Starting phenix.real_space_refine on Fri Feb 14 01:49:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rkm_24500/02_2025/7rkm_24500.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rkm_24500/02_2025/7rkm_24500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rkm_24500/02_2025/7rkm_24500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rkm_24500/02_2025/7rkm_24500.map" model { file = "/net/cci-nas-00/data/ceres_data/7rkm_24500/02_2025/7rkm_24500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rkm_24500/02_2025/7rkm_24500.cif" } resolution = 3.5 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= 0.000 sd= 0.004 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 72 5.16 5 C 6056 2.51 5 N 1604 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9491 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1747 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2592 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Conformer: "B" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} bond proxies already assigned to first conformer: 2622 Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "D" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "L" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 531 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 65} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PCA:plan-2': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2395 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.81, per 1000 atoms: 0.72 Number of scatterers: 9491 At special positions: 0 Unit cell: (98.4, 134.48, 132.84, 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 72 16.00 O 1759 8.00 N 1604 7.00 C 6056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Simple disulfide: pdb=" SG CYS L 8 " - pdb=" SG CYS L 34 " distance=2.04 Simple disulfide: pdb=" SG CYS L 12 " - pdb=" SG CYS L 50 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 173 " 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: 2.57 Conformation dependent library (CDL) restraints added in 1.3 seconds 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 36.3% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.701A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.390A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.746A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.784A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.794A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.722A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 43 Processing helix chain 'C' and resid 44 through 48 removed outlier: 3.625A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.655A pdb=" N SER D 31 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 removed outlier: 3.771A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.870A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.538A pdb=" N VAL L 5 " --> pdb=" O HIS L 2 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR L 6 " --> pdb=" O HIS L 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2 through 6' Processing helix chain 'L' and resid 56 through 67 removed outlier: 3.511A pdb=" N ASP L 60 " --> pdb=" O GLN L 56 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP L 66 " --> pdb=" O MET L 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 59 Proline residue: R 34 - end of helix removed outlier: 3.610A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 95 removed outlier: 3.556A pdb=" N VAL R 70 " --> pdb=" O CYS R 66 " (cutoff:3.500A) Proline residue: R 87 - end of helix removed outlier: 4.240A pdb=" N ASP R 95 " --> pdb=" O GLN R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 134 Processing helix chain 'R' and resid 140 through 158 removed outlier: 3.799A pdb=" N LEU R 146 " --> pdb=" O LYS R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 164 Processing helix chain 'R' and resid 183 through 195 removed outlier: 4.150A pdb=" N GLU R 191 " --> pdb=" O ILE R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 218 removed outlier: 3.541A pdb=" N VAL R 217 " --> pdb=" O ARG R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 256 removed outlier: 3.787A pdb=" N VAL R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Proline residue: R 243 - end of helix Processing helix chain 'R' and resid 263 through 292 removed outlier: 3.527A pdb=" N ARG R 267 " --> pdb=" O CYS R 263 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 295 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.082A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.772A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.764A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.206A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.782A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.093A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.670A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.445A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.972A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'D' and resid 134 through 136 removed outlier: 4.037A pdb=" N GLU D 234 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.657A pdb=" N THR L 11 " --> pdb=" O CYS R 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 24 through 29 Processing sheet with id=AB6, first strand: chain 'R' and resid 167 through 168 450 hydrogen bonds defined for protein. 1266 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: 2.36 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2923 1.34 - 1.46: 2284 1.46 - 1.58: 4390 1.58 - 1.71: 0 1.71 - 1.83: 100 Bond restraints: 9697 Sorted by residual: bond pdb=" N PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 1.345 1.463 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" CB MET B 262 " pdb=" CG MET B 262 " ideal model delta sigma weight residual 1.520 1.447 0.073 3.00e-02 1.11e+03 5.88e+00 bond pdb=" C ILE R 160 " pdb=" N PRO R 161 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.96e+00 bond pdb=" SD MET B 262 " pdb=" CE MET B 262 " ideal model delta sigma weight residual 1.791 1.736 0.055 2.50e-02 1.60e+03 4.88e+00 bond pdb=" C ASN R 287 " pdb=" N PRO R 288 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.72e+00 ... (remaining 9692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 13054 4.60 - 9.19: 84 9.19 - 13.79: 5 13.79 - 18.39: 0 18.39 - 22.99: 1 Bond angle restraints: 13144 Sorted by residual: angle pdb=" CB MET B 262 " pdb=" CG MET B 262 " pdb=" SD MET B 262 " ideal model delta sigma weight residual 112.70 89.71 22.99 3.00e+00 1.11e-01 5.87e+01 angle pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 121.54 131.97 -10.43 1.91e+00 2.74e-01 2.98e+01 angle pdb=" CB MET R 174 " pdb=" CG MET R 174 " pdb=" SD MET R 174 " ideal model delta sigma weight residual 112.70 125.74 -13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" N MET D 180 " pdb=" CA MET D 180 " pdb=" CB MET D 180 " ideal model delta sigma weight residual 110.49 117.48 -6.99 1.69e+00 3.50e-01 1.71e+01 angle pdb=" N ASN R 287 " pdb=" CA ASN R 287 " pdb=" C ASN R 287 " ideal model delta sigma weight residual 113.16 118.58 -5.42 1.42e+00 4.96e-01 1.46e+01 ... (remaining 13139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5410 17.94 - 35.89: 329 35.89 - 53.83: 71 53.83 - 71.77: 7 71.77 - 89.72: 4 Dihedral angle restraints: 5821 sinusoidal: 2317 harmonic: 3504 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 158.42 -65.42 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" CB CYS R 23 " pdb=" SG CYS R 23 " pdb=" SG CYS R 263 " pdb=" CB CYS R 263 " ideal model delta sinusoidal sigma weight residual -86.00 -131.88 45.88 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" CA ILE R 259 " pdb=" C ILE R 259 " pdb=" N SER R 260 " pdb=" CA SER R 260 " ideal model delta harmonic sigma weight residual 180.00 154.33 25.67 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 5818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1248 0.073 - 0.146: 209 0.146 - 0.219: 23 0.219 - 0.292: 9 0.292 - 0.365: 4 Chirality restraints: 1493 Sorted by residual: chirality pdb=" CA ASN R 287 " pdb=" N ASN R 287 " pdb=" C ASN R 287 " pdb=" CB ASN R 287 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB THR A 324 " pdb=" CA THR A 324 " pdb=" OG1 THR A 324 " pdb=" CG2 THR A 324 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 1490 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 57 " -0.014 2.00e-02 2.50e+03 1.69e-02 7.11e+00 pdb=" CG TRP L 57 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP L 57 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP L 57 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 57 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP L 57 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP L 57 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 57 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 57 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 57 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 44 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C PHE R 44 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE R 44 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU R 45 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 94 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C LEU R 94 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU R 94 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP R 95 " 0.014 2.00e-02 2.50e+03 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 447 2.73 - 3.27: 9397 3.27 - 3.81: 15586 3.81 - 4.36: 19326 4.36 - 4.90: 33285 Nonbonded interactions: 78041 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.181 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASN R 189 " pdb=" OG1 THR R 252 " model vdw 2.206 3.040 nonbonded pdb=" O LEU R 53 " pdb=" OG1 THR R 57 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.241 3.040 ... (remaining 78036 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.460 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 9697 Z= 0.349 Angle : 0.970 22.986 13144 Z= 0.501 Chirality : 0.060 0.365 1493 Planarity : 0.005 0.042 1654 Dihedral : 12.319 89.718 3536 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.13 (0.24), residues: 1183 helix: 0.52 (0.26), residues: 400 sheet: -1.09 (0.29), residues: 288 loop : -1.52 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP L 57 HIS 0.009 0.002 HIS B 54 PHE 0.024 0.003 PHE D 68 TYR 0.024 0.003 TYR A 320 ARG 0.009 0.001 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.070 Fit side-chains REVERT: A 26 ASP cc_start: 0.7340 (m-30) cc_final: 0.6893 (m-30) REVERT: D 6 GLU cc_start: 0.7503 (mp0) cc_final: 0.7194 (mp0) REVERT: D 127 VAL cc_start: 0.8911 (p) cc_final: 0.8640 (t) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2469 time to fit residues: 59.6315 Evaluate side-chains 143 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 189 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110322 restraints weight = 16182.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109939 restraints weight = 13898.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111635 restraints weight = 11167.656| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9697 Z= 0.216 Angle : 0.606 7.784 13144 Z= 0.321 Chirality : 0.044 0.186 1493 Planarity : 0.003 0.038 1654 Dihedral : 5.028 36.522 1370 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.87 % Allowed : 8.10 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.24), residues: 1183 helix: 0.91 (0.27), residues: 402 sheet: -0.95 (0.29), residues: 284 loop : -1.61 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 57 HIS 0.005 0.001 HIS R 245 PHE 0.031 0.002 PHE A 334 TYR 0.028 0.002 TYR R 92 ARG 0.003 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 1.090 Fit side-chains REVERT: A 26 ASP cc_start: 0.7303 (m-30) cc_final: 0.6897 (m-30) REVERT: A 52 GLN cc_start: 0.7088 (tm-30) cc_final: 0.6747 (tt0) REVERT: A 248 LYS cc_start: 0.8163 (mttm) cc_final: 0.7904 (tptp) REVERT: B 247 ASP cc_start: 0.6833 (t70) cc_final: 0.6618 (t0) REVERT: D 6 GLU cc_start: 0.7324 (mp0) cc_final: 0.7045 (mp0) REVERT: R 191 GLU cc_start: 0.7767 (tt0) cc_final: 0.7539 (tt0) outliers start: 9 outliers final: 5 residues processed: 157 average time/residue: 0.2319 time to fit residues: 49.8676 Evaluate side-chains 143 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 45 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 0.0060 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 59 optimal weight: 0.0060 chunk 51 optimal weight: 4.9990 overall best weight: 0.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 ASN L 45 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111126 restraints weight = 24126.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114383 restraints weight = 27413.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.115796 restraints weight = 14239.055| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9697 Z= 0.212 Angle : 0.583 7.724 13144 Z= 0.306 Chirality : 0.043 0.210 1493 Planarity : 0.003 0.040 1654 Dihedral : 4.926 37.117 1370 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.74 % Allowed : 9.64 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.74 (0.24), residues: 1183 helix: 1.09 (0.27), residues: 403 sheet: -0.93 (0.29), residues: 285 loop : -1.51 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS R 245 PHE 0.024 0.002 PHE A 334 TYR 0.030 0.001 TYR R 92 ARG 0.005 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 1.018 Fit side-chains REVERT: A 26 ASP cc_start: 0.7383 (m-30) cc_final: 0.6947 (m-30) REVERT: B 247 ASP cc_start: 0.6930 (t70) cc_final: 0.6727 (t0) outliers start: 18 outliers final: 11 residues processed: 161 average time/residue: 0.2315 time to fit residues: 51.5118 Evaluate side-chains 148 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 8 CYS Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 HIS L 45 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.133849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107889 restraints weight = 24234.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111920 restraints weight = 27824.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113593 restraints weight = 12155.569| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9697 Z= 0.305 Angle : 0.623 8.290 13144 Z= 0.326 Chirality : 0.044 0.218 1493 Planarity : 0.003 0.039 1654 Dihedral : 5.044 36.936 1370 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.83 % Allowed : 11.28 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.74 (0.24), residues: 1183 helix: 1.08 (0.27), residues: 403 sheet: -0.98 (0.29), residues: 278 loop : -1.46 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.007 0.001 HIS B 142 PHE 0.022 0.002 PHE A 334 TYR 0.032 0.002 TYR R 92 ARG 0.004 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 1.063 Fit side-chains REVERT: A 26 ASP cc_start: 0.7397 (m-30) cc_final: 0.6940 (m-30) REVERT: A 52 GLN cc_start: 0.6951 (tm-30) cc_final: 0.6523 (tt0) REVERT: B 247 ASP cc_start: 0.7079 (t70) cc_final: 0.6843 (t0) REVERT: D 180 MET cc_start: 0.7873 (ptm) cc_final: 0.7452 (ptm) REVERT: L 16 THR cc_start: 0.6492 (m) cc_final: 0.6232 (p) REVERT: R 16 TYR cc_start: 0.6527 (p90) cc_final: 0.6298 (p90) REVERT: R 168 LYS cc_start: 0.6636 (tptt) cc_final: 0.6403 (tptt) outliers start: 19 outliers final: 13 residues processed: 160 average time/residue: 0.2195 time to fit residues: 49.0582 Evaluate side-chains 151 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 52 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 109 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN D 3 GLN L 30 ASN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110082 restraints weight = 16127.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109255 restraints weight = 14143.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111418 restraints weight = 12164.333| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9697 Z= 0.197 Angle : 0.577 8.940 13144 Z= 0.299 Chirality : 0.042 0.214 1493 Planarity : 0.003 0.038 1654 Dihedral : 4.864 36.293 1370 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.35 % Allowed : 12.83 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.61 (0.24), residues: 1183 helix: 1.19 (0.27), residues: 403 sheet: -0.80 (0.30), residues: 272 loop : -1.47 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 PHE 0.019 0.001 PHE A 334 TYR 0.032 0.001 TYR R 92 ARG 0.006 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 1.072 Fit side-chains REVERT: A 26 ASP cc_start: 0.7314 (m-30) cc_final: 0.6883 (m-30) REVERT: B 247 ASP cc_start: 0.6869 (t70) cc_final: 0.6588 (t0) REVERT: R 16 TYR cc_start: 0.6549 (p90) cc_final: 0.6342 (p90) outliers start: 14 outliers final: 12 residues processed: 162 average time/residue: 0.2332 time to fit residues: 52.3779 Evaluate side-chains 147 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 103 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN L 45 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN R 162 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.136516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110058 restraints weight = 16098.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109062 restraints weight = 14851.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111259 restraints weight = 12582.378| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9697 Z= 0.213 Angle : 0.588 7.741 13144 Z= 0.304 Chirality : 0.043 0.322 1493 Planarity : 0.003 0.039 1654 Dihedral : 4.812 36.001 1370 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.03 % Allowed : 13.11 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.56 (0.24), residues: 1183 helix: 1.23 (0.27), residues: 402 sheet: -0.78 (0.30), residues: 274 loop : -1.42 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 PHE 0.017 0.001 PHE A 334 TYR 0.034 0.002 TYR R 92 ARG 0.006 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 1.157 Fit side-chains REVERT: A 26 ASP cc_start: 0.7326 (m-30) cc_final: 0.6872 (m-30) REVERT: B 247 ASP cc_start: 0.6888 (t70) cc_final: 0.6664 (t0) REVERT: C 25 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8383 (mt) outliers start: 21 outliers final: 14 residues processed: 164 average time/residue: 0.2217 time to fit residues: 50.9731 Evaluate side-chains 153 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN L 45 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.136826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112183 restraints weight = 24226.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113748 restraints weight = 26145.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114943 restraints weight = 17638.967| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9697 Z= 0.196 Angle : 0.583 8.483 13144 Z= 0.303 Chirality : 0.043 0.280 1493 Planarity : 0.003 0.047 1654 Dihedral : 4.744 35.609 1370 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.35 % Allowed : 14.46 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.52 (0.24), residues: 1183 helix: 1.26 (0.27), residues: 402 sheet: -0.75 (0.30), residues: 274 loop : -1.41 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 PHE 0.025 0.001 PHE D 68 TYR 0.033 0.002 TYR R 92 ARG 0.006 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7360 (m-30) cc_final: 0.6913 (m-30) REVERT: B 247 ASP cc_start: 0.6954 (t70) cc_final: 0.6717 (t0) REVERT: R 16 TYR cc_start: 0.6777 (p90) cc_final: 0.6406 (p90) outliers start: 14 outliers final: 12 residues processed: 157 average time/residue: 0.2220 time to fit residues: 48.5042 Evaluate side-chains 150 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 107 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 71 optimal weight: 0.0370 chunk 79 optimal weight: 0.4980 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.109940 restraints weight = 13930.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113117 restraints weight = 11225.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113874 restraints weight = 7104.523| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9697 Z= 0.187 Angle : 0.584 8.210 13144 Z= 0.303 Chirality : 0.043 0.261 1493 Planarity : 0.003 0.041 1654 Dihedral : 4.674 35.077 1370 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.54 % Allowed : 14.46 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.42 (0.25), residues: 1183 helix: 1.36 (0.27), residues: 402 sheet: -0.67 (0.31), residues: 273 loop : -1.37 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 PHE 0.021 0.001 PHE R 44 TYR 0.034 0.001 TYR R 92 ARG 0.005 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7276 (m-30) cc_final: 0.6837 (m-30) REVERT: A 52 GLN cc_start: 0.6922 (tm-30) cc_final: 0.6424 (tt0) REVERT: B 247 ASP cc_start: 0.6862 (t70) cc_final: 0.6628 (t0) REVERT: C 25 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8374 (mt) REVERT: R 16 TYR cc_start: 0.6702 (p90) cc_final: 0.6381 (p90) REVERT: R 65 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7375 (mm110) outliers start: 16 outliers final: 14 residues processed: 167 average time/residue: 0.2226 time to fit residues: 51.4048 Evaluate side-chains 160 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 88 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 60 optimal weight: 0.0060 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 110 ASN D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111035 restraints weight = 16666.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110468 restraints weight = 12947.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112279 restraints weight = 12829.927| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9697 Z= 0.201 Angle : 0.590 9.881 13144 Z= 0.304 Chirality : 0.043 0.249 1493 Planarity : 0.003 0.045 1654 Dihedral : 4.678 34.982 1370 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.64 % Allowed : 15.24 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.38 (0.25), residues: 1183 helix: 1.36 (0.27), residues: 403 sheet: -0.70 (0.31), residues: 275 loop : -1.29 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 PHE 0.024 0.001 PHE D 68 TYR 0.034 0.002 TYR R 92 ARG 0.007 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 1.055 Fit side-chains REVERT: A 26 ASP cc_start: 0.7319 (m-30) cc_final: 0.6936 (m-30) REVERT: B 247 ASP cc_start: 0.6933 (t0) cc_final: 0.6706 (t0) REVERT: C 25 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8374 (mt) REVERT: D 127 VAL cc_start: 0.8964 (p) cc_final: 0.8715 (t) REVERT: R 16 TYR cc_start: 0.6771 (p90) cc_final: 0.6457 (p90) outliers start: 17 outliers final: 13 residues processed: 168 average time/residue: 0.2275 time to fit residues: 52.9447 Evaluate side-chains 162 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 41 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 89 optimal weight: 0.0570 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 110 ASN D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.138265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112726 restraints weight = 18722.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112454 restraints weight = 16146.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114073 restraints weight = 13014.382| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9697 Z= 0.188 Angle : 0.602 10.122 13144 Z= 0.312 Chirality : 0.043 0.250 1493 Planarity : 0.003 0.044 1654 Dihedral : 4.642 34.686 1370 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.45 % Allowed : 15.43 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.37 (0.25), residues: 1183 helix: 1.36 (0.27), residues: 403 sheet: -0.67 (0.31), residues: 274 loop : -1.29 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 PHE 0.028 0.001 PHE D 68 TYR 0.034 0.001 TYR R 92 ARG 0.007 0.000 ARG D 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7356 (m-30) cc_final: 0.6958 (m-30) REVERT: A 52 GLN cc_start: 0.6929 (tm-30) cc_final: 0.6344 (tt0) REVERT: B 247 ASP cc_start: 0.6916 (t0) cc_final: 0.6669 (t0) REVERT: C 25 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8368 (mt) REVERT: D 127 VAL cc_start: 0.8976 (p) cc_final: 0.8703 (t) REVERT: R 16 TYR cc_start: 0.6825 (p90) cc_final: 0.6515 (p90) REVERT: R 168 LYS cc_start: 0.6103 (tptm) cc_final: 0.5872 (mmmt) outliers start: 15 outliers final: 13 residues processed: 165 average time/residue: 0.2258 time to fit residues: 51.5303 Evaluate side-chains 162 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.0370 chunk 28 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114362 restraints weight = 22386.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.116320 restraints weight = 25501.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117909 restraints weight = 16479.433| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9697 Z= 0.178 Angle : 0.590 9.975 13144 Z= 0.304 Chirality : 0.042 0.244 1493 Planarity : 0.003 0.043 1654 Dihedral : 4.624 34.224 1370 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.25 % Allowed : 15.81 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.32 (0.25), residues: 1183 helix: 1.40 (0.27), residues: 403 sheet: -0.64 (0.31), residues: 274 loop : -1.26 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 PHE 0.016 0.001 PHE R 163 TYR 0.032 0.001 TYR R 92 ARG 0.007 0.000 ARG D 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3365.76 seconds wall clock time: 61 minutes 14.64 seconds (3674.64 seconds total)