Starting phenix.real_space_refine on Sat Dec 28 12:54:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w7e_32342/12_2024/7w7e_32342.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w7e_32342/12_2024/7w7e_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7w7e_32342/12_2024/7w7e_32342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w7e_32342/12_2024/7w7e_32342.map" model { file = "/net/cci-nas-00/data/ceres_data/7w7e_32342/12_2024/7w7e_32342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w7e_32342/12_2024/7w7e_32342.cif" } resolution = 3.4 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= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'ARG:plan': 2, 'TRP:plan': 1} 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: 5.51, per 1000 atoms: 0.65 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: 2.58 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.98 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: 2.55 Time building geometry restraints manager: 2.76 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: 1.690 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.090 Find NCS groups from input model: 0.100 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.440 ------------------------------------------------------------------------------- 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 8704 Z= 0.318 Angle : 0.669 11.829 11794 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 : 8.28 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 (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: -1.54 (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 TRP 0.009 0.001 TRP R 114 HIS 0.011 0.001 HIS H 220 PHE 0.021 0.001 PHE B 241 TYR 0.030 0.001 TYR R 124 ARG 0.004 0.000 ARG R 240 *********************** 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 : 1.012 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: 0.2553 time to fit residues: 60.2720 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 : 0.973 ------------------------------------------------------------------------------- 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 90 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 446 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8704 Z= 0.289 Angle : 0.663 7.739 11794 Z= 0.349 Chirality : 0.045 0.187 1341 Planarity : 0.004 0.055 1488 Dihedral : 4.939 37.394 1192 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.16 % Allowed : 10.05 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.38 (0.26), residues: 1068 helix: 1.92 (0.28), residues: 346 sheet: -2.37 (0.32), residues: 234 loop : -2.33 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.008 0.002 HIS R 446 PHE 0.027 0.002 PHE B 241 TYR 0.032 0.002 TYR H 223 ARG 0.005 0.000 ARG B 251 *********************** 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 165 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.994 Fit side-chains REVERT: A 209 ARG cc_start: 0.8093 (ttm110) cc_final: 0.7770 (ttm110) REVERT: A 249 MET cc_start: 0.7797 (tmm) cc_final: 0.7588 (tmm) REVERT: G 21 MET cc_start: 0.7750 (tmm) cc_final: 0.7537 (tmm) REVERT: G 29 LYS cc_start: 0.7950 (tptt) cc_final: 0.7719 (tppt) REVERT: H 223 TYR cc_start: 0.5776 (OUTLIER) cc_final: 0.5531 (t80) REVERT: R 155 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7797 (mp0) outliers start: 20 outliers final: 11 residues processed: 156 average time/residue: 0.2207 time to fit residues: 46.5876 Evaluate side-chains 135 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 255 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 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 54 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8704 Z= 0.198 Angle : 0.592 6.823 11794 Z= 0.313 Chirality : 0.043 0.178 1341 Planarity : 0.004 0.048 1488 Dihedral : 4.828 37.638 1192 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.92 % Allowed : 13.08 % 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 (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: -1.12 (0.26), residues: 1068 helix: 2.07 (0.28), residues: 346 sheet: -1.90 (0.35), residues: 216 loop : -2.31 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.008 0.001 HIS R 446 PHE 0.026 0.001 PHE B 241 TYR 0.024 0.001 TYR H 223 ARG 0.003 0.000 ARG H 87 *********************** 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 173 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 209 ARG cc_start: 0.8093 (ttm110) cc_final: 0.7787 (ttm110) REVERT: B 317 CYS cc_start: 0.7949 (p) cc_final: 0.7554 (m) REVERT: H 95 TYR cc_start: 0.8129 (m-80) cc_final: 0.7793 (m-80) REVERT: R 80 LYS cc_start: 0.8305 (mttt) cc_final: 0.7809 (mmmt) REVERT: R 204 GLU cc_start: 0.6520 (tt0) cc_final: 0.6240 (tm-30) outliers start: 27 outliers final: 12 residues processed: 161 average time/residue: 0.2509 time to fit residues: 53.7637 Evaluate side-chains 142 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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 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 96 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8704 Z= 0.224 Angle : 0.596 8.288 11794 Z= 0.314 Chirality : 0.043 0.219 1341 Planarity : 0.004 0.060 1488 Dihedral : 4.697 21.463 1190 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.49 % Allowed : 14.92 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.04 (0.26), residues: 1068 helix: 2.00 (0.28), residues: 353 sheet: -1.81 (0.34), residues: 231 loop : -2.23 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.008 0.001 HIS R 446 PHE 0.022 0.001 PHE B 235 TYR 0.021 0.001 TYR H 223 ARG 0.003 0.000 ARG A 206 *********************** 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 166 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 209 ARG cc_start: 0.8090 (ttm110) cc_final: 0.7759 (ttm110) REVERT: B 234 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: B 317 CYS cc_start: 0.7954 (p) cc_final: 0.7476 (m) REVERT: R 79 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7693 (mp) REVERT: R 80 LYS cc_start: 0.8280 (mttt) cc_final: 0.7840 (mmmt) REVERT: R 204 GLU cc_start: 0.6511 (tt0) cc_final: 0.6221 (tm-30) outliers start: 23 outliers final: 16 residues processed: 157 average time/residue: 0.2285 time to fit residues: 48.6882 Evaluate side-chains 144 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 54 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain R residue 46 GLN Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 102 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8704 Z= 0.271 Angle : 0.628 8.468 11794 Z= 0.329 Chirality : 0.044 0.197 1341 Planarity : 0.004 0.057 1488 Dihedral : 4.837 21.883 1190 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.57 % Allowed : 15.68 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.04 (0.26), residues: 1068 helix: 2.02 (0.28), residues: 350 sheet: -1.79 (0.34), residues: 235 loop : -2.24 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.008 0.002 HIS R 446 PHE 0.023 0.001 PHE B 235 TYR 0.021 0.001 TYR H 223 ARG 0.006 0.000 ARG H 148 *********************** 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 164 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.908 Fit side-chains REVERT: A 209 ARG cc_start: 0.8103 (ttm110) cc_final: 0.7791 (ttm110) REVERT: A 348 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7340 (tt) REVERT: B 234 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7068 (m-80) REVERT: G 51 LEU cc_start: 0.8584 (mm) cc_final: 0.8258 (mm) REVERT: H 34 MET cc_start: 0.8066 (mmm) cc_final: 0.7725 (mtt) REVERT: R 80 LYS cc_start: 0.8314 (mttt) cc_final: 0.7936 (mmmt) REVERT: R 181 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6647 (m-10) REVERT: R 204 GLU cc_start: 0.6518 (tt0) cc_final: 0.6250 (tm-30) outliers start: 33 outliers final: 24 residues processed: 155 average time/residue: 0.2525 time to fit residues: 53.2350 Evaluate side-chains 150 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 A residue 348 LEU 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 G residue 54 VAL Chi-restraints excluded: chain H residue 22 CYS 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 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 102 ILE Chi-restraints excluded: chain R residue 124 TYR 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 216 CYS Chi-restraints excluded: chain R residue 217 ILE 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 34 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 0.0970 chunk 99 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 237 ASN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 433 ASN R 446 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8704 Z= 0.176 Angle : 0.591 9.069 11794 Z= 0.310 Chirality : 0.042 0.180 1341 Planarity : 0.004 0.061 1488 Dihedral : 4.595 21.677 1190 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.78 % Allowed : 16.54 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.27), residues: 1068 helix: 2.15 (0.29), residues: 352 sheet: -1.51 (0.34), residues: 232 loop : -2.18 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 339 HIS 0.008 0.001 HIS R 446 PHE 0.020 0.001 PHE B 241 TYR 0.017 0.001 TYR H 178 ARG 0.004 0.000 ARG H 148 *********************** 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 171 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 209 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7751 (ttm110) REVERT: B 20 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7588 (p0) REVERT: B 234 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.6980 (m-80) REVERT: B 317 CYS cc_start: 0.7813 (p) cc_final: 0.7458 (m) REVERT: B 325 MET cc_start: 0.8341 (mmm) cc_final: 0.8112 (tpp) REVERT: G 51 LEU cc_start: 0.8614 (mm) cc_final: 0.8288 (mm) REVERT: H 109 ASP cc_start: 0.8049 (m-30) cc_final: 0.7780 (m-30) REVERT: H 223 TYR cc_start: 0.6469 (OUTLIER) cc_final: 0.6033 (t80) REVERT: R 80 LYS cc_start: 0.8297 (mttt) cc_final: 0.7957 (mmmt) REVERT: R 204 GLU cc_start: 0.6438 (tt0) cc_final: 0.6205 (tm-30) REVERT: R 208 GLN cc_start: 0.5296 (OUTLIER) cc_final: 0.4686 (pp30) outliers start: 35 outliers final: 22 residues processed: 160 average time/residue: 0.2243 time to fit residues: 48.9445 Evaluate side-chains 149 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 20 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 225 HIS 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 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 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 217 ILE 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 436 LEU Chi-restraints excluded: chain R residue 439 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 0.2980 chunk 87 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN H 130 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 446 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8704 Z= 0.252 Angle : 0.624 9.405 11794 Z= 0.326 Chirality : 0.043 0.173 1341 Planarity : 0.004 0.059 1488 Dihedral : 4.695 21.806 1190 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.89 % Allowed : 18.05 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.91 (0.26), residues: 1068 helix: 1.93 (0.28), residues: 355 sheet: -1.48 (0.34), residues: 236 loop : -2.18 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 339 HIS 0.009 0.002 HIS A 322 PHE 0.025 0.001 PHE B 235 TYR 0.018 0.001 TYR H 178 ARG 0.003 0.000 ARG H 148 *********************** 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 164 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 209 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7784 (ttm110) REVERT: B 20 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7581 (p0) REVERT: B 234 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7021 (m-80) REVERT: B 317 CYS cc_start: 0.8043 (p) cc_final: 0.7478 (m) REVERT: G 51 LEU cc_start: 0.8618 (mm) cc_final: 0.8307 (mm) REVERT: H 109 ASP cc_start: 0.8042 (m-30) cc_final: 0.7762 (m-30) REVERT: H 223 TYR cc_start: 0.6522 (OUTLIER) cc_final: 0.6073 (t80) REVERT: R 80 LYS cc_start: 0.8275 (mttt) cc_final: 0.7957 (mmmt) REVERT: R 181 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.6643 (m-10) REVERT: R 204 GLU cc_start: 0.6454 (tt0) cc_final: 0.6211 (tm-30) REVERT: R 208 GLN cc_start: 0.5472 (OUTLIER) cc_final: 0.4786 (pp30) outliers start: 36 outliers final: 25 residues processed: 154 average time/residue: 0.2329 time to fit residues: 48.6264 Evaluate side-chains 155 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 20 ASP 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 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 54 VAL 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 H residue 235 LEU Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 124 TYR 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 217 ILE 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 436 LEU Chi-restraints excluded: chain R residue 439 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 0.0070 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 446 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8704 Z= 0.201 Angle : 0.615 9.846 11794 Z= 0.319 Chirality : 0.042 0.189 1341 Planarity : 0.004 0.061 1488 Dihedral : 4.598 21.659 1190 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.00 % Allowed : 18.70 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.27), residues: 1068 helix: 2.04 (0.28), residues: 352 sheet: -1.40 (0.34), residues: 232 loop : -2.12 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 339 HIS 0.008 0.001 HIS R 446 PHE 0.025 0.001 PHE A 275 TYR 0.017 0.001 TYR H 178 ARG 0.003 0.000 ARG A 206 *********************** 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 168 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 ARG cc_start: 0.8035 (ttm110) cc_final: 0.7747 (ttm110) REVERT: B 20 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7567 (p0) REVERT: B 234 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.6953 (m-80) REVERT: B 317 CYS cc_start: 0.7864 (p) cc_final: 0.7462 (m) REVERT: B 325 MET cc_start: 0.8308 (mmm) cc_final: 0.8082 (tpp) REVERT: G 51 LEU cc_start: 0.8601 (mm) cc_final: 0.8277 (mm) REVERT: H 42 GLU cc_start: 0.6901 (pm20) cc_final: 0.6697 (pm20) REVERT: H 109 ASP cc_start: 0.8048 (m-30) cc_final: 0.7774 (m-30) REVERT: H 223 TYR cc_start: 0.6570 (OUTLIER) cc_final: 0.6136 (t80) REVERT: R 80 LYS cc_start: 0.8243 (mttt) cc_final: 0.7932 (mmmt) REVERT: R 181 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.6630 (m-10) REVERT: R 204 GLU cc_start: 0.6433 (tt0) cc_final: 0.6189 (tm-30) REVERT: R 208 GLN cc_start: 0.5536 (OUTLIER) cc_final: 0.4796 (pp30) outliers start: 37 outliers final: 27 residues processed: 156 average time/residue: 0.2291 time to fit residues: 48.4830 Evaluate side-chains 158 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 20 ASP 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 225 HIS 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 54 VAL 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 H residue 235 LEU Chi-restraints excluded: chain R residue 46 GLN Chi-restraints excluded: chain R residue 57 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 181 PHE 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 400 VAL Chi-restraints excluded: chain R residue 409 TYR Chi-restraints excluded: chain R residue 418 VAL Chi-restraints excluded: chain R residue 436 LEU 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 90 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 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 ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 446 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8704 Z= 0.229 Angle : 0.617 10.286 11794 Z= 0.324 Chirality : 0.042 0.192 1341 Planarity : 0.004 0.059 1488 Dihedral : 4.625 21.431 1190 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.89 % Allowed : 18.70 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.26), residues: 1068 helix: 2.01 (0.28), residues: 352 sheet: -1.51 (0.34), residues: 233 loop : -2.15 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 339 HIS 0.008 0.001 HIS R 446 PHE 0.025 0.001 PHE A 275 TYR 0.018 0.001 TYR H 178 ARG 0.003 0.000 ARG A 206 *********************** 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 164 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7761 (ttm110) REVERT: B 20 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7623 (p0) REVERT: B 234 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7030 (m-80) REVERT: B 317 CYS cc_start: 0.8028 (p) cc_final: 0.7540 (m) REVERT: B 325 MET cc_start: 0.8285 (mmm) cc_final: 0.8084 (tpp) REVERT: G 51 LEU cc_start: 0.8610 (mm) cc_final: 0.8306 (mm) REVERT: H 42 GLU cc_start: 0.6832 (pm20) cc_final: 0.6618 (pm20) REVERT: H 109 ASP cc_start: 0.8029 (m-30) cc_final: 0.7743 (m-30) REVERT: H 223 TYR cc_start: 0.6526 (OUTLIER) cc_final: 0.6087 (t80) REVERT: R 80 LYS cc_start: 0.8247 (mttt) cc_final: 0.7966 (mmmt) REVERT: R 181 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.6641 (m-10) REVERT: R 204 GLU cc_start: 0.6398 (tt0) cc_final: 0.6150 (tm-30) REVERT: R 208 GLN cc_start: 0.5486 (OUTLIER) cc_final: 0.4789 (pp30) outliers start: 36 outliers final: 30 residues processed: 150 average time/residue: 0.2319 time to fit residues: 47.3970 Evaluate side-chains 163 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 20 ASP 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 191 SER Chi-restraints excluded: chain B residue 225 HIS 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 127 VAL 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 79 LEU Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 124 TYR 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 217 ILE 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 436 LEU 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 62 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 70 optimal weight: 0.1980 chunk 106 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 0.0270 chunk 90 optimal weight: 0.5980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 446 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8704 Z= 0.173 Angle : 0.610 12.621 11794 Z= 0.317 Chirality : 0.042 0.193 1341 Planarity : 0.004 0.061 1488 Dihedral : 4.480 21.028 1190 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.68 % Allowed : 19.24 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.27), residues: 1068 helix: 2.05 (0.28), residues: 355 sheet: -1.35 (0.34), residues: 227 loop : -2.11 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 339 HIS 0.008 0.001 HIS R 446 PHE 0.024 0.001 PHE A 275 TYR 0.017 0.001 TYR H 178 ARG 0.004 0.000 ARG A 206 ********************** 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 168 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 ARG cc_start: 0.8000 (ttm110) cc_final: 0.7703 (ttm110) REVERT: B 20 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7608 (p0) REVERT: B 234 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7046 (m-80) REVERT: B 317 CYS cc_start: 0.7776 (p) cc_final: 0.7453 (m) REVERT: G 51 LEU cc_start: 0.8592 (mm) cc_final: 0.8264 (mm) REVERT: H 42 GLU cc_start: 0.6807 (pm20) cc_final: 0.6591 (pm20) REVERT: H 109 ASP cc_start: 0.8019 (m-30) cc_final: 0.7738 (m-30) REVERT: H 223 TYR cc_start: 0.6512 (OUTLIER) cc_final: 0.6114 (t80) REVERT: R 80 LYS cc_start: 0.8229 (mttt) cc_final: 0.7922 (mmmt) REVERT: R 181 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6667 (m-10) REVERT: R 204 GLU cc_start: 0.6365 (tt0) cc_final: 0.6120 (tm-30) REVERT: R 207 ASP cc_start: 0.8587 (m-30) cc_final: 0.8346 (m-30) REVERT: R 208 GLN cc_start: 0.5479 (OUTLIER) cc_final: 0.4766 (pp30) outliers start: 34 outliers final: 22 residues processed: 155 average time/residue: 0.2178 time to fit residues: 45.6925 Evaluate side-chains 155 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 20 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN 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 127 VAL 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 124 TYR 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 217 ILE 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 26 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 chunk 4 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN G 59 ASN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 446 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100490 restraints weight = 14524.662| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.04 r_work: 0.3198 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8704 Z= 0.274 Angle : 0.645 10.343 11794 Z= 0.337 Chirality : 0.043 0.196 1341 Planarity : 0.004 0.060 1488 Dihedral : 4.653 21.092 1190 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.24 % Allowed : 19.57 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.26), residues: 1068 helix: 1.97 (0.28), residues: 355 sheet: -1.41 (0.34), residues: 233 loop : -2.16 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 339 HIS 0.008 0.002 HIS A 322 PHE 0.025 0.001 PHE A 275 TYR 0.020 0.001 TYR A 231 ARG 0.006 0.000 ARG H 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2069.11 seconds wall clock time: 38 minutes 31.93 seconds (2311.93 seconds total)