Starting phenix.real_space_refine on Sat Aug 23 02:25:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ew4_31347/08_2025/7ew4_31347.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ew4_31347/08_2025/7ew4_31347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ew4_31347/08_2025/7ew4_31347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ew4_31347/08_2025/7ew4_31347.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ew4_31347/08_2025/7ew4_31347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ew4_31347/08_2025/7ew4_31347.map" } resolution = 3.2 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= 0.002 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 48 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5692 2.51 5 N 1508 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8929 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1820 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2211 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'JF9': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.43, per 1000 atoms: 0.27 Number of scatterers: 8929 At special positions: 0 Unit cell: (92.34, 122.265, 129.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 1664 8.00 N 1508 7.00 C 5692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 178 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 269 " - pdb=" SG CYS R 274 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 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: 0.81 Conformation dependent library (CDL) restraints added in 362.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 38.3% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.718A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.519A pdb=" N PHE A 259 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 260' Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.539A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.542A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 351 removed outlier: 4.121A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 8 through 23 removed outlier: 4.357A pdb=" N ALA C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.557A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 25 removed outlier: 3.783A pdb=" N VAL R 25 " --> pdb=" O HIS R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 67 removed outlier: 3.672A pdb=" N ASN R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 102 removed outlier: 3.848A pdb=" N PHE R 77 " --> pdb=" O ARG R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 125 removed outlier: 3.602A pdb=" N PHE R 112 " --> pdb=" O PRO R 108 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET R 118 " --> pdb=" O ARG R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 142 removed outlier: 3.746A pdb=" N LYS R 142 " --> pdb=" O LEU R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 175 removed outlier: 4.142A pdb=" N VAL R 154 " --> pdb=" O LYS R 150 " (cutoff:3.500A) Proline residue: R 172 - end of helix Processing helix chain 'R' and resid 193 through 228 removed outlier: 3.580A pdb=" N ILE R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS R 228 " --> pdb=" O SER R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 269 Proline residue: R 258 - end of helix Processing helix chain 'R' and resid 279 through 301 removed outlier: 3.816A pdb=" N PHE R 283 " --> pdb=" O LYS R 279 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU R 286 " --> pdb=" O TRP R 282 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER R 291 " --> pdb=" O ALA R 287 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA R 292 " --> pdb=" O VAL R 288 " (cutoff:3.500A) Proline residue: R 295 - end of helix removed outlier: 3.765A pdb=" N ALA R 301 " --> pdb=" O ILE R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 312 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.993A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.687A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.687A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.853A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.075A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.123A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.536A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.332A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.731A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.694A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.874A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.516A pdb=" N THR S 141 " --> pdb=" O ARG S 160 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 5.484A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 225 through 227 460 hydrogen bonds defined for protein. 1287 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: 1.44 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1448 1.31 - 1.43: 2470 1.43 - 1.56: 5093 1.56 - 1.69: 2 1.69 - 1.82: 93 Bond restraints: 9106 Sorted by residual: bond pdb=" C14 JF9 R 401 " pdb=" N7 JF9 R 401 " ideal model delta sigma weight residual 1.338 1.497 -0.159 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C19 JF9 R 401 " pdb=" C21 JF9 R 401 " ideal model delta sigma weight residual 1.459 1.540 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C8 JF9 R 401 " pdb=" N7 JF9 R 401 " ideal model delta sigma weight residual 1.467 1.516 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C14 JF9 R 401 " pdb=" O15 JF9 R 401 " ideal model delta sigma weight residual 1.223 1.178 0.045 2.00e-02 2.50e+03 4.96e+00 bond pdb=" C14 JF9 R 401 " pdb=" C16 JF9 R 401 " ideal model delta sigma weight residual 1.500 1.542 -0.042 2.00e-02 2.50e+03 4.36e+00 ... (remaining 9101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 12257 2.58 - 5.17: 59 5.17 - 7.75: 6 7.75 - 10.33: 1 10.33 - 12.92: 1 Bond angle restraints: 12324 Sorted by residual: angle pdb=" C19 JF9 R 401 " pdb=" C21 JF9 R 401 " pdb=" C22 JF9 R 401 " ideal model delta sigma weight residual 121.01 133.93 -12.92 3.00e+00 1.11e-01 1.85e+01 angle pdb=" CA LEU R 97 " pdb=" CB LEU R 97 " pdb=" CG LEU R 97 " ideal model delta sigma weight residual 116.30 124.60 -8.30 3.50e+00 8.16e-02 5.63e+00 angle pdb=" C12 JF9 R 401 " pdb=" C13 JF9 R 401 " pdb=" C8 JF9 R 401 " ideal model delta sigma weight residual 109.43 116.39 -6.96 3.00e+00 1.11e-01 5.38e+00 angle pdb=" C14 JF9 R 401 " pdb=" C16 JF9 R 401 " pdb=" N17 JF9 R 401 " ideal model delta sigma weight residual 120.71 127.21 -6.50 3.00e+00 1.11e-01 4.69e+00 angle pdb=" C LYS A 54 " pdb=" N ILE A 55 " pdb=" CA ILE A 55 " ideal model delta sigma weight residual 121.70 125.54 -3.84 1.80e+00 3.09e-01 4.56e+00 ... (remaining 12319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 4891 16.98 - 33.95: 445 33.95 - 50.93: 89 50.93 - 67.91: 9 67.91 - 84.88: 8 Dihedral angle restraints: 5442 sinusoidal: 2120 harmonic: 3322 Sorted by residual: dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 52.64 40.36 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CB CYS R 178 " pdb=" SG CYS R 178 " pdb=" SG CYS R 185 " pdb=" CB CYS R 185 " ideal model delta sinusoidal sigma weight residual -86.00 -114.71 28.71 1 1.00e+01 1.00e-02 1.18e+01 dihedral pdb=" CA ASP B 195 " pdb=" CB ASP B 195 " pdb=" CG ASP B 195 " pdb=" OD1 ASP B 195 " ideal model delta sinusoidal sigma weight residual -30.00 -87.19 57.19 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 5439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1161 0.050 - 0.100: 211 0.100 - 0.150: 36 0.150 - 0.200: 3 0.200 - 0.250: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" C8 JF9 R 401 " pdb=" C13 JF9 R 401 " pdb=" C9 JF9 R 401 " pdb=" N7 JF9 R 401 " both_signs ideal model delta sigma weight residual False 2.37 2.62 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C21 JF9 R 401 " pdb=" C19 JF9 R 401 " pdb=" C22 JF9 R 401 " pdb=" C23 JF9 R 401 " both_signs ideal model delta sigma weight residual True 2.30 -2.10 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CB THR S 91 " pdb=" CA THR S 91 " pdb=" OG1 THR S 91 " pdb=" CG2 THR S 91 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 1409 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 182 " -0.062 5.00e-02 4.00e+02 9.57e-02 1.46e+01 pdb=" N PRO R 183 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO R 183 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO R 183 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN S 13 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO S 14 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO S 14 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO S 14 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO B 236 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.027 5.00e-02 4.00e+02 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1467 2.77 - 3.30: 8300 3.30 - 3.83: 14500 3.83 - 4.37: 16511 4.37 - 4.90: 29776 Nonbonded interactions: 70554 Sorted by model distance: nonbonded pdb=" OG SER R 186 " pdb=" O LEU R 189 " model vdw 2.237 3.040 nonbonded pdb=" O ILE S 138 " pdb=" OG1 THR S 238 " model vdw 2.238 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.254 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.282 3.040 nonbonded pdb=" O PHE S 29 " pdb=" NH2 ARG S 72 " model vdw 2.291 3.120 ... (remaining 70549 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.830 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 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 : 0.003 0.159 9109 Z= 0.152 Angle : 0.515 12.917 12330 Z= 0.278 Chirality : 0.040 0.250 1412 Planarity : 0.004 0.096 1550 Dihedral : 13.407 84.884 3287 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.25), residues: 1129 helix: 2.98 (0.26), residues: 399 sheet: 0.26 (0.31), residues: 288 loop : -1.21 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 18 TYR 0.019 0.001 TYR R 24 PHE 0.018 0.001 PHE R 52 TRP 0.018 0.001 TRP B 211 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9106) covalent geometry : angle 0.51462 (12324) SS BOND : bond 0.00222 ( 3) SS BOND : angle 0.90607 ( 6) hydrogen bonds : bond 0.13011 ( 443) hydrogen bonds : angle 4.89759 ( 1287) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.390 Fit side-chains REVERT: A 18 MET cc_start: 0.7675 (mtp) cc_final: 0.7467 (mtt) REVERT: R 106 LEU cc_start: 0.7822 (tp) cc_final: 0.7600 (tp) REVERT: R 257 SER cc_start: 0.7327 (m) cc_final: 0.7054 (m) REVERT: S 220 GLU cc_start: 0.7713 (mp0) cc_final: 0.7511 (mp0) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1164 time to fit residues: 21.0491 Evaluate side-chains 101 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0170 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 125 ASN R 57 ASN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.186334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148996 restraints weight = 11352.181| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.05 r_work: 0.3511 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9109 Z= 0.148 Angle : 0.543 12.180 12330 Z= 0.284 Chirality : 0.042 0.207 1412 Planarity : 0.004 0.053 1550 Dihedral : 4.225 28.600 1294 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.62 % Allowed : 8.54 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.25), residues: 1129 helix: 3.01 (0.25), residues: 397 sheet: 0.42 (0.31), residues: 282 loop : -1.34 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 67 TYR 0.012 0.002 TYR R 24 PHE 0.014 0.002 PHE R 52 TRP 0.013 0.001 TRP B 211 HIS 0.010 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9106) covalent geometry : angle 0.54293 (12324) SS BOND : bond 0.00380 ( 3) SS BOND : angle 1.21347 ( 6) hydrogen bonds : bond 0.04299 ( 443) hydrogen bonds : angle 4.22835 ( 1287) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.349 Fit side-chains REVERT: C 42 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7735 (mm-30) REVERT: R 257 SER cc_start: 0.7972 (m) cc_final: 0.7600 (m) REVERT: R 293 MET cc_start: 0.7382 (mmt) cc_final: 0.7014 (mmm) outliers start: 6 outliers final: 3 residues processed: 111 average time/residue: 0.1203 time to fit residues: 17.6707 Evaluate side-chains 98 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 99 optimal weight: 0.0370 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.180183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.139289 restraints weight = 11142.934| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.16 r_work: 0.3388 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9109 Z= 0.164 Angle : 0.544 12.370 12330 Z= 0.286 Chirality : 0.042 0.241 1412 Planarity : 0.004 0.050 1550 Dihedral : 4.505 35.992 1294 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.77 % Allowed : 11.88 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.25), residues: 1129 helix: 2.79 (0.26), residues: 403 sheet: 0.16 (0.30), residues: 283 loop : -1.36 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 67 TYR 0.012 0.002 TYR B 105 PHE 0.013 0.002 PHE B 199 TRP 0.013 0.001 TRP S 36 HIS 0.009 0.002 HIS R 21 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9106) covalent geometry : angle 0.54385 (12324) SS BOND : bond 0.00437 ( 3) SS BOND : angle 1.11555 ( 6) hydrogen bonds : bond 0.04746 ( 443) hydrogen bonds : angle 4.27676 ( 1287) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: C 42 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7771 (mm-30) REVERT: R 195 LYS cc_start: 0.5880 (tmtt) cc_final: 0.5640 (tmtt) REVERT: R 257 SER cc_start: 0.8175 (m) cc_final: 0.7784 (m) REVERT: R 293 MET cc_start: 0.7593 (mmt) cc_final: 0.7230 (mmm) REVERT: S 67 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6148 (tmm160) REVERT: S 230 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.5962 (tmm) outliers start: 17 outliers final: 7 residues processed: 116 average time/residue: 0.1261 time to fit residues: 19.2458 Evaluate side-chains 104 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 231 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 = 0.4129 r_free = 0.4129 target = 0.179197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.136976 restraints weight = 11261.658| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.34 r_work: 0.3408 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9109 Z= 0.161 Angle : 0.538 13.072 12330 Z= 0.283 Chirality : 0.042 0.240 1412 Planarity : 0.004 0.050 1550 Dihedral : 4.527 36.997 1294 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.88 % Allowed : 13.65 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.25), residues: 1129 helix: 2.81 (0.25), residues: 398 sheet: 0.09 (0.30), residues: 284 loop : -1.38 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 67 TYR 0.013 0.002 TYR R 219 PHE 0.014 0.002 PHE B 199 TRP 0.013 0.001 TRP S 36 HIS 0.007 0.001 HIS R 21 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9106) covalent geometry : angle 0.53794 (12324) SS BOND : bond 0.00428 ( 3) SS BOND : angle 1.09509 ( 6) hydrogen bonds : bond 0.04591 ( 443) hydrogen bonds : angle 4.28382 ( 1287) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7180 (m-30) cc_final: 0.6957 (m-30) REVERT: C 42 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7769 (mm-30) REVERT: C 58 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7446 (mp0) REVERT: R 257 SER cc_start: 0.8252 (m) cc_final: 0.7883 (m) REVERT: S 67 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.6151 (tmm160) REVERT: S 230 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.5902 (tmm) REVERT: S 239 PHE cc_start: 0.5305 (OUTLIER) cc_final: 0.5032 (m-10) outliers start: 18 outliers final: 7 residues processed: 112 average time/residue: 0.1158 time to fit residues: 17.4177 Evaluate side-chains 106 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 239 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.183257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141907 restraints weight = 11128.848| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.40 r_work: 0.3396 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9109 Z= 0.107 Angle : 0.493 12.662 12330 Z= 0.257 Chirality : 0.040 0.248 1412 Planarity : 0.003 0.048 1550 Dihedral : 4.166 34.568 1294 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.98 % Allowed : 14.38 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.25), residues: 1129 helix: 2.96 (0.25), residues: 397 sheet: 0.35 (0.32), residues: 268 loop : -1.36 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 67 TYR 0.014 0.001 TYR R 24 PHE 0.010 0.001 PHE A 189 TRP 0.013 0.001 TRP B 211 HIS 0.006 0.001 HIS R 21 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9106) covalent geometry : angle 0.49228 (12324) SS BOND : bond 0.00363 ( 3) SS BOND : angle 0.87778 ( 6) hydrogen bonds : bond 0.03671 ( 443) hydrogen bonds : angle 4.02733 ( 1287) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: B 338 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.7990 (mp) REVERT: C 42 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7771 (mm-30) REVERT: C 58 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7342 (mp0) REVERT: R 293 MET cc_start: 0.7406 (mmt) cc_final: 0.7068 (mmp) REVERT: S 6 GLU cc_start: 0.7192 (mp0) cc_final: 0.6969 (mp0) REVERT: S 67 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6177 (tmm160) REVERT: S 230 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.5635 (tmm) outliers start: 19 outliers final: 10 residues processed: 116 average time/residue: 0.1166 time to fit residues: 18.1307 Evaluate side-chains 110 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 231 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 = 0.4143 r_free = 0.4143 target = 0.180701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.139265 restraints weight = 11099.548| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.22 r_work: 0.3412 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9109 Z= 0.135 Angle : 0.519 12.991 12330 Z= 0.270 Chirality : 0.041 0.265 1412 Planarity : 0.003 0.049 1550 Dihedral : 4.276 34.849 1294 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.88 % Allowed : 15.10 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.25), residues: 1129 helix: 2.90 (0.25), residues: 398 sheet: 0.24 (0.31), residues: 272 loop : -1.34 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 67 TYR 0.013 0.001 TYR R 219 PHE 0.012 0.001 PHE A 189 TRP 0.010 0.001 TRP S 36 HIS 0.006 0.001 HIS R 21 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9106) covalent geometry : angle 0.51850 (12324) SS BOND : bond 0.00397 ( 3) SS BOND : angle 0.98180 ( 6) hydrogen bonds : bond 0.04140 ( 443) hydrogen bonds : angle 4.08410 ( 1287) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: B 197 ARG cc_start: 0.7403 (mmm160) cc_final: 0.7198 (mmt90) REVERT: B 262 MET cc_start: 0.8103 (ttm) cc_final: 0.7844 (ttm) REVERT: B 338 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8020 (mp) REVERT: C 42 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7802 (mm-30) REVERT: C 58 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7423 (mp0) REVERT: R 143 MET cc_start: 0.7601 (mmt) cc_final: 0.7248 (mmp) REVERT: R 293 MET cc_start: 0.7425 (mmt) cc_final: 0.7069 (mmp) REVERT: S 67 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.6299 (tmm160) REVERT: S 230 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.5746 (tmm) outliers start: 18 outliers final: 10 residues processed: 113 average time/residue: 0.1152 time to fit residues: 17.6384 Evaluate side-chains 106 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 0.0470 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 231 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 = 0.4138 r_free = 0.4138 target = 0.180201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.138867 restraints weight = 11245.578| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.24 r_work: 0.3386 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9109 Z= 0.149 Angle : 0.532 13.029 12330 Z= 0.278 Chirality : 0.042 0.279 1412 Planarity : 0.003 0.049 1550 Dihedral : 4.384 36.052 1294 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.98 % Allowed : 15.94 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.25), residues: 1129 helix: 2.82 (0.25), residues: 400 sheet: 0.22 (0.31), residues: 271 loop : -1.38 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 67 TYR 0.013 0.001 TYR R 219 PHE 0.013 0.001 PHE B 199 TRP 0.012 0.001 TRP S 36 HIS 0.009 0.001 HIS R 21 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9106) covalent geometry : angle 0.53140 (12324) SS BOND : bond 0.00443 ( 3) SS BOND : angle 1.06268 ( 6) hydrogen bonds : bond 0.04320 ( 443) hydrogen bonds : angle 4.12959 ( 1287) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: B 197 ARG cc_start: 0.7433 (mmm160) cc_final: 0.7211 (mmt90) REVERT: B 234 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.7673 (t80) REVERT: B 338 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8040 (mp) REVERT: C 42 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7788 (mm-30) REVERT: C 58 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7435 (mp0) REVERT: R 106 LEU cc_start: 0.8781 (tp) cc_final: 0.8474 (tp) REVERT: R 143 MET cc_start: 0.7674 (mmt) cc_final: 0.7391 (mmp) REVERT: R 293 MET cc_start: 0.7583 (mmt) cc_final: 0.7163 (mmm) REVERT: S 67 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6244 (tmm160) REVERT: S 230 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6135 (tmm) outliers start: 19 outliers final: 11 residues processed: 114 average time/residue: 0.1182 time to fit residues: 18.0101 Evaluate side-chains 111 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 90 optimal weight: 0.0570 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.184006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.143027 restraints weight = 11306.499| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.39 r_work: 0.3447 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9109 Z= 0.104 Angle : 0.492 13.415 12330 Z= 0.256 Chirality : 0.040 0.289 1412 Planarity : 0.003 0.047 1550 Dihedral : 4.096 33.896 1294 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.77 % Allowed : 16.25 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.25), residues: 1129 helix: 2.97 (0.26), residues: 399 sheet: 0.24 (0.31), residues: 278 loop : -1.28 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 67 TYR 0.012 0.001 TYR R 219 PHE 0.010 0.001 PHE S 212 TRP 0.012 0.001 TRP B 211 HIS 0.006 0.001 HIS R 21 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9106) covalent geometry : angle 0.49201 (12324) SS BOND : bond 0.00275 ( 3) SS BOND : angle 0.76924 ( 6) hydrogen bonds : bond 0.03494 ( 443) hydrogen bonds : angle 3.90240 ( 1287) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: B 197 ARG cc_start: 0.7249 (mmm160) cc_final: 0.7008 (mmt90) REVERT: B 234 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.7543 (t80) REVERT: B 338 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.7891 (mp) REVERT: C 42 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7746 (mm-30) REVERT: R 143 MET cc_start: 0.7546 (mmt) cc_final: 0.7206 (mmp) REVERT: R 293 MET cc_start: 0.7316 (mmt) cc_final: 0.6896 (mmm) REVERT: S 67 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6348 (tmm160) REVERT: S 83 MET cc_start: 0.7550 (mtm) cc_final: 0.7316 (mtp) REVERT: S 230 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.5308 (tmm) outliers start: 17 outliers final: 9 residues processed: 114 average time/residue: 0.1165 time to fit residues: 17.9785 Evaluate side-chains 112 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.177373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.135510 restraints weight = 11265.114| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.37 r_work: 0.3377 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 9109 Z= 0.235 Angle : 0.632 13.172 12330 Z= 0.330 Chirality : 0.045 0.316 1412 Planarity : 0.004 0.051 1550 Dihedral : 4.821 38.882 1294 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.88 % Allowed : 16.15 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.25), residues: 1129 helix: 2.59 (0.26), residues: 401 sheet: -0.06 (0.31), residues: 279 loop : -1.40 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 67 TYR 0.015 0.002 TYR S 175 PHE 0.019 0.002 PHE B 199 TRP 0.015 0.002 TRP S 36 HIS 0.009 0.002 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 9106) covalent geometry : angle 0.63178 (12324) SS BOND : bond 0.00532 ( 3) SS BOND : angle 1.34154 ( 6) hydrogen bonds : bond 0.05384 ( 443) hydrogen bonds : angle 4.38876 ( 1287) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: B 197 ARG cc_start: 0.7508 (mmm160) cc_final: 0.7290 (mmt90) REVERT: B 234 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.7665 (t80) REVERT: B 338 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8085 (mp) REVERT: C 42 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7775 (mm-30) REVERT: R 106 LEU cc_start: 0.8723 (tp) cc_final: 0.8503 (tp) REVERT: S 67 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.6247 (tmm160) REVERT: S 230 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6337 (tmm) outliers start: 18 outliers final: 10 residues processed: 110 average time/residue: 0.1177 time to fit residues: 17.4740 Evaluate side-chains 104 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 88 optimal weight: 0.0570 chunk 76 optimal weight: 0.0570 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.183277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.142576 restraints weight = 11113.834| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.18 r_work: 0.3455 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9109 Z= 0.105 Angle : 0.511 13.783 12330 Z= 0.267 Chirality : 0.041 0.291 1412 Planarity : 0.003 0.047 1550 Dihedral : 4.197 34.796 1294 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.35 % Allowed : 16.77 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.25), residues: 1129 helix: 2.87 (0.26), residues: 400 sheet: 0.30 (0.32), residues: 269 loop : -1.39 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 67 TYR 0.017 0.001 TYR R 24 PHE 0.010 0.001 PHE A 189 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS R 21 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9106) covalent geometry : angle 0.51061 (12324) SS BOND : bond 0.00444 ( 3) SS BOND : angle 0.87193 ( 6) hydrogen bonds : bond 0.03430 ( 443) hydrogen bonds : angle 3.94680 ( 1287) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.6976 (m-30) cc_final: 0.6655 (m-30) REVERT: B 197 ARG cc_start: 0.7429 (mmm160) cc_final: 0.7164 (mmt90) REVERT: B 234 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7607 (t80) REVERT: B 323 ASP cc_start: 0.7783 (p0) cc_final: 0.7552 (p0) REVERT: B 338 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.7919 (mp) REVERT: C 42 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7821 (mm-30) REVERT: R 106 LEU cc_start: 0.8722 (tp) cc_final: 0.8514 (tp) REVERT: R 143 MET cc_start: 0.7765 (mmt) cc_final: 0.7536 (mmp) REVERT: R 293 MET cc_start: 0.7561 (mmt) cc_final: 0.7126 (mmm) REVERT: S 67 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6286 (tmm160) outliers start: 13 outliers final: 8 residues processed: 109 average time/residue: 0.1278 time to fit residues: 18.4142 Evaluate side-chains 110 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 37 optimal weight: 0.0970 chunk 45 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.178128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.136284 restraints weight = 11174.600| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.29 r_work: 0.3383 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9109 Z= 0.201 Angle : 0.605 13.574 12330 Z= 0.315 Chirality : 0.044 0.316 1412 Planarity : 0.004 0.049 1550 Dihedral : 4.656 37.945 1294 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.67 % Allowed : 16.46 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.25), residues: 1129 helix: 2.66 (0.26), residues: 399 sheet: -0.10 (0.31), residues: 278 loop : -1.41 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 67 TYR 0.017 0.002 TYR R 24 PHE 0.017 0.002 PHE B 199 TRP 0.014 0.001 TRP S 36 HIS 0.008 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 9106) covalent geometry : angle 0.60460 (12324) SS BOND : bond 0.00529 ( 3) SS BOND : angle 1.27447 ( 6) hydrogen bonds : bond 0.04971 ( 443) hydrogen bonds : angle 4.29070 ( 1287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2856.77 seconds wall clock time: 49 minutes 45.30 seconds (2985.30 seconds total)