Starting phenix.real_space_refine on Wed Sep 25 00:45:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/09_2024/7ew4_31347.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/09_2024/7ew4_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/09_2024/7ew4_31347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/09_2024/7ew4_31347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/09_2024/7ew4_31347.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/09_2024/7ew4_31347.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} 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: 5.58, per 1000 atoms: 0.62 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: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.17 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: 2.51 Time building geometry restraints manager: 2.69 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.350 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.840 ------------------------------------------------------------------------------- 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 9106 Z= 0.210 Angle : 0.515 12.917 12324 Z= 0.277 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 : 7.77 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.001 TRP B 211 HIS 0.003 0.001 HIS B 54 PHE 0.018 0.001 PHE R 52 TYR 0.019 0.001 TYR R 24 ARG 0.006 0.000 ARG S 18 *********************** 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 fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.060 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: 0.2405 time to fit residues: 43.5495 Evaluate side-chains 101 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 65 optimal weight: 0.0170 chunk 101 optimal weight: 3.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 57 ASN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9106 Z= 0.175 Angle : 0.503 12.270 12324 Z= 0.262 Chirality : 0.040 0.206 1412 Planarity : 0.004 0.055 1550 Dihedral : 3.959 25.765 1294 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.42 % Allowed : 8.23 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1129 helix: 3.29 (0.25), residues: 389 sheet: 0.41 (0.31), residues: 287 loop : -1.24 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.007 0.001 HIS B 225 PHE 0.014 0.001 PHE R 52 TYR 0.010 0.001 TYR R 24 ARG 0.011 0.000 ARG S 67 *********************** 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 116 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.073 Fit side-chains REVERT: A 18 MET cc_start: 0.7733 (mtp) cc_final: 0.7532 (mtt) REVERT: R 257 SER cc_start: 0.7554 (m) cc_final: 0.7237 (m) outliers start: 4 outliers final: 2 residues processed: 115 average time/residue: 0.2451 time to fit residues: 38.1076 Evaluate side-chains 100 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 161 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 56 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 0.0370 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9106 Z= 0.136 Angle : 0.463 12.309 12324 Z= 0.240 Chirality : 0.040 0.215 1412 Planarity : 0.003 0.049 1550 Dihedral : 3.848 28.902 1294 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.25 % Allowed : 10.62 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1129 helix: 3.14 (0.25), residues: 398 sheet: 0.40 (0.31), residues: 285 loop : -1.22 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.007 0.001 HIS R 21 PHE 0.010 0.001 PHE A 189 TYR 0.012 0.001 TYR R 24 ARG 0.007 0.000 ARG S 67 *********************** 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 120 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: R 257 SER cc_start: 0.7639 (m) cc_final: 0.7299 (m) REVERT: R 293 MET cc_start: 0.7362 (mmp) cc_final: 0.7112 (mmm) outliers start: 12 outliers final: 6 residues processed: 115 average time/residue: 0.2379 time to fit residues: 36.9275 Evaluate side-chains 103 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain R residue 97 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 30.0000 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9106 Z= 0.252 Angle : 0.536 12.866 12324 Z= 0.280 Chirality : 0.042 0.253 1412 Planarity : 0.004 0.050 1550 Dihedral : 4.305 33.713 1294 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.56 % Allowed : 11.77 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1129 helix: 2.99 (0.26), residues: 398 sheet: 0.20 (0.30), residues: 288 loop : -1.29 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 36 HIS 0.008 0.001 HIS B 225 PHE 0.013 0.002 PHE A 189 TYR 0.013 0.002 TYR S 102 ARG 0.006 0.000 ARG S 67 *********************** 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 113 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: R 257 SER cc_start: 0.7731 (m) cc_final: 0.7361 (m) REVERT: R 293 MET cc_start: 0.7374 (mmp) cc_final: 0.7131 (mmm) REVERT: S 230 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.5945 (tmm) outliers start: 15 outliers final: 7 residues processed: 108 average time/residue: 0.2558 time to fit residues: 37.2608 Evaluate side-chains 99 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 96 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN S 194 ASN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 0.004 0.048 9106 Z= 0.251 Angle : 0.536 13.092 12324 Z= 0.281 Chirality : 0.042 0.250 1412 Planarity : 0.004 0.049 1550 Dihedral : 4.434 35.309 1294 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.08 % Allowed : 13.02 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1129 helix: 2.94 (0.25), residues: 393 sheet: 0.26 (0.31), residues: 273 loop : -1.34 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 36 HIS 0.009 0.001 HIS R 21 PHE 0.013 0.002 PHE B 199 TYR 0.014 0.002 TYR R 24 ARG 0.007 0.000 ARG S 67 *********************** 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 123 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: R 257 SER cc_start: 0.7818 (m) cc_final: 0.7472 (m) REVERT: R 293 MET cc_start: 0.7338 (mmp) cc_final: 0.7123 (mmm) REVERT: S 67 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.5807 (tmm160) REVERT: S 230 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6103 (tmm) outliers start: 20 outliers final: 9 residues processed: 115 average time/residue: 0.2456 time to fit residues: 38.2383 Evaluate side-chains 107 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 331 SER 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 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 97 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9106 Z= 0.166 Angle : 0.497 13.285 12324 Z= 0.259 Chirality : 0.040 0.258 1412 Planarity : 0.003 0.047 1550 Dihedral : 4.137 33.309 1294 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.67 % Allowed : 14.27 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1129 helix: 3.03 (0.25), residues: 393 sheet: 0.35 (0.31), residues: 272 loop : -1.26 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.007 0.001 HIS R 21 PHE 0.010 0.001 PHE A 189 TYR 0.012 0.001 TYR R 219 ARG 0.006 0.000 ARG S 67 *********************** 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 122 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: B 338 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7889 (mp) REVERT: R 257 SER cc_start: 0.7720 (m) cc_final: 0.7351 (m) REVERT: S 67 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6084 (tmm160) REVERT: S 230 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.5768 (tmm) outliers start: 16 outliers final: 7 residues processed: 117 average time/residue: 0.2444 time to fit residues: 38.2883 Evaluate side-chains 107 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 0.0050 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.0770 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.5352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9106 Z= 0.143 Angle : 0.488 12.992 12324 Z= 0.251 Chirality : 0.040 0.270 1412 Planarity : 0.003 0.047 1550 Dihedral : 3.932 31.197 1294 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.46 % Allowed : 14.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1129 helix: 3.11 (0.26), residues: 393 sheet: 0.24 (0.30), residues: 289 loop : -1.18 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.006 0.001 HIS R 21 PHE 0.010 0.001 PHE S 212 TYR 0.010 0.001 TYR R 219 ARG 0.005 0.000 ARG S 67 *********************** 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 117 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: B 338 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7839 (mp) REVERT: R 257 SER cc_start: 0.7660 (m) cc_final: 0.7283 (m) REVERT: R 293 MET cc_start: 0.7243 (mmp) cc_final: 0.6839 (mmm) REVERT: S 67 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6180 (tmm160) REVERT: S 230 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6083 (tmm) outliers start: 14 outliers final: 9 residues processed: 112 average time/residue: 0.2572 time to fit residues: 38.8305 Evaluate side-chains 109 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 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 64 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.0070 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9106 Z= 0.143 Angle : 0.485 13.106 12324 Z= 0.250 Chirality : 0.040 0.284 1412 Planarity : 0.003 0.047 1550 Dihedral : 3.837 30.428 1294 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.35 % Allowed : 15.10 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1129 helix: 2.93 (0.26), residues: 401 sheet: 0.27 (0.30), residues: 287 loop : -1.26 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS R 21 PHE 0.009 0.001 PHE A 189 TYR 0.010 0.001 TYR R 219 ARG 0.004 0.000 ARG S 67 *********************** 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 114 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 318 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6576 (pm20) REVERT: B 338 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7821 (mp) REVERT: R 118 MET cc_start: 0.6530 (mmp) cc_final: 0.6182 (mmt) REVERT: R 257 SER cc_start: 0.7642 (m) cc_final: 0.7266 (m) REVERT: R 293 MET cc_start: 0.7213 (mmp) cc_final: 0.6805 (mmm) REVERT: S 67 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6231 (tmm160) REVERT: S 230 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6050 (tmm) outliers start: 13 outliers final: 9 residues processed: 110 average time/residue: 0.2530 time to fit residues: 37.2491 Evaluate side-chains 111 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 247 ASP 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 94 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9106 Z= 0.163 Angle : 0.494 12.892 12324 Z= 0.256 Chirality : 0.040 0.297 1412 Planarity : 0.003 0.048 1550 Dihedral : 3.897 31.190 1294 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.56 % Allowed : 14.69 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1129 helix: 3.08 (0.26), residues: 395 sheet: 0.24 (0.31), residues: 284 loop : -1.24 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.005 0.001 HIS R 21 PHE 0.010 0.001 PHE A 189 TYR 0.012 0.001 TYR R 24 ARG 0.004 0.000 ARG S 67 *********************** 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 117 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: B 338 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7898 (mp) REVERT: R 257 SER cc_start: 0.7700 (m) cc_final: 0.7307 (m) REVERT: R 293 MET cc_start: 0.7208 (mmp) cc_final: 0.6820 (mmm) REVERT: S 67 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6190 (tmm160) REVERT: S 230 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.5949 (tmm) outliers start: 15 outliers final: 9 residues processed: 113 average time/residue: 0.2482 time to fit residues: 37.7494 Evaluate side-chains 110 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 247 ASP 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 64 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 0.2980 chunk 102 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9106 Z= 0.159 Angle : 0.505 13.038 12324 Z= 0.260 Chirality : 0.040 0.303 1412 Planarity : 0.003 0.048 1550 Dihedral : 3.869 31.265 1294 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.35 % Allowed : 15.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1129 helix: 3.11 (0.26), residues: 394 sheet: 0.27 (0.31), residues: 282 loop : -1.17 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.005 0.001 HIS R 21 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR R 24 ARG 0.004 0.000 ARG S 67 ********************** 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 fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 318 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6559 (pm20) REVERT: B 234 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7509 (t80) REVERT: B 338 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7892 (mp) REVERT: R 257 SER cc_start: 0.7690 (m) cc_final: 0.7291 (m) REVERT: R 293 MET cc_start: 0.7215 (mmp) cc_final: 0.6837 (mmm) REVERT: S 67 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6278 (tmm160) REVERT: S 230 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.5975 (tmm) outliers start: 13 outliers final: 8 residues processed: 110 average time/residue: 0.2477 time to fit residues: 36.5961 Evaluate side-chains 112 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 247 ASP 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 27 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 0.2980 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.184042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143380 restraints weight = 11099.391| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.19 r_work: 0.3464 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9106 Z= 0.176 Angle : 0.511 12.929 12324 Z= 0.264 Chirality : 0.041 0.311 1412 Planarity : 0.003 0.048 1550 Dihedral : 3.933 31.980 1294 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.67 % Allowed : 14.79 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1129 helix: 3.07 (0.25), residues: 395 sheet: 0.26 (0.31), residues: 280 loop : -1.23 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.005 0.001 HIS R 21 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR R 219 ARG 0.004 0.000 ARG S 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2102.90 seconds wall clock time: 38 minutes 20.35 seconds (2300.35 seconds total)