 91.2, 115.9, 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 31 16.00 P 2 15.00 O 1133 8.00 N 1041 7.00 C 3840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 114 " distance=2.04 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.04 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: 0.52 Conformation dependent library (CDL) restraints added in 228.3 milliseconds 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1394 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 54.3% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 13 through 41 Processing helix chain 'A' and resid 45 through 84 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 88 through 103 removed outlier: 3.508A pdb=" N ILE A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 136 removed outlier: 3.999A pdb=" N LEU A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 136 " --> pdb=" O PHE A 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 122 removed outlier: 3.643A pdb=" N VAL B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 166 Proline residue: B 146 - end of helix removed outlier: 4.131A pdb=" N ASN B 151 " --> pdb=" O PHE B 147 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 104 through 125 removed outlier: 3.806A pdb=" N THR C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS C 110 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR C 112 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET C 116 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 147 Processing helix chain 'C' and resid 147 through 152 Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 165 through 172 removed outlier: 3.911A pdb=" N SER C 168 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 172 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 193 Processing helix chain 'C' and resid 257 through 263 removed outlier: 3.845A pdb=" N VAL C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 285 through 296 Processing helix chain 'C' and resid 296 through 308 Processing helix chain 'C' and resid 309 through 317 removed outlier: 3.873A pdb=" N LEU C 313 " --> pdb=" O ASP C 309 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS C 315 " --> pdb=" O LYS C 311 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TRP C 316 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 335 removed outlier: 3.634A pdb=" N PHE C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE C 332 " --> pdb=" O GLN C 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 46 removed outlier: 3.595A pdb=" N CYS D 32 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 35 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N PHE D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA D 41 " --> pdb=" O PHE D 37 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ALA D 43 " --> pdb=" O GLY D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 77 removed outlier: 3.544A pdb=" N LEU D 56 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE D 76 " --> pdb=" O SER D 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 109 removed outlier: 4.139A pdb=" N THR H 109 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 148 removed outlier: 3.745A pdb=" N UNK E 145 " --> pdb=" O UNK E 141 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N UNK E 146 " --> pdb=" O UNK E 142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 337 through 356 removed outlier: 6.973A pdb=" N ASP C 340 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG C 378 " --> pdb=" O ASP C 340 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ARG C 342 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N LEU C 376 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LEU C 344 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N ILE C 374 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE C 346 " --> pdb=" O GLN C 372 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLN C 372 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY C 348 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG C 370 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C 366 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA C 354 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 364 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR C 377 " --> pdb=" O ALA C 386 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 337 through 356 removed outlier: 6.973A pdb=" N ASP C 340 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG C 378 " --> pdb=" O ASP C 340 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ARG C 342 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N LEU C 376 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LEU C 344 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N ILE C 374 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE C 346 " --> pdb=" O GLN C 372 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLN C 372 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY C 348 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG C 370 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C 366 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA C 354 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 364 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ARG C 404 " --> pdb=" O PRO C 363 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER C 397 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG C 424 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA C 399 " --> pdb=" O PHE C 422 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE C 422 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL C 401 " --> pdb=" O LEU C 420 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA4, first strand: chain 'H' and resid 76 through 78 removed outlier: 4.843A pdb=" N LEU H 64 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER H 59 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY H 68 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY H 52 " --> pdb=" O TYR H 117 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR H 117 " --> pdb=" O GLY H 52 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE H 111 " --> pdb=" O GLN H 58 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR H 125 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 76 through 78 removed outlier: 4.843A pdb=" N LEU H 64 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER H 59 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY H 68 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY H 52 " --> pdb=" O TYR H 117 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR H 117 " --> pdb=" O GLY H 52 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE H 111 " --> pdb=" O GLN H 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 25 through 26 Processing sheet with id=AA7, first strand: chain 'L' and resid 30 through 33 removed outlier: 7.016A pdb=" N MET L 57 " --> pdb=" O TYR L 73 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N TYR L 73 " --> pdb=" O MET L 57 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 50 through 51 375 hydrogen bonds defined for protein. 1071 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: 0.90 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1015 1.32 - 1.45: 1643 1.45 - 1.57: 3453 1.57 - 1.69: 4 1.69 - 1.82: 51 Bond restraints: 6166 Sorted by residual: bond pdb=" OB5 CDL A 301 " pdb=" PB2 CDL A 301 " ideal model delta sigma weight residual 1.657 1.572 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" OA5 CDL A 301 " pdb=" PA1 CDL A 301 " ideal model delta sigma weight residual 1.651 1.579 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" OA2 CDL A 301 " pdb=" PA1 CDL A 301 " ideal model delta sigma weight residual 1.639 1.578 0.061 2.00e-02 2.50e+03 9.42e+00 bond pdb=" OB2 CDL A 301 " pdb=" PB2 CDL A 301 " ideal model delta sigma weight residual 1.636 1.577 0.059 2.00e-02 2.50e+03 8.76e+00 bond pdb=" C GLN D 12 " pdb=" N PRO D 13 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.81e+00 ... (remaining 6161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 8100 1.98 - 3.96: 174 3.96 - 5.94: 16 5.94 - 7.92: 14 7.92 - 9.90: 6 Bond angle restraints: 8310 Sorted by residual: angle pdb=" C GLU L 117 " pdb=" N VAL L 118 " pdb=" CA VAL L 118 " ideal model delta sigma weight residual 120.24 123.35 -3.11 6.30e-01 2.52e+00 2.43e+01 angle pdb=" C TRP B 93 " pdb=" N THR B 94 " pdb=" CA THR B 94 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.88e+01 angle pdb=" C GLY B 92 " pdb=" N TRP B 93 " pdb=" CA TRP B 93 " ideal model delta sigma weight residual 121.54 129.52 -7.98 1.91e+00 2.74e-01 1.75e+01 angle pdb=" N GLY H 27 " pdb=" CA GLY H 27 " pdb=" C GLY H 27 " ideal model delta sigma weight residual 112.34 120.71 -8.37 2.04e+00 2.40e-01 1.69e+01 angle pdb=" C GLU C 407 " pdb=" N GLN C 408 " pdb=" CA GLN C 408 " ideal model delta sigma weight residual 121.54 128.46 -6.92 1.91e+00 2.74e-01 1.31e+01 ... (remaining 8305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 3264 15.12 - 30.25: 262 30.25 - 45.37: 92 45.37 - 60.49: 49 60.49 - 75.62: 6 Dihedral angle restraints: 3673 sinusoidal: 1474 harmonic: 2199 Sorted by residual: dihedral pdb=" CB CYS A 10 " pdb=" SG CYS A 10 " pdb=" SG CYS A 77 " pdb=" CB CYS A 77 " ideal model delta sinusoidal sigma weight residual 93.00 136.60 -43.60 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CA ALA C 358 " pdb=" C ALA C 358 " pdb=" N PRO C 359 " pdb=" CA PRO C 359 " ideal model delta harmonic sigma weight residual 180.00 155.78 24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA ILE A 92 " pdb=" C ILE A 92 " pdb=" N ILE A 93 " pdb=" CA ILE A 93 " ideal model delta harmonic sigma weight residual -180.00 -157.90 -22.10 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 3670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 591 0.039 - 0.077: 210 0.077 - 0.116: 73 0.116 - 0.155: 24 0.155 - 0.193: 2 Chirality restraints: 900 Sorted by residual: chirality pdb=" CA THR B 94 " pdb=" N THR B 94 " pdb=" C THR B 94 " pdb=" CB THR B 94 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CA SER L 27 " pdb=" N SER L 27 " pdb=" C SER L 27 " pdb=" CB SER L 27 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CA GLN C 408 " pdb=" N GLN C 408 " pdb=" C GLN C 408 " pdb=" CB GLN C 408 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 897 not shown) Planarity restraints: 1065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 99 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" C GLY A 99 " 0.043 2.00e-02 2.50e+03 pdb=" O GLY A 99 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A 100 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 8 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO A 9 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 9 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 9 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 358 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO C 359 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 359 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 359 " -0.026 5.00e-02 4.00e+02 ... (remaining 1062 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1494 2.80 - 3.32: 5178 3.32 - 3.85: 9633 3.85 - 4.37: 10053 4.37 - 4.90: 18523 Nonbonded interactions: 44881 Sorted by model distance: nonbonded pdb=" OH TYR C 296 " pdb=" OE2 GLU C 413 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR C 176 " pdb=" OE1 GLN C 179 " model vdw 2.322 3.040 nonbonded pdb=" O ILE B 161 " pdb=" OG1 THR B 165 " model vdw 2.325 3.040 nonbonded pdb=" O GLY A 37 " pdb=" OG SER A 41 " model vdw 2.336 3.040 nonbonded pdb=" O ASN C 286 " pdb=" OG1 THR C 290 " model vdw 2.342 3.040 ... (remaining 44876 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.480 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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 : 0.005 0.085 6169 Z= 0.237 Angle : 0.769 9.895 8316 Z= 0.411 Chirality : 0.048 0.193 900 Planarity : 0.006 0.052 1065 Dihedral : 14.643 75.616 2270 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.66 % Allowed : 9.55 % Favored : 84.79 % 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: -1.43 (0.27), residues: 761 helix: -0.41 (0.23), residues: 364 sheet: -0.30 (0.44), residues: 152 loop : -2.00 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 180 TYR 0.016 0.002 TYR H 117 PHE 0.019 0.002 PHE H 99 TRP 0.010 0.001 TRP H 66 HIS 0.002 0.001 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.24 ( 6166) covalent geometry : angle 0.76780 / 0.41 ( 8310) SS BOND : bond 0.00467 / 0.23 ( 3) SS BOND : angle 1.46305 / 0.62 ( 6) hydrogen bonds : bond 0.14168 / 9.80 ( 362) hydrogen bonds : angle 6.21413 / 4.73 ( 1071) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 12 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8507 (pt) REVERT: A 97 PHE cc_start: 0.7915 (m-10) cc_final: 0.7694 (m-10) REVERT: A 105 ARG cc_start: 0.6332 (ttm170) cc_final: 0.5387 (tpt170) REVERT: A 109 ARG cc_start: 0.8100 (mpt-90) cc_final: 0.7828 (mtm-85) REVERT: B 95 ASP cc_start: 0.6354 (t0) cc_final: 0.5759 (t0) REVERT: C 264 PHE cc_start: 0.8648 (t80) cc_final: 0.8261 (t80) REVERT: C 423 VAL cc_start: 0.9090 (t) cc_final: 0.8836 (m) REVERT: D 24 MET cc_start: 0.7018 (mtt) cc_final: 0.6785 (ttt) REVERT: H 124 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8807 (p0) REVERT: L 35 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7787 (tp) outliers start: 35 outliers final: 8 residues processed: 220 average time/residue: 0.0814 time to fit residues: 23.0208 Evaluate side-chains 148 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain L residue 35 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 92 ASN L 26 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.139436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.110633 restraints weight = 12082.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.110128 restraints weight = 8633.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111117 restraints weight = 7351.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111392 restraints weight = 5889.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.111994 restraints weight = 5659.762| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6169 Z= 0.134 Angle : 0.639 12.482 8316 Z= 0.323 Chirality : 0.042 0.162 900 Planarity : 0.005 0.041 1065 Dihedral : 10.332 58.741 933 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.05 % Allowed : 16.18 % Favored : 79.77 % 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: 0.15 (0.30), residues: 761 helix: 1.22 (0.26), residues: 368 sheet: 0.09 (0.46), residues: 141 loop : -1.54 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 180 TYR 0.016 0.002 TYR C 156 PHE 0.017 0.002 PHE A 96 TRP 0.013 0.001 TRP B 93 HIS 0.001 0.000 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 6166) covalent geometry : angle 0.63870 / 0.32 ( 8310) SS BOND : bond 0.00511 / 0.25 ( 3) SS BOND : angle 0.76823 / 0.42 ( 6) hydrogen bonds : bond 0.04011 / 2.77 ( 362) hydrogen bonds : angle 4.23861 / 3.14 ( 1071) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.248 Fit side-chains REVERT: A 36 LYS cc_start: 0.9369 (mmmm) cc_final: 0.8966 (mmmm) REVERT: A 105 ARG cc_start: 0.6751 (ttm170) cc_final: 0.5490 (tpt170) REVERT: A 109 ARG cc_start: 0.8100 (mpt-90) cc_final: 0.7878 (mmm-85) REVERT: A 131 MET cc_start: 0.7657 (mpp) cc_final: 0.7138 (mpp) REVERT: A 135 TYR cc_start: 0.7305 (m-80) cc_final: 0.6946 (m-10) REVERT: A 138 TRP cc_start: 0.5177 (p-90) cc_final: 0.3216 (m100) REVERT: B 95 ASP cc_start: 0.6504 (t0) cc_final: 0.6238 (t0) REVERT: C 118 HIS cc_start: 0.7092 (OUTLIER) cc_final: 0.6533 (p90) REVERT: C 264 PHE cc_start: 0.8624 (t80) cc_final: 0.8275 (t80) REVERT: H 124 ASP cc_start: 0.8904 (p0) cc_final: 0.8701 (p0) REVERT: L 35 LEU cc_start: 0.8196 (mm) cc_final: 0.7829 (tp) outliers start: 25 outliers final: 15 residues processed: 169 average time/residue: 0.0827 time to fit residues: 18.3893 Evaluate side-chains 157 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 20 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 179 GLN C 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.139064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.108098 restraints weight = 12458.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.107005 restraints weight = 8393.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.107996 restraints weight = 8993.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.108378 restraints weight = 6256.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.108977 restraints weight = 5896.526| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6169 Z= 0.142 Angle : 0.605 10.952 8316 Z= 0.306 Chirality : 0.042 0.146 900 Planarity : 0.004 0.041 1065 Dihedral : 9.627 59.490 925 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.34 % Allowed : 17.64 % Favored : 77.02 % 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: 0.49 (0.30), residues: 761 helix: 1.66 (0.27), residues: 370 sheet: 0.11 (0.45), residues: 145 loop : -1.64 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 184 TYR 0.013 0.002 TYR B 159 PHE 0.014 0.001 PHE H 99 TRP 0.018 0.001 TRP B 93 HIS 0.001 0.000 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6166) covalent geometry : angle 0.60367 / 0.31 ( 8310) SS BOND : bond 0.00626 / 0.30 ( 3) SS BOND : angle 1.41093 / 0.74 ( 6) hydrogen bonds : bond 0.03733 / 2.58 ( 362) hydrogen bonds : angle 4.04012 / 2.99 ( 1071) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.253 Fit side-chains REVERT: A 36 LYS cc_start: 0.9345 (mmmm) cc_final: 0.9071 (mmmm) REVERT: A 105 ARG cc_start: 0.6770 (ttm170) cc_final: 0.5395 (tpt170) REVERT: A 109 ARG cc_start: 0.8272 (mpt-90) cc_final: 0.7919 (mmm-85) REVERT: A 131 MET cc_start: 0.7893 (mpp) cc_final: 0.7236 (mpp) REVERT: B 95 ASP cc_start: 0.6997 (t0) cc_final: 0.6794 (t0) REVERT: C 295 GLU cc_start: 0.7612 (pt0) cc_final: 0.7385 (pt0) REVERT: D 24 MET cc_start: 0.7892 (mtt) cc_final: 0.7112 (ttt) REVERT: D 25 MET cc_start: 0.8034 (mmm) cc_final: 0.7771 (tpp) REVERT: H 124 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8492 (p0) REVERT: L 35 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7871 (tp) outliers start: 33 outliers final: 22 residues processed: 169 average time/residue: 0.0833 time to fit residues: 18.5651 Evaluate side-chains 164 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 TRP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 99 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 57 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.138802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109332 restraints weight = 12255.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107569 restraints weight = 9028.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.109254 restraints weight = 7847.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.109216 restraints weight = 6060.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.109771 restraints weight = 5984.815| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6169 Z= 0.119 Angle : 0.586 10.991 8316 Z= 0.293 Chirality : 0.041 0.150 900 Planarity : 0.004 0.043 1065 Dihedral : 9.196 57.479 925 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.37 % Allowed : 19.58 % Favored : 76.05 % 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: 0.78 (0.31), residues: 761 helix: 1.92 (0.27), residues: 370 sheet: 0.23 (0.45), residues: 145 loop : -1.52 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 184 TYR 0.013 0.001 TYR C 296 PHE 0.014 0.001 PHE A 96 TRP 0.022 0.001 TRP B 93 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 6166) covalent geometry : angle 0.58574 / 0.29 ( 8310) SS BOND : bond 0.00547 / 0.26 ( 3) SS BOND : angle 1.23783 / 0.66 ( 6) hydrogen bonds : bond 0.03489 / 2.40 ( 362) hydrogen bonds : angle 3.82435 / 2.83 ( 1071) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.257 Fit side-chains REVERT: A 36 LYS cc_start: 0.9312 (mmmm) cc_final: 0.9055 (mmmm) REVERT: A 105 ARG cc_start: 0.6707 (ttm170) cc_final: 0.5623 (tpt170) REVERT: A 109 ARG cc_start: 0.8176 (mpt-90) cc_final: 0.7922 (mmm-85) REVERT: A 131 MET cc_start: 0.7741 (mpp) cc_final: 0.7257 (mpp) REVERT: C 181 ARG cc_start: 0.8227 (mpt180) cc_final: 0.7948 (mpt180) REVERT: D 24 MET cc_start: 0.7712 (mtt) cc_final: 0.7079 (ttt) REVERT: D 25 MET cc_start: 0.8092 (mmm) cc_final: 0.7835 (tpp) REVERT: L 35 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7878 (tp) outliers start: 27 outliers final: 19 residues processed: 157 average time/residue: 0.0827 time to fit residues: 17.0832 Evaluate side-chains 158 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 99 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 72 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 69 optimal weight: 0.0040 chunk 60 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 0.0170 chunk 15 optimal weight: 1.9990 overall best weight: 0.5030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.140342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109358 restraints weight = 12722.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.108987 restraints weight = 8583.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109985 restraints weight = 8116.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.110602 restraints weight = 5841.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.110977 restraints weight = 5458.652| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6169 Z= 0.115 Angle : 0.574 9.500 8316 Z= 0.288 Chirality : 0.041 0.148 900 Planarity : 0.004 0.044 1065 Dihedral : 8.447 59.522 924 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.05 % Allowed : 20.23 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.31), residues: 761 helix: 2.06 (0.26), residues: 376 sheet: 0.28 (0.45), residues: 143 loop : -1.58 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 184 TYR 0.014 0.001 TYR C 296 PHE 0.011 0.001 PHE A 72 TRP 0.024 0.001 TRP B 93 HIS 0.003 0.001 HIS C 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 6166) covalent geometry : angle 0.57404 / 0.29 ( 8310) SS BOND : bond 0.00499 / 0.24 ( 3) SS BOND : angle 0.93807 / 0.49 ( 6) hydrogen bonds : bond 0.03343 / 2.31 ( 362) hydrogen bonds : angle 3.72173 / 2.76 ( 1071) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.258 Fit side-chains REVERT: A 36 LYS cc_start: 0.9326 (mmmm) cc_final: 0.9063 (mmmm) REVERT: A 105 ARG cc_start: 0.6530 (ttm170) cc_final: 0.5574 (tpt170) REVERT: A 109 ARG cc_start: 0.8200 (mpt-90) cc_final: 0.7882 (mmm-85) REVERT: C 118 HIS cc_start: 0.6943 (OUTLIER) cc_final: 0.6682 (p90) REVERT: C 181 ARG cc_start: 0.8279 (mpt180) cc_final: 0.7994 (mpt180) REVERT: C 332 PHE cc_start: 0.8351 (m-10) cc_final: 0.8007 (m-10) REVERT: D 24 MET cc_start: 0.7650 (mtt) cc_final: 0.7028 (ttt) REVERT: L 35 LEU cc_start: 0.8235 (mm) cc_final: 0.7876 (tp) outliers start: 25 outliers final: 19 residues processed: 159 average time/residue: 0.0754 time to fit residues: 15.7665 Evaluate side-chains 160 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 TRP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 128 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.138061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108668 restraints weight = 12378.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107064 restraints weight = 9037.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.108285 restraints weight = 7966.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.108497 restraints weight = 6249.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.109271 restraints weight = 6073.316| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6169 Z= 0.133 Angle : 0.602 11.531 8316 Z= 0.301 Chirality : 0.042 0.150 900 Planarity : 0.004 0.047 1065 Dihedral : 7.740 54.533 922 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.37 % Allowed : 21.36 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.31), residues: 761 helix: 2.11 (0.26), residues: 377 sheet: 0.16 (0.44), residues: 149 loop : -1.44 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 184 TYR 0.010 0.001 TYR C 377 PHE 0.013 0.001 PHE H 99 TRP 0.019 0.001 TRP B 93 HIS 0.003 0.001 HIS C 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 6166) covalent geometry : angle 0.60129 / 0.30 ( 8310) SS BOND : bond 0.00659 / 0.33 ( 3) SS BOND : angle 1.43703 / 0.76 ( 6) hydrogen bonds : bond 0.03480 / 2.41 ( 362) hydrogen bonds : angle 3.72352 / 2.76 ( 1071) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9289 (mmmm) cc_final: 0.9043 (mmmm) REVERT: A 83 ARG cc_start: 0.6899 (ttp-170) cc_final: 0.6578 (ttp-170) REVERT: A 105 ARG cc_start: 0.6933 (ttm170) cc_final: 0.5709 (tpt170) REVERT: A 109 ARG cc_start: 0.8154 (mpt-90) cc_final: 0.7904 (mmm-85) REVERT: B 161 ILE cc_start: 0.8714 (mm) cc_final: 0.8507 (tt) REVERT: C 332 PHE cc_start: 0.8263 (m-10) cc_final: 0.7672 (m-10) REVERT: D 24 MET cc_start: 0.7221 (mtt) cc_final: 0.6983 (ttt) REVERT: L 35 LEU cc_start: 0.8194 (mm) cc_final: 0.7905 (tp) outliers start: 27 outliers final: 22 residues processed: 157 average time/residue: 0.0844 time to fit residues: 17.1753 Evaluate side-chains 163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 108 TRP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 128 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 0.0270 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.140105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108922 restraints weight = 12585.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.107949 restraints weight = 8371.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.108900 restraints weight = 8647.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.109635 restraints weight = 6108.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110031 restraints weight = 5596.812| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6169 Z= 0.120 Angle : 0.616 16.382 8316 Z= 0.303 Chirality : 0.041 0.149 900 Planarity : 0.004 0.046 1065 Dihedral : 7.405 53.878 922 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.05 % Allowed : 22.33 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.31), residues: 761 helix: 2.23 (0.26), residues: 374 sheet: 0.30 (0.45), residues: 143 loop : -1.48 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 91 TYR 0.007 0.001 TYR H 113 PHE 0.017 0.001 PHE B 114 TRP 0.020 0.001 TRP B 93 HIS 0.004 0.001 HIS C 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 6166) covalent geometry : angle 0.61528 / 0.30 ( 8310) SS BOND : bond 0.00701 / 0.34 ( 3) SS BOND : angle 0.93205 / 0.50 ( 6) hydrogen bonds : bond 0.03345 / 2.31 ( 362) hydrogen bonds : angle 3.67266 / 2.72 ( 1071) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9316 (mmmm) cc_final: 0.9086 (mmmm) REVERT: A 105 ARG cc_start: 0.6620 (ttm170) cc_final: 0.5613 (tpt170) REVERT: A 109 ARG cc_start: 0.8210 (mpt-90) cc_final: 0.7893 (mmm-85) REVERT: C 118 HIS cc_start: 0.6882 (OUTLIER) cc_final: 0.6644 (p90) REVERT: C 328 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7737 (tm-30) REVERT: D 24 MET cc_start: 0.7403 (mtt) cc_final: 0.7043 (ttt) REVERT: L 35 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7954 (tp) outliers start: 25 outliers final: 17 residues processed: 157 average time/residue: 0.0844 time to fit residues: 17.2237 Evaluate side-chains 160 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 TRP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 35 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 27 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 58 optimal weight: 0.2980 chunk 25 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.140181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108961 restraints weight = 12633.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.108720 restraints weight = 8408.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.109660 restraints weight = 8151.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110221 restraints weight = 5701.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110798 restraints weight = 5300.740| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6169 Z= 0.122 Angle : 0.612 13.631 8316 Z= 0.304 Chirality : 0.042 0.150 900 Planarity : 0.004 0.046 1065 Dihedral : 7.301 53.857 922 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.72 % Allowed : 23.30 % Favored : 72.98 % 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: 1.09 (0.31), residues: 761 helix: 2.24 (0.26), residues: 374 sheet: 0.11 (0.43), residues: 153 loop : -1.40 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 91 TYR 0.010 0.001 TYR C 377 PHE 0.017 0.001 PHE A 132 TRP 0.017 0.001 TRP B 93 HIS 0.004 0.001 HIS C 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6166) covalent geometry : angle 0.61145 / 0.30 ( 8310) SS BOND : bond 0.00689 / 0.34 ( 3) SS BOND : angle 0.84632 / 0.46 ( 6) hydrogen bonds : bond 0.03362 / 2.33 ( 362) hydrogen bonds : angle 3.71049 / 2.75 ( 1071) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9323 (mmmm) cc_final: 0.8956 (mmmm) REVERT: A 83 ARG cc_start: 0.6288 (ttp-170) cc_final: 0.5932 (ttp-170) REVERT: A 105 ARG cc_start: 0.6705 (ttm170) cc_final: 0.5606 (tpt170) REVERT: A 109 ARG cc_start: 0.8196 (mpt-90) cc_final: 0.7907 (mmm-85) REVERT: B 96 ASP cc_start: 0.7413 (m-30) cc_final: 0.7170 (m-30) REVERT: C 116 MET cc_start: 0.7388 (tpp) cc_final: 0.7106 (tpt) REVERT: C 118 HIS cc_start: 0.6910 (OUTLIER) cc_final: 0.6707 (p90) REVERT: D 24 MET cc_start: 0.7211 (mtt) cc_final: 0.6848 (ttt) REVERT: L 35 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7900 (tp) outliers start: 23 outliers final: 19 residues processed: 153 average time/residue: 0.0871 time to fit residues: 17.2991 Evaluate side-chains 161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 54 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 19 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.138393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.107690 restraints weight = 12645.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.106554 restraints weight = 8552.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107564 restraints weight = 8888.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108322 restraints weight = 6280.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108782 restraints weight = 5751.968| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6169 Z= 0.143 Angle : 0.647 12.037 8316 Z= 0.321 Chirality : 0.042 0.150 900 Planarity : 0.004 0.046 1065 Dihedral : 7.421 55.102 922 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.40 % Allowed : 24.27 % Favored : 72.33 % 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: 1.09 (0.31), residues: 761 helix: 2.20 (0.26), residues: 377 sheet: 0.31 (0.45), residues: 142 loop : -1.46 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 91 TYR 0.011 0.001 TYR H 117 PHE 0.021 0.002 PHE C 332 TRP 0.016 0.001 TRP B 93 HIS 0.004 0.001 HIS C 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 6166) covalent geometry : angle 0.64711 / 0.32 ( 8310) SS BOND : bond 0.00639 / 0.31 ( 3) SS BOND : angle 0.90887 / 0.49 ( 6) hydrogen bonds : bond 0.03457 / 2.38 ( 362) hydrogen bonds : angle 3.80102 / 2.81 ( 1071) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9322 (mmmm) cc_final: 0.8964 (mmmm) REVERT: A 105 ARG cc_start: 0.6972 (ttm170) cc_final: 0.5608 (tpt170) REVERT: A 109 ARG cc_start: 0.8209 (mpt-90) cc_final: 0.7945 (mmm-85) REVERT: A 133 GLN cc_start: 0.8412 (tp40) cc_final: 0.8206 (tp40) REVERT: B 96 ASP cc_start: 0.7455 (m-30) cc_final: 0.7190 (m-30) REVERT: C 167 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8269 (tp30) REVERT: C 332 PHE cc_start: 0.8234 (m-10) cc_final: 0.8023 (m-10) REVERT: D 24 MET cc_start: 0.7319 (mtt) cc_final: 0.6919 (ttt) REVERT: L 35 LEU cc_start: 0.8186 (mm) cc_final: 0.7923 (tp) outliers start: 21 outliers final: 17 residues processed: 155 average time/residue: 0.0791 time to fit residues: 15.7873 Evaluate side-chains 155 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 54 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 40 optimal weight: 0.0000 chunk 18 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.137843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106752 restraints weight = 12545.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107729 restraints weight = 8167.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108474 restraints weight = 7201.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108529 restraints weight = 5639.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.108650 restraints weight = 5132.697| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6169 Z= 0.163 Angle : 0.671 11.605 8316 Z= 0.336 Chirality : 0.043 0.154 900 Planarity : 0.004 0.046 1065 Dihedral : 7.573 55.514 922 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.40 % Allowed : 25.40 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.31), residues: 761 helix: 2.17 (0.26), residues: 378 sheet: 0.21 (0.45), residues: 138 loop : -1.51 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 91 TYR 0.012 0.001 TYR H 117 PHE 0.020 0.002 PHE C 332 TRP 0.027 0.001 TRP B 93 HIS 0.004 0.001 HIS C 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 6166) covalent geometry : angle 0.67066 / 0.34 ( 8310) SS BOND : bond 0.00708 / 0.35 ( 3) SS BOND : angle 1.09739 / 0.59 ( 6) hydrogen bonds : bond 0.03544 / 2.44 ( 362) hydrogen bonds : angle 3.88946 / 2.88 ( 1071) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ILE cc_start: 0.8695 (pt) cc_final: 0.8346 (mt) REVERT: A 36 LYS cc_start: 0.9316 (mmmm) cc_final: 0.9091 (mmmm) REVERT: A 105 ARG cc_start: 0.7020 (ttm170) cc_final: 0.5496 (tpt170) REVERT: A 109 ARG cc_start: 0.8218 (mpt-90) cc_final: 0.8001 (mmm-85) REVERT: C 116 MET cc_start: 0.7393 (tpp) cc_final: 0.7066 (tpt) REVERT: C 118 HIS cc_start: 0.6308 (p90) cc_final: 0.5852 (p90) REVERT: C 156 TYR cc_start: 0.6001 (m-80) cc_final: 0.5361 (m-80) REVERT: C 274 TYR cc_start: 0.9079 (m-80) cc_final: 0.8748 (m-80) REVERT: L 35 LEU cc_start: 0.8280 (mm) cc_final: 0.7992 (tp) outliers start: 21 outliers final: 17 residues processed: 154 average time/residue: 0.0618 time to fit residues: 12.5675 Evaluate side-chains 156 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 41 optimal weight: 0.3980 chunk 75 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.139434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.109135 restraints weight = 12257.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.109499 restraints weight = 8233.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.110395 restraints weight = 7680.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.110832 restraints weight = 5567.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.110893 restraints weight = 5432.045| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6169 Z= 0.130 Angle : 0.670 14.775 8316 Z= 0.333 Chirality : 0.042 0.151 900 Planarity : 0.004 0.045 1065 Dihedral : 7.369 54.789 922 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.07 % Allowed : 25.73 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.31), residues: 761 helix: 2.18 (0.26), residues: 378 sheet: 0.27 (0.45), residues: 143 loop : -1.35 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 184 TYR 0.007 0.001 TYR L 73 PHE 0.021 0.001 PHE B 114 TRP 0.028 0.001 TRP B 93 HIS 0.004 0.001 HIS C 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 6166) covalent geometry : angle 0.66746 / 0.33 ( 8310) SS BOND : bond 0.00567 / 0.28 ( 3) SS BOND : angle 2.36493 / 1.28 ( 6) hydrogen bonds : bond 0.03357 / 2.31 ( 362) hydrogen bonds : angle 3.82214 / 2.82 ( 1071) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1161.66 seconds wall clock time: 20 minutes 46.98 seconds (1246.98 seconds total)