Starting phenix.real_space_refine on Thu Jul 2 11:36:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hqn_34951/07_2026/8hqn_34951.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hqn_34951/07_2026/8hqn_34951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hqn_34951/07_2026/8hqn_34951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hqn_34951/07_2026/8hqn_34951.map" model { file = "/net/cci-nas-00/data/ceres_data/8hqn_34951/07_2026/8hqn_34951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hqn_34951/07_2026/8hqn_34951.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hqn_34951/07_2026/8hqn_34951.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hqn_34951/07_2026/8hqn_34951.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.019 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 64 5.16 5 C 5468 2.51 5 N 1460 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8605 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2246 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 291} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 418 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} 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: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2467 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 6, 'TRANS': 303} Chain: "A" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1668 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 212} Chain breaks: 3 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'9HO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.13, per 1000 atoms: 0.25 Number of scatterers: 8605 At special positions: 0 Unit cell: (113.92, 111.25, 136.17, 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 64 16.00 O 1613 8.00 N 1460 7.00 C 5468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 516.0 milliseconds 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 13 sheets defined 36.9% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'C' and resid 10 through 21 removed outlier: 4.211A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.698A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'R' and resid 38 through 71 Proline residue: R 58 - end of helix removed outlier: 3.820A pdb=" N TRP R 65 " --> pdb=" O CYS R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 87 removed outlier: 3.774A pdb=" N VAL R 79 " --> pdb=" O ASN R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 102 Proline residue: R 96 - end of helix Processing helix chain 'R' and resid 112 through 145 Processing helix chain 'R' and resid 146 through 154 removed outlier: 4.126A pdb=" N ARG R 151 " --> pdb=" O ALA R 147 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLY R 152 " --> pdb=" O LEU R 148 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG R 153 " --> pdb=" O GLU R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 180 removed outlier: 3.961A pdb=" N LEU R 161 " --> pdb=" O ARG R 157 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE R 162 " --> pdb=" O THR R 158 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER R 163 " --> pdb=" O ALA R 159 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA R 164 " --> pdb=" O ILE R 160 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS R 165 " --> pdb=" O LEU R 161 " (cutoff:3.500A) Proline residue: R 176 - end of helix Processing helix chain 'R' and resid 194 through 208 Processing helix chain 'R' and resid 208 through 228 Processing helix chain 'R' and resid 233 through 271 Proline residue: R 257 - end of helix removed outlier: 4.622A pdb=" N LYS R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA R 266 " --> pdb=" O LEU R 262 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA R 267 " --> pdb=" O LEU R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 311 Proline residue: R 305 - end of helix removed outlier: 3.613A pdb=" N ALA R 311 " --> pdb=" O ILE R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 331 removed outlier: 3.977A pdb=" N GLN R 317 " --> pdb=" O ASP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 346 removed outlier: 3.840A pdb=" N GLU R 346 " --> pdb=" O ARG R 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.378A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.801A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 50 removed outlier: 7.400A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.527A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.878A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 150 removed outlier: 4.130A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.058A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.809A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 244 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 242 " --> pdb=" O CYS B 233 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 276 through 278 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.883A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.701A pdb=" N TYR H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG H 98 " --> pdb=" O PHE H 110 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 129 through 130 Processing sheet with id=AB2, first strand: chain 'H' and resid 182 through 183 removed outlier: 6.915A pdb=" N TRP H 164 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR H 178 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU H 162 " --> pdb=" O TYR H 178 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY H 213 " --> pdb=" O LEU H 233 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 194 through 195 Processing sheet with id=AB4, first strand: chain 'A' and resid 185 through 191 removed outlier: 5.645A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2254 1.33 - 1.46: 2033 1.46 - 1.58: 4402 1.58 - 1.70: 0 1.70 - 1.83: 89 Bond restraints: 8778 Sorted by residual: bond pdb=" C11 9HO R 401 " pdb=" C12 9HO R 401 " ideal model delta sigma weight residual 1.455 1.551 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" N LEU R 95 " pdb=" CA LEU R 95 " ideal model delta sigma weight residual 1.462 1.491 -0.029 7.70e-03 1.69e+04 1.38e+01 bond pdb=" C ILE R 210 " pdb=" N PRO R 211 " ideal model delta sigma weight residual 1.334 1.389 -0.055 1.51e-02 4.39e+03 1.31e+01 bond pdb=" N LYS B 57 " pdb=" CA LYS B 57 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.36e+00 bond pdb=" N VAL B 320 " pdb=" CA VAL B 320 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.14e-02 7.69e+03 9.32e+00 ... (remaining 8773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.48: 11883 7.48 - 14.96: 12 14.96 - 22.45: 0 22.45 - 29.93: 0 29.93 - 37.41: 1 Bond angle restraints: 11896 Sorted by residual: angle pdb=" C10 9HO R 401 " pdb=" C11 9HO R 401 " pdb=" C12 9HO R 401 " ideal model delta sigma weight residual 122.56 85.15 37.41 3.00e+00 1.11e-01 1.55e+02 angle pdb=" C GLN H 167 " pdb=" N ARG H 168 " pdb=" CA ARG H 168 " ideal model delta sigma weight residual 120.49 130.38 -9.89 1.42e+00 4.96e-01 4.85e+01 angle pdb=" C LYS A 192 " pdb=" CA LYS A 192 " pdb=" CB LYS A 192 " ideal model delta sigma weight residual 117.23 110.18 7.05 1.36e+00 5.41e-01 2.68e+01 angle pdb=" CA LYS A 192 " pdb=" C LYS A 192 " pdb=" N ASP A 193 " ideal model delta sigma weight residual 119.98 115.62 4.36 8.50e-01 1.38e+00 2.64e+01 angle pdb=" C11 9HO R 401 " pdb=" C10 9HO R 401 " pdb=" C9 9HO R 401 " ideal model delta sigma weight residual 126.07 111.47 14.60 3.00e+00 1.11e-01 2.37e+01 ... (remaining 11891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4590 17.91 - 35.83: 479 35.83 - 53.74: 93 53.74 - 71.66: 15 71.66 - 89.57: 3 Dihedral angle restraints: 5180 sinusoidal: 1968 harmonic: 3212 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 6.91 86.09 1 1.00e+01 1.00e-02 8.95e+01 dihedral pdb=" CB CYS H 147 " pdb=" SG CYS H 147 " pdb=" SG CYS H 217 " pdb=" CB CYS H 217 " ideal model delta sinusoidal sigma weight residual 93.00 54.22 38.78 1 1.00e+01 1.00e-02 2.12e+01 dihedral pdb=" CA LEU R 310 " pdb=" C LEU R 310 " pdb=" N ALA R 311 " pdb=" CA ALA R 311 " ideal model delta harmonic sigma weight residual -180.00 -157.46 -22.54 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 5177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1218 0.090 - 0.180: 134 0.180 - 0.269: 8 0.269 - 0.359: 1 0.359 - 0.449: 2 Chirality restraints: 1363 Sorted by residual: chirality pdb=" CG LEU R 262 " pdb=" CB LEU R 262 " pdb=" CD1 LEU R 262 " pdb=" CD2 LEU R 262 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CG LEU R 89 " pdb=" CB LEU R 89 " pdb=" CD1 LEU R 89 " pdb=" CD2 LEU R 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" C9 9HO R 401 " pdb=" C10 9HO R 401 " pdb=" C8 9HO R 401 " pdb=" O3 9HO R 401 " both_signs ideal model delta sigma weight residual False 2.23 2.50 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 1360 not shown) Planarity restraints: 1502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 70 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C GLN R 70 " 0.045 2.00e-02 2.50e+03 pdb=" O GLN R 70 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL R 71 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET H 180 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C MET H 180 " -0.040 2.00e-02 2.50e+03 pdb=" O MET H 180 " 0.015 2.00e-02 2.50e+03 pdb=" N SER H 181 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 210 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO R 211 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " -0.028 5.00e-02 4.00e+02 ... (remaining 1499 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1911 2.78 - 3.31: 8222 3.31 - 3.84: 14161 3.84 - 4.37: 15822 4.37 - 4.90: 27140 Nonbonded interactions: 67256 Sorted by model distance: nonbonded pdb=" OG SER B 227 " pdb=" OD1 ASP B 228 " model vdw 2.253 3.040 nonbonded pdb=" CB PHE R 123 " pdb=" O1 9HO R 401 " model vdw 2.259 3.440 nonbonded pdb=" OG SER B 201 " pdb=" NE1 TRP B 211 " model vdw 2.290 3.120 nonbonded pdb=" O PHE A 336 " pdb=" OG1 THR A 340 " model vdw 2.293 3.040 nonbonded pdb=" NE2 GLN H 167 " pdb=" O ARG H 168 " model vdw 2.295 3.120 ... (remaining 67251 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.680 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.160 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 0.096 8780 Z= 0.313 Angle : 1.055 37.410 11900 Z= 0.572 Chirality : 0.057 0.449 1363 Planarity : 0.006 0.049 1502 Dihedral : 14.851 89.571 3104 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.54 % Allowed : 15.87 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.23), residues: 1089 helix: -0.18 (0.26), residues: 373 sheet: -0.75 (0.32), residues: 236 loop : -1.93 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 256 TYR 0.027 0.003 TYR R 91 PHE 0.019 0.003 PHE A 189 TRP 0.018 0.002 TRP R 98 HIS 0.010 0.002 HIS R 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.31 ( 8778) covalent geometry : angle 1.05451 / 0.57 (11896) SS BOND : bond 0.00344 / 0.18 ( 2) SS BOND : angle 2.05772 / 1.09 ( 4) hydrogen bonds : bond 0.14549 / 10.14 ( 394) hydrogen bonds : angle 7.17662 / 5.06 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: C 19 LEU cc_start: 0.9058 (mt) cc_final: 0.8842 (mp) outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 0.4943 time to fit residues: 39.2795 Evaluate side-chains 50 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 335 VAL Chi-restraints excluded: chain A residue 54 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.0020 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN C 11 GLN A 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.062439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.055685 restraints weight = 39569.922| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.99 r_work: 0.2758 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8780 Z= 0.170 Angle : 0.596 6.880 11900 Z= 0.318 Chirality : 0.042 0.144 1363 Planarity : 0.004 0.042 1502 Dihedral : 5.945 59.765 1221 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.81 % Allowed : 15.77 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.24), residues: 1089 helix: 0.80 (0.27), residues: 378 sheet: -0.75 (0.30), residues: 260 loop : -1.67 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 205 TYR 0.016 0.002 TYR R 91 PHE 0.018 0.002 PHE A 354 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 8778) covalent geometry : angle 0.59478 / 0.32 (11896) SS BOND : bond 0.00182 / 0.09 ( 2) SS BOND : angle 1.75117 / 0.95 ( 4) hydrogen bonds : bond 0.04625 / 3.15 ( 394) hydrogen bonds : angle 5.37361 / 3.81 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: B 58 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8125 (mp) REVERT: R 304 ASP cc_start: 0.9126 (t70) cc_final: 0.8808 (t0) REVERT: A 18 MET cc_start: 0.8420 (tpp) cc_final: 0.8180 (tpp) REVERT: A 256 ASN cc_start: 0.9019 (m-40) cc_final: 0.8558 (m-40) outliers start: 26 outliers final: 7 residues processed: 77 average time/residue: 0.4268 time to fit residues: 35.5736 Evaluate side-chains 54 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain A residue 233 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 53 optimal weight: 0.0060 overall best weight: 2.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 GLN R 105 GLN A 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.062217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.055399 restraints weight = 39292.128| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.97 r_work: 0.2755 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8780 Z= 0.142 Angle : 0.544 6.074 11900 Z= 0.292 Chirality : 0.041 0.137 1363 Planarity : 0.003 0.038 1502 Dihedral : 5.463 55.612 1216 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.92 % Allowed : 16.52 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.25), residues: 1089 helix: 1.22 (0.28), residues: 376 sheet: -0.74 (0.30), residues: 275 loop : -1.48 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 205 TYR 0.015 0.001 TYR B 59 PHE 0.014 0.002 PHE H 29 TRP 0.011 0.001 TRP B 297 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 8778) covalent geometry : angle 0.54373 / 0.29 (11896) SS BOND : bond 0.00245 / 0.13 ( 2) SS BOND : angle 1.35158 / 0.70 ( 4) hydrogen bonds : bond 0.04187 / 2.84 ( 394) hydrogen bonds : angle 4.98497 / 3.55 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 46 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: H 154 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9470 (tt) REVERT: A 256 ASN cc_start: 0.9108 (m-40) cc_final: 0.8686 (m110) outliers start: 27 outliers final: 4 residues processed: 68 average time/residue: 0.4353 time to fit residues: 32.0332 Evaluate side-chains 50 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 261 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 4 optimal weight: 6.9990 chunk 49 optimal weight: 0.1980 chunk 21 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 GLN A 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.064658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.057822 restraints weight = 39551.307| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.01 r_work: 0.2817 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8780 Z= 0.093 Angle : 0.507 6.041 11900 Z= 0.268 Chirality : 0.040 0.187 1363 Planarity : 0.003 0.038 1502 Dihedral : 5.193 52.882 1216 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.69 % Rotamer: Outliers : 2.70 % Allowed : 18.25 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.25), residues: 1089 helix: 1.51 (0.28), residues: 376 sheet: -0.55 (0.31), residues: 266 loop : -1.34 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.011 0.001 TYR H 178 PHE 0.010 0.001 PHE A 354 TRP 0.012 0.001 TRP B 332 HIS 0.005 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.09 ( 8778) covalent geometry : angle 0.50695 / 0.27 (11896) SS BOND : bond 0.00077 / 0.04 ( 2) SS BOND : angle 0.79558 / 0.37 ( 4) hydrogen bonds : bond 0.03533 / 2.38 ( 394) hydrogen bonds : angle 4.61083 / 3.29 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: H 154 LEU cc_start: 0.9702 (OUTLIER) cc_final: 0.9476 (tt) REVERT: A 233 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.7896 (m) REVERT: A 256 ASN cc_start: 0.9125 (m-40) cc_final: 0.8754 (m110) outliers start: 25 outliers final: 7 residues processed: 76 average time/residue: 0.4151 time to fit residues: 34.1823 Evaluate side-chains 53 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain A residue 233 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN C 11 GLN A 213 HIS ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.060999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.054139 restraints weight = 40369.000| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.99 r_work: 0.2723 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8780 Z= 0.218 Angle : 0.590 7.770 11900 Z= 0.314 Chirality : 0.043 0.161 1363 Planarity : 0.003 0.038 1502 Dihedral : 5.400 56.227 1216 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.59 % Rotamer: Outliers : 3.02 % Allowed : 18.57 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1089 helix: 1.33 (0.28), residues: 378 sheet: -0.56 (0.31), residues: 275 loop : -1.28 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 205 TYR 0.015 0.002 TYR H 178 PHE 0.019 0.002 PHE R 38 TRP 0.014 0.002 TRP B 339 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 ( 8778) covalent geometry : angle 0.58992 / 0.31 (11896) SS BOND : bond 0.00290 / 0.15 ( 2) SS BOND : angle 1.41081 / 0.75 ( 4) hydrogen bonds : bond 0.04376 / 2.96 ( 394) hydrogen bonds : angle 4.98856 / 3.57 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 47 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: B 76 ASP cc_start: 0.9511 (t0) cc_final: 0.9284 (t0) REVERT: H 154 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9472 (tt) REVERT: A 256 ASN cc_start: 0.9205 (m-40) cc_final: 0.8857 (m110) outliers start: 28 outliers final: 8 residues processed: 72 average time/residue: 0.4192 time to fit residues: 32.7169 Evaluate side-chains 54 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 158 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain A residue 233 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 93 optimal weight: 0.2980 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN C 11 GLN R 73 GLN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.061057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.054221 restraints weight = 39779.637| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.98 r_work: 0.2723 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8780 Z= 0.183 Angle : 0.572 9.353 11900 Z= 0.302 Chirality : 0.042 0.157 1363 Planarity : 0.003 0.038 1502 Dihedral : 5.370 54.836 1216 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.22 % Favored : 95.68 % Rotamer: Outliers : 1.94 % Allowed : 20.73 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.25), residues: 1089 helix: 1.28 (0.28), residues: 378 sheet: -0.61 (0.30), residues: 268 loop : -1.23 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.015 0.001 TYR H 178 PHE 0.016 0.002 PHE A 189 TRP 0.012 0.001 TRP B 332 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 8778) covalent geometry : angle 0.57199 / 0.30 (11896) SS BOND : bond 0.00241 / 0.13 ( 2) SS BOND : angle 1.19778 / 0.63 ( 4) hydrogen bonds : bond 0.04191 / 2.84 ( 394) hydrogen bonds : angle 4.96797 / 3.57 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: B 76 ASP cc_start: 0.9481 (t0) cc_final: 0.9236 (t0) REVERT: H 154 LEU cc_start: 0.9721 (OUTLIER) cc_final: 0.9465 (tt) outliers start: 18 outliers final: 8 residues processed: 65 average time/residue: 0.4483 time to fit residues: 31.4868 Evaluate side-chains 53 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 158 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain A residue 233 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 14 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN C 11 GLN ** A 347 ASN ** 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 = 0.2995 r_free = 0.2995 target = 0.062383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.055497 restraints weight = 39536.122| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.01 r_work: 0.2760 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8780 Z= 0.115 Angle : 0.528 8.517 11900 Z= 0.276 Chirality : 0.041 0.176 1363 Planarity : 0.003 0.038 1502 Dihedral : 5.258 58.269 1216 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.13 % Favored : 95.78 % Rotamer: Outliers : 2.05 % Allowed : 21.06 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.25), residues: 1089 helix: 1.47 (0.28), residues: 377 sheet: -0.62 (0.30), residues: 276 loop : -1.24 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.012 0.001 TYR H 178 PHE 0.014 0.001 PHE A 189 TRP 0.014 0.001 TRP B 332 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 8778) covalent geometry : angle 0.52808 / 0.28 (11896) SS BOND : bond 0.00154 / 0.08 ( 2) SS BOND : angle 0.90678 / 0.46 ( 4) hydrogen bonds : bond 0.03773 / 2.55 ( 394) hydrogen bonds : angle 4.74732 / 3.41 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: H 154 LEU cc_start: 0.9712 (OUTLIER) cc_final: 0.9476 (tt) REVERT: A 256 ASN cc_start: 0.9081 (m-40) cc_final: 0.8814 (m110) outliers start: 19 outliers final: 10 residues processed: 66 average time/residue: 0.4413 time to fit residues: 31.6564 Evaluate side-chains 55 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 158 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain A residue 233 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 99 optimal weight: 0.0870 chunk 67 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 43 optimal weight: 0.0170 chunk 41 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN R 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.065432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.058528 restraints weight = 38426.472| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.03 r_work: 0.2842 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8780 Z= 0.087 Angle : 0.504 9.308 11900 Z= 0.262 Chirality : 0.040 0.157 1363 Planarity : 0.003 0.036 1502 Dihedral : 4.953 52.452 1216 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.69 % Rotamer: Outliers : 1.84 % Allowed : 21.92 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.26), residues: 1089 helix: 1.70 (0.28), residues: 380 sheet: -0.47 (0.30), residues: 282 loop : -1.17 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.010 0.001 TYR H 178 PHE 0.009 0.001 PHE H 80 TRP 0.015 0.001 TRP B 332 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00173 / 0.09 ( 8778) covalent geometry : angle 0.50364 / 0.26 (11896) SS BOND : bond 0.00123 / 0.06 ( 2) SS BOND : angle 0.70958 / 0.33 ( 4) hydrogen bonds : bond 0.03229 / 2.17 ( 394) hydrogen bonds : angle 4.37140 / 3.16 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: H 154 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9494 (tt) REVERT: A 256 ASN cc_start: 0.9079 (m-40) cc_final: 0.8870 (m110) outliers start: 17 outliers final: 7 residues processed: 66 average time/residue: 0.4363 time to fit residues: 31.2678 Evaluate side-chains 53 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain A residue 233 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 37 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN C 11 GLN R 73 GLN R 104 ASN ** A 347 ASN ** 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 = 0.2940 r_free = 0.2940 target = 0.059993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.053112 restraints weight = 40217.573| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.00 r_work: 0.2701 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 8780 Z= 0.285 Angle : 0.643 9.898 11900 Z= 0.338 Chirality : 0.044 0.156 1363 Planarity : 0.004 0.039 1502 Dihedral : 5.484 56.644 1216 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.22 % Rotamer: Outliers : 2.05 % Allowed : 21.49 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.25), residues: 1089 helix: 1.17 (0.28), residues: 379 sheet: -0.67 (0.31), residues: 275 loop : -1.21 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 205 TYR 0.021 0.002 TYR H 50 PHE 0.024 0.002 PHE R 38 TRP 0.022 0.002 TRP B 339 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.29 ( 8778) covalent geometry : angle 0.64202 / 0.34 (11896) SS BOND : bond 0.00325 / 0.17 ( 2) SS BOND : angle 1.51647 / 0.82 ( 4) hydrogen bonds : bond 0.04645 / 3.14 ( 394) hydrogen bonds : angle 5.04037 / 3.62 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: H 154 LEU cc_start: 0.9733 (OUTLIER) cc_final: 0.9527 (tt) REVERT: R 73 GLN cc_start: 0.9363 (mt0) cc_final: 0.8741 (pp30) REVERT: A 256 ASN cc_start: 0.9139 (m-40) cc_final: 0.8871 (m110) outliers start: 19 outliers final: 9 residues processed: 63 average time/residue: 0.6058 time to fit residues: 40.8319 Evaluate side-chains 51 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 158 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain A residue 233 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.061027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.054125 restraints weight = 39806.552| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.99 r_work: 0.2725 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8780 Z= 0.183 Angle : 0.590 9.272 11900 Z= 0.308 Chirality : 0.042 0.158 1363 Planarity : 0.003 0.044 1502 Dihedral : 5.393 57.880 1216 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.13 % Favored : 95.78 % Rotamer: Outliers : 1.19 % Allowed : 22.46 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.25), residues: 1089 helix: 1.17 (0.28), residues: 379 sheet: -0.70 (0.30), residues: 277 loop : -1.16 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 52 TYR 0.015 0.001 TYR H 178 PHE 0.015 0.002 PHE R 38 TRP 0.010 0.001 TRP B 332 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 8778) covalent geometry : angle 0.59012 / 0.31 (11896) SS BOND : bond 0.00236 / 0.12 ( 2) SS BOND : angle 1.14562 / 0.60 ( 4) hydrogen bonds : bond 0.04175 / 2.82 ( 394) hydrogen bonds : angle 4.92170 / 3.54 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: R 73 GLN cc_start: 0.9393 (mt0) cc_final: 0.8777 (pp30) REVERT: A 256 ASN cc_start: 0.9116 (m-40) cc_final: 0.8873 (m110) outliers start: 11 outliers final: 6 residues processed: 52 average time/residue: 0.5464 time to fit residues: 30.4857 Evaluate side-chains 47 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 42 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN ** A 347 ASN ** 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 = 0.3000 r_free = 0.3000 target = 0.062548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.055630 restraints weight = 39861.072| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.03 r_work: 0.2764 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8780 Z= 0.115 Angle : 0.547 8.915 11900 Z= 0.282 Chirality : 0.040 0.151 1363 Planarity : 0.003 0.038 1502 Dihedral : 5.190 54.730 1216 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.76 % Favored : 96.14 % Rotamer: Outliers : 0.97 % Allowed : 22.57 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.26), residues: 1089 helix: 1.38 (0.28), residues: 380 sheet: -0.66 (0.31), residues: 270 loop : -1.17 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 52 TYR 0.012 0.001 TYR H 178 PHE 0.010 0.001 PHE H 29 TRP 0.013 0.001 TRP B 332 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 8778) covalent geometry : angle 0.54722 / 0.28 (11896) SS BOND : bond 0.00158 / 0.08 ( 2) SS BOND : angle 0.88560 / 0.45 ( 4) hydrogen bonds : bond 0.03718 / 2.50 ( 394) hydrogen bonds : angle 4.67039 / 3.35 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2119.22 seconds wall clock time: 37 minutes 5.22 seconds (2225.22 seconds total)