Starting phenix.real_space_refine on Sat Dec 28 13:09:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hqn_34951/12_2024/8hqn_34951.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hqn_34951/12_2024/8hqn_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_34951/12_2024/8hqn_34951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hqn_34951/12_2024/8hqn_34951.map" model { file = "/net/cci-nas-00/data/ceres_data/8hqn_34951/12_2024/8hqn_34951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hqn_34951/12_2024/8hqn_34951.cif" } resolution = 3.0 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= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG: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, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP: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: 5.13, per 1000 atoms: 0.60 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.98 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: 2.40 Time building geometry restraints manager: 2.65 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 - 35.64: 5067 35.64 - 71.28: 113 71.28 - 106.92: 3 106.92 - 142.56: 0 142.56 - 178.20: 1 Dihedral angle restraints: 5184 sinusoidal: 1972 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=" C11 9HO R 401 " pdb=" C10 9HO R 401 " pdb=" C9 9HO R 401 " pdb=" O3 9HO R 401 " ideal model delta sinusoidal sigma weight residual 1.74 179.94 -178.20 1 3.00e+01 1.11e-03 2.13e+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 ... (remaining 5181 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: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.970 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 8778 Z= 0.383 Angle : 1.055 37.410 11896 Z= 0.572 Chirality : 0.057 0.449 1363 Planarity : 0.006 0.049 1502 Dihedral : 15.246 178.201 3108 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.80 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 (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: -1.62 (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 TRP 0.018 0.002 TRP R 98 HIS 0.010 0.002 HIS R 242 PHE 0.019 0.003 PHE A 189 TYR 0.027 0.003 TYR R 91 ARG 0.006 0.001 ARG B 256 *********************** 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 : 1.065 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: 1.3912 time to fit residues: 111.3742 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 : 1.014 ------------------------------------------------------------------------------- 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 92 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN C 11 GLN A 213 HIS A 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8778 Z= 0.303 Angle : 0.620 6.920 11896 Z= 0.331 Chirality : 0.043 0.146 1363 Planarity : 0.004 0.041 1502 Dihedral : 7.277 131.468 1225 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.48 % Allowed : 16.74 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.24), residues: 1089 helix: 0.71 (0.27), residues: 378 sheet: -0.74 (0.30), residues: 265 loop : -1.69 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS H 35 PHE 0.018 0.002 PHE H 29 TYR 0.016 0.002 TYR H 178 ARG 0.005 0.000 ARG A 205 *********************** 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 76 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.956 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 73 average time/residue: 1.2288 time to fit residues: 96.7913 Evaluate side-chains 51 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR 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 55 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN R 105 GLN A 304 GLN A 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8778 Z= 0.181 Angle : 0.550 6.910 11896 Z= 0.293 Chirality : 0.041 0.181 1363 Planarity : 0.003 0.038 1502 Dihedral : 6.732 116.500 1220 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.81 % Allowed : 16.85 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.54 (0.25), residues: 1089 helix: 1.16 (0.28), residues: 376 sheet: -0.66 (0.30), residues: 282 loop : -1.47 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.005 0.001 HIS H 35 PHE 0.013 0.001 PHE H 29 TYR 0.018 0.001 TYR B 59 ARG 0.004 0.000 ARG A 205 *********************** 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: 26 poor density : 47 time to evaluate : 1.090 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 4 residues processed: 69 average time/residue: 1.1004 time to fit residues: 82.5981 Evaluate side-chains 49 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 97 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN A 213 HIS A 256 ASN A 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8778 Z= 0.209 Angle : 0.540 5.921 11896 Z= 0.288 Chirality : 0.041 0.166 1363 Planarity : 0.003 0.038 1502 Dihedral : 6.603 109.266 1220 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 3.24 % Allowed : 17.82 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1089 helix: 1.31 (0.28), residues: 377 sheet: -0.59 (0.31), residues: 261 loop : -1.37 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 332 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.001 PHE A 354 TYR 0.014 0.001 TYR H 178 ARG 0.003 0.000 ARG A 205 *********************** 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 77 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 47 time to evaluate : 1.039 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 7 residues processed: 73 average time/residue: 1.0302 time to fit residues: 81.8043 Evaluate side-chains 51 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 327 VAL Chi-restraints excluded: chain R residue 57 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN C 11 GLN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8778 Z= 0.176 Angle : 0.535 7.923 11896 Z= 0.281 Chirality : 0.040 0.164 1363 Planarity : 0.003 0.036 1502 Dihedral : 6.517 105.408 1220 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 2.59 % Allowed : 19.11 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1089 helix: 1.43 (0.28), residues: 376 sheet: -0.53 (0.31), residues: 261 loop : -1.33 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 332 HIS 0.005 0.001 HIS H 35 PHE 0.015 0.001 PHE A 189 TYR 0.013 0.001 TYR H 178 ARG 0.002 0.000 ARG A 205 *********************** 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 71 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 47 time to evaluate : 1.040 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 70 average time/residue: 1.0595 time to fit residues: 80.7134 Evaluate side-chains 58 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 69 LEU 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 94 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 0.0470 chunk 34 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 overall best weight: 5.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN A 213 HIS A 256 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8778 Z= 0.348 Angle : 0.600 7.556 11896 Z= 0.319 Chirality : 0.043 0.163 1363 Planarity : 0.004 0.039 1502 Dihedral : 6.709 105.707 1220 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.41 % Favored : 95.50 % Rotamer: Outliers : 3.24 % Allowed : 19.87 % 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 (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: -0.46 (0.25), residues: 1089 helix: 1.20 (0.28), residues: 378 sheet: -0.74 (0.31), residues: 270 loop : -1.30 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.003 0.001 HIS H 35 PHE 0.018 0.002 PHE R 38 TYR 0.016 0.002 TYR H 178 ARG 0.004 0.000 ARG A 205 *********************** 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 75 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 45 time to evaluate : 1.100 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 73 average time/residue: 1.0461 time to fit residues: 83.0305 Evaluate side-chains 57 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 69 LEU 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 Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN R 73 GLN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8778 Z= 0.242 Angle : 0.562 9.399 11896 Z= 0.296 Chirality : 0.042 0.170 1363 Planarity : 0.003 0.036 1502 Dihedral : 6.626 105.971 1220 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.59 % Favored : 95.32 % Rotamer: Outliers : 2.27 % Allowed : 21.06 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.25), residues: 1089 helix: 1.27 (0.28), residues: 376 sheet: -0.70 (0.30), residues: 282 loop : -1.21 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 332 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.002 PHE A 189 TYR 0.014 0.001 TYR H 178 ARG 0.003 0.000 ARG A 205 *********************** 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 65 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 0.979 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 63 average time/residue: 1.1751 time to fit residues: 80.0827 Evaluate side-chains 57 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 B residue 327 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 69 LEU 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 Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN A 256 ASN A 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8778 Z= 0.176 Angle : 0.537 9.361 11896 Z= 0.280 Chirality : 0.040 0.160 1363 Planarity : 0.003 0.037 1502 Dihedral : 6.525 103.477 1220 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.67 % Favored : 96.24 % Rotamer: Outliers : 2.48 % Allowed : 21.49 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.24 (0.26), residues: 1089 helix: 1.43 (0.28), residues: 377 sheet: -0.64 (0.30), residues: 276 loop : -1.20 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 332 HIS 0.005 0.001 HIS H 35 PHE 0.011 0.001 PHE A 189 TYR 0.013 0.001 TYR H 178 ARG 0.003 0.000 ARG A 205 *********************** 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 68 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 1.029 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 68 average time/residue: 1.0873 time to fit residues: 80.1726 Evaluate side-chains 54 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 B residue 327 VAL Chi-restraints excluded: chain H residue 162 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 Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.0970 chunk 30 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 346 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8778 Z= 0.142 Angle : 0.529 9.813 11896 Z= 0.275 Chirality : 0.040 0.155 1363 Planarity : 0.003 0.035 1502 Dihedral : 6.439 98.684 1220 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.76 % Favored : 96.14 % Rotamer: Outliers : 1.84 % Allowed : 21.81 % 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 (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: -0.09 (0.26), residues: 1089 helix: 1.62 (0.28), residues: 375 sheet: -0.53 (0.30), residues: 281 loop : -1.20 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 332 HIS 0.005 0.001 HIS H 35 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR H 178 ARG 0.003 0.000 ARG A 205 *********************** 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 63 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7781 (mtp) cc_final: 0.7348 (mtp) outliers start: 17 outliers final: 10 residues processed: 61 average time/residue: 1.1165 time to fit residues: 74.0028 Evaluate side-chains 54 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 162 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 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 49 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN C 11 GLN ** R 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8778 Z= 0.190 Angle : 0.560 9.966 11896 Z= 0.291 Chirality : 0.040 0.152 1363 Planarity : 0.003 0.038 1502 Dihedral : 6.388 96.358 1220 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 1.30 % Allowed : 22.46 % 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 (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: -0.13 (0.26), residues: 1089 helix: 1.55 (0.28), residues: 377 sheet: -0.49 (0.30), residues: 281 loop : -1.24 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.001 PHE A 189 TYR 0.013 0.001 TYR H 178 ARG 0.003 0.000 ARG A 205 ********************** 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 55 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7769 (mtp) cc_final: 0.7331 (mtp) outliers start: 12 outliers final: 10 residues processed: 55 average time/residue: 1.2663 time to fit residues: 75.0400 Evaluate side-chains 52 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 162 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 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 79 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 86 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 4 optimal weight: 0.0570 chunk 62 optimal weight: 4.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 73 GLN R 104 ASN A 346 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.064444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.057541 restraints weight = 38528.456| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.02 r_work: 0.2820 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8778 Z= 0.129 Angle : 0.534 9.620 11896 Z= 0.273 Chirality : 0.040 0.151 1363 Planarity : 0.003 0.035 1502 Dihedral : 6.338 93.011 1220 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 1.30 % Allowed : 22.57 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1089 helix: 1.72 (0.28), residues: 376 sheet: -0.39 (0.31), residues: 282 loop : -1.14 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 332 HIS 0.006 0.001 HIS H 35 PHE 0.012 0.001 PHE A 189 TYR 0.011 0.001 TYR H 178 ARG 0.003 0.000 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2341.02 seconds wall clock time: 43 minutes 27.84 seconds (2607.84 seconds total)