Starting phenix.real_space_refine on Tue Mar 3 20:16:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w7e_32342/03_2026/7w7e_32342.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w7e_32342/03_2026/7w7e_32342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w7e_32342/03_2026/7w7e_32342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w7e_32342/03_2026/7w7e_32342.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w7e_32342/03_2026/7w7e_32342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w7e_32342/03_2026/7w7e_32342.map" } resolution = 3.4 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= -0.001 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5440 2.51 5 N 1449 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8524 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1649 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "H" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2083 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'W58': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 2.14, per 1000 atoms: 0.25 Number of scatterers: 8524 At special positions: 0 Unit cell: (91.8, 115.6, 124.95, 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 59 16.00 O 1576 8.00 N 1449 7.00 C 5440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 121 " - pdb=" SG CYS R 203 " 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: 0.90 Conformation dependent library (CDL) restraints added in 336.2 milliseconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2036 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 14 sheets defined 34.5% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 6 through 29 removed outlier: 3.976A pdb=" N ARG A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.588A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 296 through 311 removed outlier: 3.685A pdb=" N ALA A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 348 removed outlier: 3.505A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.826A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.594A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.712A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.539A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'R' and resid 46 through 76 removed outlier: 3.601A pdb=" N PHE R 74 " --> pdb=" O ILE R 70 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER R 76 " --> pdb=" O ALA R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 111 removed outlier: 3.501A pdb=" N VAL R 88 " --> pdb=" O ASN R 84 " (cutoff:3.500A) Proline residue: R 103 - end of helix Processing helix chain 'R' and resid 121 through 152 removed outlier: 4.014A pdb=" N LEU R 139 " --> pdb=" O SER R 135 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS R 140 " --> pdb=" O ILE R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 158 removed outlier: 3.558A pdb=" N TYR R 156 " --> pdb=" O GLN R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 181 removed outlier: 3.509A pdb=" N ILE R 165 " --> pdb=" O THR R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 220 removed outlier: 3.976A pdb=" N VAL R 212 " --> pdb=" O GLN R 208 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE R 213 " --> pdb=" O LYS R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 242 removed outlier: 3.536A pdb=" N ILE R 234 " --> pdb=" O VAL R 230 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR R 242 " --> pdb=" O ALA R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 380 through 415 removed outlier: 4.076A pdb=" N GLU R 384 " --> pdb=" O ARG R 380 " (cutoff:3.500A) Proline residue: R 404 - end of helix removed outlier: 4.105A pdb=" N VAL R 414 " --> pdb=" O THR R 410 " (cutoff:3.500A) Processing helix chain 'R' and resid 421 through 443 removed outlier: 3.989A pdb=" N PHE R 425 " --> pdb=" O THR R 421 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER R 434 " --> pdb=" O GLY R 430 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER R 435 " --> pdb=" O TYR R 431 " (cutoff:3.500A) Proline residue: R 438 - end of helix Processing helix chain 'R' and resid 445 through 457 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188 removed outlier: 3.529A pdb=" N LEU A 195 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 192 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 188 removed outlier: 6.629A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.615A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.938A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 112 through 114 removed outlier: 3.528A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 Processing sheet with id=AA7, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.569A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.939A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 253 through 254 removed outlier: 3.877A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.437A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.792A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 47 through 51 removed outlier: 6.667A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 182 through 183 removed outlier: 5.825A pdb=" N LEU H 175 " --> pdb=" O LEU H 166 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU H 166 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE H 177 " --> pdb=" O TRP H 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 193 through 195 339 hydrogen bonds defined for protein. 966 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: 1.27 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1372 1.31 - 1.44: 2436 1.44 - 1.56: 4813 1.56 - 1.68: 1 1.68 - 1.81: 82 Bond restraints: 8704 Sorted by residual: bond pdb=" C13 W58 R 501 " pdb=" N12 W58 R 501 " ideal model delta sigma weight residual 1.463 1.191 0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" C13 W58 R 501 " pdb=" C14 W58 R 501 " ideal model delta sigma weight residual 1.523 1.713 -0.190 2.00e-02 2.50e+03 9.02e+01 bond pdb=" C1 W58 R 501 " pdb=" C2 W58 R 501 " ideal model delta sigma weight residual 1.339 1.491 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C1 W58 R 501 " pdb=" C14 W58 R 501 " ideal model delta sigma weight residual 1.500 1.360 0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C11 W58 R 501 " pdb=" N12 W58 R 501 " ideal model delta sigma weight residual 1.462 1.580 -0.118 2.00e-02 2.50e+03 3.50e+01 ... (remaining 8699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 11622 2.37 - 4.73: 144 4.73 - 7.10: 24 7.10 - 9.46: 3 9.46 - 11.83: 1 Bond angle restraints: 11794 Sorted by residual: angle pdb=" C SER H 133 " pdb=" N SER H 134 " pdb=" CA SER H 134 " ideal model delta sigma weight residual 121.50 133.33 -11.83 1.43e+00 4.89e-01 6.84e+01 angle pdb=" C ALA B 309 " pdb=" N GLY B 310 " pdb=" CA GLY B 310 " ideal model delta sigma weight residual 120.00 127.46 -7.46 1.10e+00 8.26e-01 4.60e+01 angle pdb=" N TYR R 409 " pdb=" CA TYR R 409 " pdb=" C TYR R 409 " ideal model delta sigma weight residual 111.07 104.64 6.43 1.07e+00 8.73e-01 3.62e+01 angle pdb=" C ASP R 128 " pdb=" N VAL R 129 " pdb=" CA VAL R 129 " ideal model delta sigma weight residual 120.56 113.46 7.10 1.26e+00 6.30e-01 3.17e+01 angle pdb=" C ASP R 128 " pdb=" CA ASP R 128 " pdb=" CB ASP R 128 " ideal model delta sigma weight residual 110.88 102.43 8.45 1.57e+00 4.06e-01 2.90e+01 ... (remaining 11789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 4615 17.22 - 34.45: 439 34.45 - 51.67: 69 51.67 - 68.89: 12 68.89 - 86.11: 7 Dihedral angle restraints: 5142 sinusoidal: 1987 harmonic: 3155 Sorted by residual: dihedral pdb=" CB CYS R 121 " pdb=" SG CYS R 121 " pdb=" SG CYS R 203 " pdb=" CB CYS R 203 " ideal model delta sinusoidal sigma weight residual 93.00 171.50 -78.50 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" C ASP R 128 " pdb=" N ASP R 128 " pdb=" CA ASP R 128 " pdb=" CB ASP R 128 " ideal model delta harmonic sigma weight residual -122.60 -111.52 -11.08 0 2.50e+00 1.60e-01 1.97e+01 dihedral pdb=" CA ARG R 420 " pdb=" C ARG R 420 " pdb=" N THR R 421 " pdb=" CA THR R 421 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 5139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1227 0.074 - 0.148: 102 0.148 - 0.222: 7 0.222 - 0.296: 3 0.296 - 0.370: 2 Chirality restraints: 1341 Sorted by residual: chirality pdb=" CA TYR H 223 " pdb=" N TYR H 223 " pdb=" C TYR H 223 " pdb=" CB TYR H 223 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA TYR R 409 " pdb=" N TYR R 409 " pdb=" C TYR R 409 " pdb=" CB TYR R 409 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA ASP R 128 " pdb=" N ASP R 128 " pdb=" C ASP R 128 " pdb=" CB ASP R 128 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 1338 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 123 " -0.026 2.00e-02 2.50e+03 5.26e-02 2.77e+01 pdb=" C ILE R 123 " 0.091 2.00e-02 2.50e+03 pdb=" O ILE R 123 " -0.034 2.00e-02 2.50e+03 pdb=" N TYR R 124 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 22 " -0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C GLU G 22 " 0.072 2.00e-02 2.50e+03 pdb=" O GLU G 22 " -0.027 2.00e-02 2.50e+03 pdb=" N ALA G 23 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 220 " -0.012 2.00e-02 2.50e+03 2.59e-02 6.71e+00 pdb=" C HIS H 220 " 0.045 2.00e-02 2.50e+03 pdb=" O HIS H 220 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU H 221 " -0.015 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 214 2.68 - 3.23: 8641 3.23 - 3.79: 12221 3.79 - 4.34: 16341 4.34 - 4.90: 27782 Nonbonded interactions: 65199 Sorted by model distance: nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.120 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.153 3.040 nonbonded pdb=" N GLU R 122 " pdb=" OE1 GLU R 122 " model vdw 2.187 3.120 nonbonded pdb=" O ILE H 145 " pdb=" OG1 THR H 201 " model vdw 2.206 3.040 nonbonded pdb=" O GLY H 16 " pdb=" OG SER H 17 " model vdw 2.227 3.040 ... (remaining 65194 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=0.00 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: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.580 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.006 0.272 8706 Z= 0.325 Angle : 0.669 11.829 11798 Z= 0.422 Chirality : 0.046 0.370 1341 Planarity : 0.003 0.053 1488 Dihedral : 13.827 86.113 3100 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 0.32 % Allowed : 1.08 % Favored : 98.59 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.27), residues: 1068 helix: 1.90 (0.29), residues: 337 sheet: -2.75 (0.34), residues: 218 loop : -2.31 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 240 TYR 0.030 0.001 TYR R 124 PHE 0.021 0.001 PHE B 241 TRP 0.009 0.001 TRP R 114 HIS 0.011 0.001 HIS H 220 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 8704) covalent geometry : angle 0.66926 (11794) SS BOND : bond 0.00256 ( 2) SS BOND : angle 0.83418 ( 4) hydrogen bonds : bond 0.18900 ( 335) hydrogen bonds : angle 6.87058 ( 966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 177 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 209 ARG cc_start: 0.8121 (ttm110) cc_final: 0.7790 (ttm110) REVERT: A 249 MET cc_start: 0.7753 (tmm) cc_final: 0.7546 (tmm) REVERT: B 32 GLN cc_start: 0.8401 (pt0) cc_final: 0.8198 (pm20) REVERT: B 317 CYS cc_start: 0.8036 (p) cc_final: 0.7536 (m) REVERT: G 21 MET cc_start: 0.7741 (tmm) cc_final: 0.7541 (tmm) REVERT: G 29 LYS cc_start: 0.7976 (tptt) cc_final: 0.7763 (tppt) REVERT: R 155 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7801 (mp0) REVERT: R 453 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8503 (mptt) outliers start: 3 outliers final: 1 residues processed: 179 average time/residue: 0.1116 time to fit residues: 26.4801 Evaluate side-chains 133 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 175 GLN B 239 ASN H 220 HIS R 433 ASN R 437 ASN R 446 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.142890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104836 restraints weight = 14256.615| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.15 r_work: 0.3253 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8706 Z= 0.198 Angle : 0.672 7.811 11798 Z= 0.354 Chirality : 0.045 0.178 1341 Planarity : 0.004 0.056 1488 Dihedral : 4.980 37.530 1192 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.16 % Allowed : 10.27 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.26), residues: 1068 helix: 1.89 (0.28), residues: 346 sheet: -2.39 (0.32), residues: 233 loop : -2.33 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.031 0.002 TYR H 223 PHE 0.027 0.002 PHE B 241 TRP 0.015 0.001 TRP B 339 HIS 0.008 0.002 HIS R 446 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 8704) covalent geometry : angle 0.67163 (11794) SS BOND : bond 0.00531 ( 2) SS BOND : angle 0.75793 ( 4) hydrogen bonds : bond 0.05427 ( 335) hydrogen bonds : angle 4.96476 ( 966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.337 Fit side-chains REVERT: A 209 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7885 (ttm110) REVERT: A 249 MET cc_start: 0.8284 (tmm) cc_final: 0.7944 (tmm) REVERT: G 21 MET cc_start: 0.7971 (tmm) cc_final: 0.7668 (tmm) REVERT: G 29 LYS cc_start: 0.7993 (tptt) cc_final: 0.7756 (tppt) REVERT: H 223 TYR cc_start: 0.5947 (OUTLIER) cc_final: 0.5594 (t80) REVERT: R 155 GLU cc_start: 0.8650 (mm-30) cc_final: 0.7971 (mp0) outliers start: 20 outliers final: 12 residues processed: 154 average time/residue: 0.1024 time to fit residues: 21.2920 Evaluate side-chains 136 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 223 TYR Chi-restraints excluded: chain R residue 46 GLN Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 124 TYR Chi-restraints excluded: chain R residue 208 GLN Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 436 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 85 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 0.0570 chunk 8 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 GLN R 437 ASN R 446 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.145040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.107135 restraints weight = 14135.311| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.15 r_work: 0.3289 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8706 Z= 0.125 Angle : 0.588 6.788 11798 Z= 0.310 Chirality : 0.042 0.175 1341 Planarity : 0.004 0.047 1488 Dihedral : 4.807 37.617 1192 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.24 % Allowed : 12.76 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.26), residues: 1068 helix: 2.11 (0.29), residues: 346 sheet: -1.89 (0.35), residues: 217 loop : -2.32 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.024 0.001 TYR H 223 PHE 0.026 0.001 PHE B 241 TRP 0.008 0.001 TRP B 82 HIS 0.008 0.001 HIS R 446 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8704) covalent geometry : angle 0.58785 (11794) SS BOND : bond 0.00514 ( 2) SS BOND : angle 0.36960 ( 4) hydrogen bonds : bond 0.04362 ( 335) hydrogen bonds : angle 4.54103 ( 966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8263 (p0) cc_final: 0.8020 (p0) REVERT: A 209 ARG cc_start: 0.8183 (ttm110) cc_final: 0.7840 (ttm110) REVERT: A 249 MET cc_start: 0.8237 (tmm) cc_final: 0.7917 (tmm) REVERT: B 317 CYS cc_start: 0.8508 (p) cc_final: 0.7801 (m) REVERT: G 21 MET cc_start: 0.8008 (tmm) cc_final: 0.7732 (tmm) REVERT: R 80 LYS cc_start: 0.8117 (mttt) cc_final: 0.7604 (mmmt) REVERT: R 155 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8407 (mm-30) REVERT: R 204 GLU cc_start: 0.6589 (tt0) cc_final: 0.6194 (tm-30) outliers start: 30 outliers final: 14 residues processed: 165 average time/residue: 0.1041 time to fit residues: 23.0775 Evaluate side-chains 144 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain R residue 46 GLN Chi-restraints excluded: chain R residue 53 CYS Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 208 GLN Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 409 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 70 optimal weight: 0.0970 chunk 57 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 chunk 36 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.140397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.104012 restraints weight = 14448.511| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.05 r_work: 0.3247 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8706 Z= 0.114 Angle : 0.563 6.626 11798 Z= 0.299 Chirality : 0.042 0.226 1341 Planarity : 0.004 0.057 1488 Dihedral : 4.549 21.279 1190 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.16 % Allowed : 14.49 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.27), residues: 1068 helix: 2.10 (0.28), residues: 353 sheet: -1.78 (0.34), residues: 227 loop : -2.23 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.018 0.001 TYR H 223 PHE 0.022 0.001 PHE B 241 TRP 0.014 0.001 TRP B 339 HIS 0.008 0.001 HIS R 446 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8704) covalent geometry : angle 0.56345 (11794) SS BOND : bond 0.00455 ( 2) SS BOND : angle 0.37585 ( 4) hydrogen bonds : bond 0.03875 ( 335) hydrogen bonds : angle 4.33680 ( 966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8225 (p0) cc_final: 0.7945 (p0) REVERT: A 209 ARG cc_start: 0.8132 (ttm110) cc_final: 0.7839 (ttm110) REVERT: A 249 MET cc_start: 0.8324 (tmm) cc_final: 0.7968 (tmm) REVERT: B 317 CYS cc_start: 0.8271 (p) cc_final: 0.7749 (m) REVERT: G 21 MET cc_start: 0.7937 (tmm) cc_final: 0.7695 (tmm) REVERT: R 80 LYS cc_start: 0.8190 (mttt) cc_final: 0.7697 (mmmt) REVERT: R 155 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8363 (mm-30) REVERT: R 204 GLU cc_start: 0.6520 (tt0) cc_final: 0.6187 (tm-30) outliers start: 20 outliers final: 15 residues processed: 160 average time/residue: 0.1037 time to fit residues: 22.3673 Evaluate side-chains 143 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain R residue 46 GLN Chi-restraints excluded: chain R residue 124 TYR Chi-restraints excluded: chain R residue 208 GLN Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 409 TYR Chi-restraints excluded: chain R residue 436 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 78 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 0.0980 chunk 72 optimal weight: 0.0040 chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.140894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103898 restraints weight = 14617.057| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.10 r_work: 0.3252 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8706 Z= 0.112 Angle : 0.560 6.125 11798 Z= 0.295 Chirality : 0.042 0.205 1341 Planarity : 0.004 0.057 1488 Dihedral : 4.458 21.565 1190 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.92 % Allowed : 15.46 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.27), residues: 1068 helix: 2.09 (0.28), residues: 356 sheet: -1.53 (0.35), residues: 220 loop : -2.15 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 206 TYR 0.016 0.001 TYR H 178 PHE 0.021 0.001 PHE B 241 TRP 0.018 0.001 TRP B 339 HIS 0.008 0.001 HIS R 446 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8704) covalent geometry : angle 0.56042 (11794) SS BOND : bond 0.00495 ( 2) SS BOND : angle 0.43702 ( 4) hydrogen bonds : bond 0.03735 ( 335) hydrogen bonds : angle 4.24180 ( 966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 209 ARG cc_start: 0.8098 (ttm110) cc_final: 0.7765 (ttm110) REVERT: A 249 MET cc_start: 0.8324 (tmm) cc_final: 0.7962 (tmm) REVERT: B 234 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: B 317 CYS cc_start: 0.8304 (p) cc_final: 0.7802 (m) REVERT: G 21 MET cc_start: 0.7933 (tmm) cc_final: 0.7709 (tmm) REVERT: G 51 LEU cc_start: 0.8482 (mm) cc_final: 0.8137 (mm) REVERT: H 34 MET cc_start: 0.8625 (mmm) cc_final: 0.8327 (mtt) REVERT: R 80 LYS cc_start: 0.8140 (mttt) cc_final: 0.7694 (mmmt) REVERT: R 155 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8355 (mm-30) REVERT: R 204 GLU cc_start: 0.6469 (tt0) cc_final: 0.6153 (tm-30) outliers start: 27 outliers final: 21 residues processed: 155 average time/residue: 0.1019 time to fit residues: 21.4689 Evaluate side-chains 151 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain R residue 46 GLN Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 124 TYR Chi-restraints excluded: chain R residue 208 GLN Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 409 TYR Chi-restraints excluded: chain R residue 418 VAL Chi-restraints excluded: chain R residue 436 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 0.0770 chunk 63 optimal weight: 0.0970 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 0.0370 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN B 17 GLN R 446 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.142627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.106138 restraints weight = 14229.010| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.05 r_work: 0.3281 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8706 Z= 0.106 Angle : 0.561 7.034 11798 Z= 0.293 Chirality : 0.041 0.186 1341 Planarity : 0.004 0.062 1488 Dihedral : 4.313 21.208 1190 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.81 % Allowed : 16.86 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.27), residues: 1068 helix: 2.25 (0.28), residues: 353 sheet: -1.42 (0.34), residues: 222 loop : -2.12 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 148 TYR 0.015 0.001 TYR H 178 PHE 0.020 0.001 PHE A 275 TRP 0.016 0.001 TRP B 339 HIS 0.008 0.001 HIS R 446 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8704) covalent geometry : angle 0.56076 (11794) SS BOND : bond 0.00516 ( 2) SS BOND : angle 0.50596 ( 4) hydrogen bonds : bond 0.03464 ( 335) hydrogen bonds : angle 4.10630 ( 966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 ARG cc_start: 0.8060 (ttm110) cc_final: 0.7592 (ttp80) REVERT: A 249 MET cc_start: 0.8325 (tmm) cc_final: 0.7931 (tmm) REVERT: B 217 MET cc_start: 0.8312 (pmm) cc_final: 0.8076 (pmm) REVERT: B 234 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7192 (m-80) REVERT: B 297 TRP cc_start: 0.8878 (m100) cc_final: 0.8589 (m100) REVERT: B 317 CYS cc_start: 0.8291 (p) cc_final: 0.7876 (m) REVERT: B 325 MET cc_start: 0.8802 (mmm) cc_final: 0.8552 (tpp) REVERT: G 21 MET cc_start: 0.7867 (tmm) cc_final: 0.7641 (tmm) REVERT: G 51 LEU cc_start: 0.8532 (mm) cc_final: 0.8186 (mm) REVERT: H 34 MET cc_start: 0.8590 (mmm) cc_final: 0.8270 (mtt) REVERT: H 109 ASP cc_start: 0.8253 (m-30) cc_final: 0.7952 (m-30) REVERT: H 223 TYR cc_start: 0.5954 (OUTLIER) cc_final: 0.5507 (t80) REVERT: R 76 SER cc_start: 0.8205 (t) cc_final: 0.7466 (m) REVERT: R 80 LYS cc_start: 0.8100 (mttt) cc_final: 0.7701 (mmmt) REVERT: R 155 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8356 (mm-30) outliers start: 26 outliers final: 18 residues processed: 167 average time/residue: 0.0969 time to fit residues: 22.0896 Evaluate side-chains 158 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 223 TYR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain R residue 124 TYR Chi-restraints excluded: chain R residue 208 GLN Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 409 TYR Chi-restraints excluded: chain R residue 418 VAL Chi-restraints excluded: chain R residue 436 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 74 optimal weight: 0.0040 chunk 71 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 70 optimal weight: 0.0010 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.141556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.105100 restraints weight = 14447.172| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.06 r_work: 0.3271 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8706 Z= 0.115 Angle : 0.572 8.298 11798 Z= 0.298 Chirality : 0.041 0.196 1341 Planarity : 0.004 0.059 1488 Dihedral : 4.291 21.602 1190 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.24 % Allowed : 17.73 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.27), residues: 1068 helix: 2.30 (0.28), residues: 351 sheet: -1.47 (0.33), residues: 232 loop : -2.12 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 206 TYR 0.016 0.001 TYR H 178 PHE 0.031 0.001 PHE R 427 TRP 0.025 0.001 TRP B 339 HIS 0.011 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8704) covalent geometry : angle 0.57181 (11794) SS BOND : bond 0.00509 ( 2) SS BOND : angle 0.38294 ( 4) hydrogen bonds : bond 0.03615 ( 335) hydrogen bonds : angle 4.09445 ( 966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 209 ARG cc_start: 0.8071 (ttm110) cc_final: 0.7606 (ttp80) REVERT: A 249 MET cc_start: 0.8353 (tmm) cc_final: 0.7958 (tmm) REVERT: B 163 ASP cc_start: 0.6650 (p0) cc_final: 0.6428 (p0) REVERT: B 217 MET cc_start: 0.8295 (pmm) cc_final: 0.8033 (pmm) REVERT: B 234 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.7159 (m-80) REVERT: B 297 TRP cc_start: 0.8878 (m100) cc_final: 0.8590 (m100) REVERT: B 317 CYS cc_start: 0.8333 (p) cc_final: 0.7869 (m) REVERT: B 325 MET cc_start: 0.8777 (mmm) cc_final: 0.8529 (tpp) REVERT: G 21 MET cc_start: 0.7836 (tmm) cc_final: 0.7612 (tmm) REVERT: G 51 LEU cc_start: 0.8543 (mm) cc_final: 0.8213 (mm) REVERT: H 223 TYR cc_start: 0.6048 (OUTLIER) cc_final: 0.5636 (t80) REVERT: R 76 SER cc_start: 0.8113 (t) cc_final: 0.7435 (m) REVERT: R 80 LYS cc_start: 0.8116 (mttt) cc_final: 0.7744 (mmmt) REVERT: R 155 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8356 (mm-30) REVERT: R 208 GLN cc_start: 0.5328 (OUTLIER) cc_final: 0.4686 (pp30) outliers start: 30 outliers final: 18 residues processed: 156 average time/residue: 0.0975 time to fit residues: 20.7674 Evaluate side-chains 157 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 223 TYR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 124 TYR Chi-restraints excluded: chain R residue 208 GLN Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 400 VAL Chi-restraints excluded: chain R residue 409 TYR Chi-restraints excluded: chain R residue 418 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 95 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.139985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.103235 restraints weight = 14443.862| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.06 r_work: 0.3237 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8706 Z= 0.136 Angle : 0.583 7.011 11798 Z= 0.308 Chirality : 0.042 0.202 1341 Planarity : 0.004 0.062 1488 Dihedral : 4.381 21.478 1190 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.24 % Allowed : 17.62 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.27), residues: 1068 helix: 2.21 (0.28), residues: 352 sheet: -1.49 (0.33), residues: 236 loop : -2.10 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 206 TYR 0.017 0.001 TYR H 178 PHE 0.026 0.001 PHE R 427 TRP 0.031 0.001 TRP B 339 HIS 0.009 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8704) covalent geometry : angle 0.58340 (11794) SS BOND : bond 0.00548 ( 2) SS BOND : angle 0.42280 ( 4) hydrogen bonds : bond 0.03848 ( 335) hydrogen bonds : angle 4.14339 ( 966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8432 (p0) cc_final: 0.8194 (p0) REVERT: A 209 ARG cc_start: 0.8081 (ttm110) cc_final: 0.7802 (ttm110) REVERT: A 249 MET cc_start: 0.8380 (tmm) cc_final: 0.7973 (tmm) REVERT: B 163 ASP cc_start: 0.6670 (p0) cc_final: 0.6461 (p0) REVERT: B 217 MET cc_start: 0.8307 (pmm) cc_final: 0.8034 (pmm) REVERT: B 234 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7165 (m-80) REVERT: B 317 CYS cc_start: 0.8412 (p) cc_final: 0.7798 (m) REVERT: B 325 MET cc_start: 0.8790 (mmm) cc_final: 0.8534 (tpp) REVERT: G 21 MET cc_start: 0.7843 (tmm) cc_final: 0.7624 (tmm) REVERT: G 51 LEU cc_start: 0.8538 (mm) cc_final: 0.8188 (mm) REVERT: H 34 MET cc_start: 0.8676 (mmm) cc_final: 0.8336 (mtt) REVERT: H 223 TYR cc_start: 0.6354 (OUTLIER) cc_final: 0.5832 (t80) REVERT: R 76 SER cc_start: 0.8210 (t) cc_final: 0.7479 (m) REVERT: R 80 LYS cc_start: 0.8137 (mttt) cc_final: 0.7760 (mmmt) REVERT: R 155 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8346 (mm-30) REVERT: R 181 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.6730 (m-10) REVERT: R 208 GLN cc_start: 0.5435 (OUTLIER) cc_final: 0.5024 (pm20) outliers start: 30 outliers final: 21 residues processed: 152 average time/residue: 0.1035 time to fit residues: 21.2434 Evaluate side-chains 152 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 223 TYR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain R residue 46 GLN Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 181 PHE Chi-restraints excluded: chain R residue 208 GLN Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 400 VAL Chi-restraints excluded: chain R residue 409 TYR Chi-restraints excluded: chain R residue 418 VAL Chi-restraints excluded: chain R residue 439 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN R 446 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101243 restraints weight = 14581.495| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.05 r_work: 0.3208 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8706 Z= 0.160 Angle : 0.611 6.367 11798 Z= 0.323 Chirality : 0.043 0.205 1341 Planarity : 0.004 0.060 1488 Dihedral : 4.545 21.368 1190 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.24 % Allowed : 18.05 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.26), residues: 1068 helix: 2.09 (0.28), residues: 354 sheet: -1.42 (0.33), residues: 237 loop : -2.11 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 206 TYR 0.018 0.001 TYR H 178 PHE 0.024 0.001 PHE R 427 TRP 0.038 0.002 TRP B 339 HIS 0.009 0.002 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8704) covalent geometry : angle 0.61129 (11794) SS BOND : bond 0.00614 ( 2) SS BOND : angle 0.51036 ( 4) hydrogen bonds : bond 0.04186 ( 335) hydrogen bonds : angle 4.26264 ( 966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.268 Fit side-chains REVERT: A 33 ASP cc_start: 0.8465 (p0) cc_final: 0.8236 (p0) REVERT: A 209 ARG cc_start: 0.8078 (ttm110) cc_final: 0.7785 (ttm110) REVERT: A 249 MET cc_start: 0.8360 (tmm) cc_final: 0.7969 (tmm) REVERT: B 163 ASP cc_start: 0.6656 (p0) cc_final: 0.6408 (p0) REVERT: B 191 SER cc_start: 0.8929 (t) cc_final: 0.8542 (t) REVERT: B 217 MET cc_start: 0.8243 (pmm) cc_final: 0.7969 (pmm) REVERT: B 234 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7010 (m-80) REVERT: B 317 CYS cc_start: 0.8444 (p) cc_final: 0.7759 (m) REVERT: B 325 MET cc_start: 0.8796 (mmm) cc_final: 0.8539 (tpp) REVERT: G 21 MET cc_start: 0.7794 (tmm) cc_final: 0.7589 (tmm) REVERT: G 51 LEU cc_start: 0.8572 (mm) cc_final: 0.8221 (mm) REVERT: H 34 MET cc_start: 0.8671 (mmm) cc_final: 0.8326 (mtt) REVERT: H 223 TYR cc_start: 0.6533 (OUTLIER) cc_final: 0.5981 (t80) REVERT: R 80 LYS cc_start: 0.8182 (mttt) cc_final: 0.7836 (mmmt) REVERT: R 155 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8344 (mm-30) REVERT: R 181 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.6773 (m-10) REVERT: R 204 GLU cc_start: 0.6461 (tt0) cc_final: 0.6107 (tm-30) REVERT: R 208 GLN cc_start: 0.5572 (OUTLIER) cc_final: 0.5168 (pm20) outliers start: 30 outliers final: 23 residues processed: 147 average time/residue: 0.1009 time to fit residues: 19.7936 Evaluate side-chains 147 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 223 TYR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain R residue 46 GLN Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 181 PHE Chi-restraints excluded: chain R residue 208 GLN Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 400 VAL Chi-restraints excluded: chain R residue 409 TYR Chi-restraints excluded: chain R residue 418 VAL Chi-restraints excluded: chain R residue 439 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 68 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN R 446 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.138660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.101514 restraints weight = 14674.331| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.08 r_work: 0.3213 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8706 Z= 0.150 Angle : 0.617 6.902 11798 Z= 0.328 Chirality : 0.043 0.207 1341 Planarity : 0.004 0.060 1488 Dihedral : 4.532 21.008 1190 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.24 % Allowed : 19.03 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.26), residues: 1068 helix: 2.11 (0.28), residues: 352 sheet: -1.38 (0.33), residues: 234 loop : -2.13 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.017 0.001 TYR H 178 PHE 0.027 0.001 PHE R 427 TRP 0.039 0.001 TRP B 339 HIS 0.008 0.002 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8704) covalent geometry : angle 0.61749 (11794) SS BOND : bond 0.00620 ( 2) SS BOND : angle 0.34871 ( 4) hydrogen bonds : bond 0.04019 ( 335) hydrogen bonds : angle 4.24144 ( 966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.324 Fit side-chains REVERT: A 33 ASP cc_start: 0.8471 (p0) cc_final: 0.8222 (p0) REVERT: A 209 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7590 (ttp80) REVERT: A 249 MET cc_start: 0.8379 (tmm) cc_final: 0.7975 (tmm) REVERT: B 163 ASP cc_start: 0.6575 (p0) cc_final: 0.6307 (p0) REVERT: B 217 MET cc_start: 0.8319 (pmm) cc_final: 0.8027 (pmm) REVERT: B 234 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: B 317 CYS cc_start: 0.8362 (p) cc_final: 0.7742 (m) REVERT: G 21 MET cc_start: 0.7838 (tmm) cc_final: 0.7636 (tmm) REVERT: G 51 LEU cc_start: 0.8570 (mm) cc_final: 0.8217 (mm) REVERT: H 34 MET cc_start: 0.8707 (mmm) cc_final: 0.8310 (mtt) REVERT: H 109 ASP cc_start: 0.8263 (m-30) cc_final: 0.7963 (m-30) REVERT: H 223 TYR cc_start: 0.6569 (OUTLIER) cc_final: 0.5981 (t80) REVERT: R 80 LYS cc_start: 0.8193 (mttt) cc_final: 0.7852 (mmmt) REVERT: R 155 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8344 (mm-30) REVERT: R 181 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.6751 (m-10) REVERT: R 204 GLU cc_start: 0.6479 (tt0) cc_final: 0.6111 (tm-30) REVERT: R 208 GLN cc_start: 0.5566 (OUTLIER) cc_final: 0.5148 (pm20) outliers start: 30 outliers final: 25 residues processed: 145 average time/residue: 0.1029 time to fit residues: 20.3329 Evaluate side-chains 152 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 223 TYR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain R residue 46 GLN Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 181 PHE Chi-restraints excluded: chain R residue 208 GLN Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 400 VAL Chi-restraints excluded: chain R residue 409 TYR Chi-restraints excluded: chain R residue 418 VAL Chi-restraints excluded: chain R residue 439 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 7 optimal weight: 0.0070 chunk 62 optimal weight: 0.3980 chunk 78 optimal weight: 0.0170 chunk 42 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 overall best weight: 0.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN R 446 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.142121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.105287 restraints weight = 14394.834| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.06 r_work: 0.3271 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8706 Z= 0.112 Angle : 0.583 7.311 11798 Z= 0.310 Chirality : 0.041 0.199 1341 Planarity : 0.004 0.060 1488 Dihedral : 4.337 19.762 1190 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.49 % Allowed : 19.89 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.27), residues: 1068 helix: 2.16 (0.28), residues: 354 sheet: -1.23 (0.33), residues: 236 loop : -2.10 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 206 TYR 0.017 0.001 TYR A 231 PHE 0.030 0.001 PHE R 427 TRP 0.012 0.001 TRP B 339 HIS 0.009 0.001 HIS R 446 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8704) covalent geometry : angle 0.58273 (11794) SS BOND : bond 0.00537 ( 2) SS BOND : angle 0.24505 ( 4) hydrogen bonds : bond 0.03510 ( 335) hydrogen bonds : angle 4.16081 ( 966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2132.90 seconds wall clock time: 37 minutes 21.10 seconds (2241.10 seconds total)