Starting phenix.real_space_refine on Fri Aug 22 21:25:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iyh_35822/08_2025/8iyh_35822.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iyh_35822/08_2025/8iyh_35822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iyh_35822/08_2025/8iyh_35822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iyh_35822/08_2025/8iyh_35822.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iyh_35822/08_2025/8iyh_35822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iyh_35822/08_2025/8iyh_35822.map" } resolution = 3.3 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= 0.000 sd= 0.039 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 48 5.16 5 C 5108 2.51 5 N 1392 2.21 5 O 1487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8035 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2410 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 8, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1538 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "D" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2001 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 485 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 5, 'ASP:plan': 6, 'ASN:plan1': 4, 'ARG:plan': 8, 'PHE:plan': 9, 'TRP:plan': 5, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 215 Chain: "G" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 400 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1658 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'FI7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.90, per 1000 atoms: 0.24 Number of scatterers: 8035 At special positions: 0 Unit cell: (89.995, 117.432, 133.895, 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 48 16.00 O 1487 8.00 N 1392 7.00 C 5108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 183 " distance=2.37 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 266 " distance=2.03 Simple disulfide: pdb=" SG CYS D 100 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " 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: 0.60 Conformation dependent library (CDL) restraints added in 451.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 38.3% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 3 through 26 Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'B' and resid 8 through 31 Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.712A pdb=" N LYS B 211 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 257 through 261 removed outlier: 4.044A pdb=" N ILE B 261 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 279 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 330 through 351 Processing helix chain 'D' and resid 24 through 54 Proline residue: D 31 - end of helix removed outlier: 3.961A pdb=" N LEU D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 89 Proline residue: D 81 - end of helix Processing helix chain 'D' and resid 96 through 130 removed outlier: 3.502A pdb=" N PHE D 105 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 139 removed outlier: 3.663A pdb=" N ILE D 139 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 187 through 218 removed outlier: 3.980A pdb=" N ALA D 191 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Proline residue: D 200 - end of helix Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 230 through 262 removed outlier: 3.905A pdb=" N VAL D 236 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) Proline residue: D 246 - end of helix Processing helix chain 'D' and resid 265 through 268 removed outlier: 4.228A pdb=" N VAL D 268 " --> pdb=" O ASN D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 268' Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 280 through 289 removed outlier: 3.745A pdb=" N TYR D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER D 287 " --> pdb=" O THR D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 295 removed outlier: 4.090A pdb=" N TYR D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.612A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.814A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.673A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.546A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.566A pdb=" N LEU A 336 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 63 removed outlier: 3.935A pdb=" N LYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU A 79 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA A 92 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A 81 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 105 removed outlier: 6.981A pdb=" N GLY A 115 " --> pdb=" O MET A 101 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS A 103 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA A 113 " --> pdb=" O CYS A 103 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR A 105 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR A 111 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY A 116 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 137 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASN A 125 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL A 135 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 151 removed outlier: 5.896A pdb=" N ASP A 170 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLN A 176 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192 removed outlier: 3.865A pdb=" N SER A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN A 220 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP A 212 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS A 218 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 234 removed outlier: 6.822A pdb=" N CYS A 250 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR A 263 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 252 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 259 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 273 through 278 removed outlier: 6.262A pdb=" N GLY A 288 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL A 276 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 286 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE A 278 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU A 284 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS A 294 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL A 307 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 296 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 186 through 192 removed outlier: 3.643A pdb=" N VAL B 186 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 34 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE B 200 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU B 36 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N ALA B 221 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS B 35 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE B 223 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU B 37 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N CYS B 225 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 39 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ASP B 227 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 13 removed outlier: 4.036A pdb=" N ILE D 182 " --> pdb=" O CYS D 19 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 169 through 171 Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.556A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.898A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 149 removed outlier: 6.073A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1212 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: 1.02 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1399 1.32 - 1.45: 2223 1.45 - 1.57: 4518 1.57 - 1.69: 1 1.69 - 1.81: 64 Bond restraints: 8205 Sorted by residual: bond pdb=" N PHE D 186 " pdb=" CA PHE D 186 " ideal model delta sigma weight residual 1.455 1.528 -0.073 1.23e-02 6.61e+03 3.50e+01 bond pdb=" CA PHE D 186 " pdb=" C PHE D 186 " ideal model delta sigma weight residual 1.522 1.581 -0.060 1.22e-02 6.72e+03 2.39e+01 bond pdb=" C20 FI7 D 401 " pdb=" N19 FI7 D 401 " ideal model delta sigma weight residual 1.396 1.327 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C22 FI7 D 401 " pdb=" O23 FI7 D 401 " ideal model delta sigma weight residual 1.269 1.203 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C LYS B 24 " pdb=" O LYS B 24 " ideal model delta sigma weight residual 1.236 1.201 0.036 1.15e-02 7.56e+03 9.75e+00 ... (remaining 8200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 10882 1.96 - 3.91: 253 3.91 - 5.87: 42 5.87 - 7.82: 10 7.82 - 9.78: 4 Bond angle restraints: 11191 Sorted by residual: angle pdb=" CA PHE D 186 " pdb=" C PHE D 186 " pdb=" O PHE D 186 " ideal model delta sigma weight residual 120.70 112.56 8.14 1.08e+00 8.57e-01 5.68e+01 angle pdb=" N HIS D 184 " pdb=" CA HIS D 184 " pdb=" C HIS D 184 " ideal model delta sigma weight residual 113.19 120.64 -7.45 1.19e+00 7.06e-01 3.92e+01 angle pdb=" N PHE D 186 " pdb=" CA PHE D 186 " pdb=" C PHE D 186 " ideal model delta sigma weight residual 109.40 119.18 -9.78 1.63e+00 3.76e-01 3.60e+01 angle pdb=" O LEU B 23 " pdb=" C LEU B 23 " pdb=" N LYS B 24 " ideal model delta sigma weight residual 122.07 116.90 5.17 1.03e+00 9.43e-01 2.52e+01 angle pdb=" CA LEU B 23 " pdb=" C LEU B 23 " pdb=" N LYS B 24 " ideal model delta sigma weight residual 117.07 122.14 -5.07 1.14e+00 7.69e-01 1.98e+01 ... (remaining 11186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4372 17.56 - 35.11: 339 35.11 - 52.67: 70 52.67 - 70.22: 10 70.22 - 87.78: 3 Dihedral angle restraints: 4794 sinusoidal: 1561 harmonic: 3233 Sorted by residual: dihedral pdb=" CB CYS D 18 " pdb=" SG CYS D 18 " pdb=" SG CYS D 183 " pdb=" CB CYS D 183 " ideal model delta sinusoidal sigma weight residual 93.00 53.07 39.93 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CA ARG H 191 " pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA VAL D 29 " pdb=" C VAL D 29 " pdb=" N LEU D 30 " pdb=" CA LEU D 30 " ideal model delta harmonic sigma weight residual -180.00 -162.14 -17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 938 0.044 - 0.088: 263 0.088 - 0.132: 91 0.132 - 0.177: 8 0.177 - 0.221: 3 Chirality restraints: 1303 Sorted by residual: chirality pdb=" CA ILE D 182 " pdb=" N ILE D 182 " pdb=" C ILE D 182 " pdb=" CB ILE D 182 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ILE D 242 " pdb=" N ILE D 242 " pdb=" C ILE D 242 " pdb=" CB ILE D 242 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE D 13 " pdb=" N ILE D 13 " pdb=" C ILE D 13 " pdb=" CB ILE D 13 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 1300 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C04 FI7 D 401 " 0.064 2.00e-02 2.50e+03 5.71e-02 5.72e+01 pdb=" C05 FI7 D 401 " -0.021 2.00e-02 2.50e+03 pdb=" C07 FI7 D 401 " -0.063 2.00e-02 2.50e+03 pdb=" C08 FI7 D 401 " 0.091 2.00e-02 2.50e+03 pdb=" N06 FI7 D 401 " -0.075 2.00e-02 2.50e+03 pdb=" N15 FI7 D 401 " -0.013 2.00e-02 2.50e+03 pdb=" O16 FI7 D 401 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 FI7 D 401 " 0.081 2.00e-02 2.50e+03 4.11e-02 3.38e+01 pdb=" C08 FI7 D 401 " -0.040 2.00e-02 2.50e+03 pdb=" C09 FI7 D 401 " -0.032 2.00e-02 2.50e+03 pdb=" C10 FI7 D 401 " -0.010 2.00e-02 2.50e+03 pdb=" C11 FI7 D 401 " -0.001 2.00e-02 2.50e+03 pdb=" C13 FI7 D 401 " -0.014 2.00e-02 2.50e+03 pdb=" N14 FI7 D 401 " -0.036 2.00e-02 2.50e+03 pdb=" O12 FI7 D 401 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 232 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C PHE D 232 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE D 232 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE D 233 " -0.022 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 744 2.74 - 3.28: 8075 3.28 - 3.82: 13000 3.82 - 4.36: 15067 4.36 - 4.90: 27511 Nonbonded interactions: 64397 Sorted by model distance: nonbonded pdb=" OD1 ASP A 27 " pdb=" OG SER G 31 " model vdw 2.204 3.040 nonbonded pdb=" O ALA B 41 " pdb=" OG SER B 44 " model vdw 2.212 3.040 nonbonded pdb=" O GLY D 44 " pdb=" OH TYR D 295 " model vdw 2.213 3.040 nonbonded pdb=" NZ LYS G 32 " pdb=" OD2 ASP G 36 " model vdw 2.273 3.120 nonbonded pdb=" OG SER A 281 " pdb=" OD2 ASP G 48 " model vdw 2.278 3.040 ... (remaining 64392 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: 2.240 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.910 Find NCS groups from input model: 0.030 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 0.341 8210 Z= 0.321 Angle : 0.742 14.122 11201 Z= 0.439 Chirality : 0.046 0.221 1303 Planarity : 0.005 0.075 1440 Dihedral : 13.480 87.775 2689 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.08 % Allowed : 15.16 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.53 (0.26), residues: 1099 helix: 0.81 (0.28), residues: 372 sheet: 0.26 (0.31), residues: 273 loop : 0.21 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 349 TYR 0.010 0.001 TYR H 190 PHE 0.015 0.001 PHE D 232 TRP 0.017 0.002 TRP A 82 HIS 0.004 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 8205) covalent geometry : angle 0.72339 (11191) SS BOND : bond 0.15274 ( 5) SS BOND : angle 5.50223 ( 10) hydrogen bonds : bond 0.16971 ( 435) hydrogen bonds : angle 7.06853 ( 1212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.196 Fit side-chains REVERT: A 46 ARG cc_start: 0.7274 (mtm110) cc_final: 0.7028 (ttp80) REVERT: B 24 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6812 (pttm) REVERT: B 26 ASP cc_start: 0.8047 (t0) cc_final: 0.7726 (t0) REVERT: B 210 LYS cc_start: 0.7393 (ptmm) cc_final: 0.6892 (pttm) REVERT: B 273 ASP cc_start: 0.7963 (m-30) cc_final: 0.7631 (p0) REVERT: D 84 MET cc_start: 0.6521 (tpt) cc_final: 0.6267 (tpt) REVERT: D 225 LYS cc_start: 0.6333 (mmtp) cc_final: 0.6041 (mttt) outliers start: 8 outliers final: 1 residues processed: 136 average time/residue: 0.0870 time to fit residues: 15.9050 Evaluate side-chains 110 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain D residue 232 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN B 189 HIS ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN G 24 ASN H 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.189506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.143959 restraints weight = 9095.471| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.67 r_work: 0.3235 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8210 Z= 0.209 Angle : 0.618 6.954 11201 Z= 0.330 Chirality : 0.046 0.169 1303 Planarity : 0.005 0.051 1440 Dihedral : 6.644 59.553 1217 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.92 % Allowed : 13.26 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.50 (0.25), residues: 1099 helix: 1.08 (0.27), residues: 374 sheet: -0.09 (0.30), residues: 301 loop : 0.17 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 349 TYR 0.018 0.002 TYR H 190 PHE 0.024 0.002 PHE H 68 TRP 0.018 0.002 TRP A 169 HIS 0.005 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 8205) covalent geometry : angle 0.61656 (11191) SS BOND : bond 0.00851 ( 5) SS BOND : angle 1.51502 ( 10) hydrogen bonds : bond 0.04297 ( 435) hydrogen bonds : angle 5.05539 ( 1212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.275 Fit side-chains REVERT: A 46 ARG cc_start: 0.7668 (mtm110) cc_final: 0.7294 (ttp80) REVERT: A 160 SER cc_start: 0.9036 (p) cc_final: 0.8707 (p) REVERT: B 210 LYS cc_start: 0.7387 (ptmm) cc_final: 0.6908 (pttm) REVERT: B 273 ASP cc_start: 0.8002 (m-30) cc_final: 0.7389 (p0) REVERT: D 232 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7100 (t80) outliers start: 29 outliers final: 18 residues processed: 136 average time/residue: 0.0770 time to fit residues: 14.6535 Evaluate side-chains 129 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.183648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135244 restraints weight = 8949.260| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 3.13 r_work: 0.3041 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8210 Z= 0.180 Angle : 0.563 8.488 11201 Z= 0.301 Chirality : 0.044 0.163 1303 Planarity : 0.004 0.041 1440 Dihedral : 6.424 59.454 1213 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.79 % Allowed : 14.34 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.49 (0.26), residues: 1099 helix: 1.32 (0.28), residues: 368 sheet: -0.22 (0.30), residues: 291 loop : 0.02 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 349 TYR 0.018 0.001 TYR H 190 PHE 0.018 0.002 PHE A 235 TRP 0.016 0.002 TRP A 169 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8205) covalent geometry : angle 0.56203 (11191) SS BOND : bond 0.00674 ( 5) SS BOND : angle 1.34171 ( 10) hydrogen bonds : bond 0.03883 ( 435) hydrogen bonds : angle 4.72889 ( 1212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.275 Fit side-chains REVERT: A 155 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8162 (t0) REVERT: A 160 SER cc_start: 0.9125 (p) cc_final: 0.8814 (p) REVERT: B 210 LYS cc_start: 0.7312 (ptmm) cc_final: 0.6806 (pttm) REVERT: B 258 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7194 (ptpp) REVERT: B 273 ASP cc_start: 0.8032 (m-30) cc_final: 0.7339 (p0) outliers start: 28 outliers final: 16 residues processed: 131 average time/residue: 0.0759 time to fit residues: 13.7155 Evaluate side-chains 129 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.180808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120412 restraints weight = 9126.401| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.68 r_work: 0.3136 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8210 Z= 0.153 Angle : 0.524 6.887 11201 Z= 0.280 Chirality : 0.043 0.170 1303 Planarity : 0.004 0.045 1440 Dihedral : 6.147 59.476 1211 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.06 % Allowed : 15.56 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.56 (0.26), residues: 1099 helix: 1.49 (0.28), residues: 369 sheet: -0.34 (0.30), residues: 294 loop : 0.09 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 218 TYR 0.018 0.001 TYR H 190 PHE 0.017 0.001 PHE A 235 TRP 0.015 0.001 TRP A 169 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8205) covalent geometry : angle 0.52329 (11191) SS BOND : bond 0.00455 ( 5) SS BOND : angle 1.10963 ( 10) hydrogen bonds : bond 0.03485 ( 435) hydrogen bonds : angle 4.52525 ( 1212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.239 Fit side-chains REVERT: A 160 SER cc_start: 0.9152 (p) cc_final: 0.8863 (p) REVERT: B 210 LYS cc_start: 0.7142 (ptmm) cc_final: 0.6651 (pttm) REVERT: B 258 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7257 (ptpp) REVERT: B 273 ASP cc_start: 0.7956 (m-30) cc_final: 0.7312 (p0) outliers start: 30 outliers final: 19 residues processed: 132 average time/residue: 0.0836 time to fit residues: 14.9149 Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.183167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.119331 restraints weight = 9065.819| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.35 r_work: 0.3092 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8210 Z= 0.179 Angle : 0.541 6.684 11201 Z= 0.289 Chirality : 0.044 0.171 1303 Planarity : 0.004 0.041 1440 Dihedral : 5.949 55.284 1211 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.87 % Allowed : 16.10 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.57 (0.26), residues: 1099 helix: 1.59 (0.28), residues: 372 sheet: -0.49 (0.30), residues: 282 loop : 0.09 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 313 TYR 0.017 0.001 TYR H 190 PHE 0.018 0.002 PHE A 235 TRP 0.013 0.002 TRP A 169 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 8205) covalent geometry : angle 0.54060 (11191) SS BOND : bond 0.00440 ( 5) SS BOND : angle 0.93146 ( 10) hydrogen bonds : bond 0.03541 ( 435) hydrogen bonds : angle 4.48682 ( 1212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.196 Fit side-chains REVERT: A 160 SER cc_start: 0.9181 (p) cc_final: 0.8895 (p) REVERT: B 210 LYS cc_start: 0.7145 (ptmm) cc_final: 0.6661 (pttm) REVERT: B 258 LYS cc_start: 0.8051 (ttpt) cc_final: 0.7269 (ptpp) REVERT: B 273 ASP cc_start: 0.7928 (m-30) cc_final: 0.7257 (p0) REVERT: D 120 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7635 (p) REVERT: D 198 PHE cc_start: 0.6858 (OUTLIER) cc_final: 0.6313 (m-10) REVERT: D 218 ARG cc_start: 0.7566 (mtp85) cc_final: 0.7331 (mmm-85) REVERT: H 19 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7114 (tptp) outliers start: 36 outliers final: 25 residues processed: 137 average time/residue: 0.0845 time to fit residues: 15.6906 Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 64 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.177636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121050 restraints weight = 9006.439| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.35 r_work: 0.3143 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8210 Z= 0.153 Angle : 0.517 6.149 11201 Z= 0.277 Chirality : 0.043 0.169 1303 Planarity : 0.004 0.041 1440 Dihedral : 5.589 48.657 1211 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.74 % Allowed : 16.24 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.56 (0.26), residues: 1099 helix: 1.62 (0.28), residues: 373 sheet: -0.47 (0.30), residues: 295 loop : 0.05 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 313 TYR 0.017 0.001 TYR H 190 PHE 0.015 0.001 PHE A 235 TRP 0.013 0.001 TRP A 169 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8205) covalent geometry : angle 0.51611 (11191) SS BOND : bond 0.00664 ( 5) SS BOND : angle 1.34632 ( 10) hydrogen bonds : bond 0.03339 ( 435) hydrogen bonds : angle 4.36677 ( 1212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.212 Fit side-chains REVERT: A 160 SER cc_start: 0.9247 (p) cc_final: 0.8994 (p) REVERT: B 210 LYS cc_start: 0.7199 (ptmm) cc_final: 0.6662 (pttm) REVERT: B 258 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7260 (ptpp) REVERT: B 273 ASP cc_start: 0.8051 (m-30) cc_final: 0.7300 (p0) REVERT: D 120 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7969 (p) REVERT: D 198 PHE cc_start: 0.6912 (OUTLIER) cc_final: 0.6392 (m-10) REVERT: D 232 PHE cc_start: 0.7895 (m-80) cc_final: 0.7477 (t80) outliers start: 35 outliers final: 26 residues processed: 135 average time/residue: 0.0872 time to fit residues: 16.0149 Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 42 optimal weight: 0.0270 chunk 62 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.179561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123949 restraints weight = 9006.301| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.27 r_work: 0.3112 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8210 Z= 0.174 Angle : 0.538 8.658 11201 Z= 0.287 Chirality : 0.044 0.171 1303 Planarity : 0.004 0.044 1440 Dihedral : 5.251 40.158 1211 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.47 % Allowed : 17.19 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.52 (0.26), residues: 1099 helix: 1.64 (0.28), residues: 372 sheet: -0.61 (0.31), residues: 282 loop : 0.04 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 218 TYR 0.017 0.001 TYR H 190 PHE 0.017 0.002 PHE A 235 TRP 0.012 0.001 TRP A 82 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8205) covalent geometry : angle 0.53727 (11191) SS BOND : bond 0.00546 ( 5) SS BOND : angle 1.24451 ( 10) hydrogen bonds : bond 0.03391 ( 435) hydrogen bonds : angle 4.37347 ( 1212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.216 Fit side-chains REVERT: A 160 SER cc_start: 0.9127 (p) cc_final: 0.8855 (p) REVERT: B 210 LYS cc_start: 0.7186 (ptmm) cc_final: 0.6742 (pttm) REVERT: B 258 LYS cc_start: 0.8099 (ttpt) cc_final: 0.7356 (ptpp) REVERT: D 120 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7930 (p) REVERT: D 198 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.6365 (m-10) REVERT: D 232 PHE cc_start: 0.7879 (m-80) cc_final: 0.7483 (t80) REVERT: D 292 VAL cc_start: 0.6124 (p) cc_final: 0.5705 (p) REVERT: H 19 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7140 (tptp) outliers start: 33 outliers final: 25 residues processed: 137 average time/residue: 0.0872 time to fit residues: 16.2830 Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 98 optimal weight: 0.0670 chunk 92 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 72 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 8 optimal weight: 0.0870 chunk 73 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.180087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116918 restraints weight = 8868.148| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.29 r_work: 0.3183 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8210 Z= 0.106 Angle : 0.488 8.186 11201 Z= 0.259 Chirality : 0.042 0.162 1303 Planarity : 0.004 0.043 1440 Dihedral : 4.573 26.354 1211 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.92 % Allowed : 17.32 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.71 (0.26), residues: 1099 helix: 1.77 (0.28), residues: 373 sheet: -0.48 (0.30), residues: 292 loop : 0.18 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 218 TYR 0.017 0.001 TYR H 190 PHE 0.016 0.001 PHE A 292 TRP 0.017 0.001 TRP A 169 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8205) covalent geometry : angle 0.48721 (11191) SS BOND : bond 0.00467 ( 5) SS BOND : angle 0.97547 ( 10) hydrogen bonds : bond 0.02942 ( 435) hydrogen bonds : angle 4.18902 ( 1212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.289 Fit side-chains REVERT: A 45 MET cc_start: 0.8186 (ptt) cc_final: 0.7616 (ptt) REVERT: A 160 SER cc_start: 0.9192 (p) cc_final: 0.8933 (p) REVERT: B 210 LYS cc_start: 0.7083 (ptmm) cc_final: 0.6551 (pttm) REVERT: B 258 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7199 (ptpp) REVERT: D 120 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7652 (p) REVERT: D 198 PHE cc_start: 0.6781 (OUTLIER) cc_final: 0.6257 (m-10) REVERT: D 218 ARG cc_start: 0.7635 (mmm-85) cc_final: 0.7025 (mtp85) REVERT: D 232 PHE cc_start: 0.7799 (m-80) cc_final: 0.7374 (t80) REVERT: D 292 VAL cc_start: 0.6198 (p) cc_final: 0.5756 (p) REVERT: H 19 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7200 (tptp) outliers start: 29 outliers final: 15 residues processed: 130 average time/residue: 0.0875 time to fit residues: 15.6082 Evaluate side-chains 131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 102 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.183045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.135333 restraints weight = 8886.044| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.13 r_work: 0.3046 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8210 Z= 0.150 Angle : 0.521 8.298 11201 Z= 0.277 Chirality : 0.043 0.161 1303 Planarity : 0.004 0.041 1440 Dihedral : 4.531 26.024 1211 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.98 % Allowed : 18.13 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.66 (0.26), residues: 1099 helix: 1.81 (0.28), residues: 372 sheet: -0.57 (0.30), residues: 295 loop : 0.13 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 218 TYR 0.017 0.001 TYR H 190 PHE 0.016 0.001 PHE A 235 TRP 0.011 0.001 TRP A 169 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8205) covalent geometry : angle 0.51999 (11191) SS BOND : bond 0.00477 ( 5) SS BOND : angle 0.98452 ( 10) hydrogen bonds : bond 0.03189 ( 435) hydrogen bonds : angle 4.25379 ( 1212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.243 Fit side-chains REVERT: A 160 SER cc_start: 0.9201 (p) cc_final: 0.8960 (p) REVERT: B 210 LYS cc_start: 0.7244 (ptmm) cc_final: 0.6761 (pttm) REVERT: B 258 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7296 (ptpp) REVERT: D 120 VAL cc_start: 0.8330 (OUTLIER) cc_final: 0.8110 (p) REVERT: D 198 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.6474 (m-10) REVERT: D 218 ARG cc_start: 0.7728 (mmm-85) cc_final: 0.6963 (mtp85) REVERT: D 232 PHE cc_start: 0.7998 (m-80) cc_final: 0.7595 (t80) REVERT: D 292 VAL cc_start: 0.6322 (p) cc_final: 0.5875 (p) REVERT: H 19 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7225 (tptp) outliers start: 22 outliers final: 17 residues processed: 131 average time/residue: 0.0825 time to fit residues: 14.7974 Evaluate side-chains 133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 102 optimal weight: 0.1980 chunk 65 optimal weight: 0.0970 chunk 41 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 3 optimal weight: 0.0070 chunk 107 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.192178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.146829 restraints weight = 9031.094| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.98 r_work: 0.3195 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8210 Z= 0.105 Angle : 0.490 8.035 11201 Z= 0.260 Chirality : 0.042 0.158 1303 Planarity : 0.004 0.041 1440 Dihedral : 4.347 26.099 1211 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.98 % Allowed : 18.27 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.76 (0.26), residues: 1099 helix: 1.87 (0.28), residues: 373 sheet: -0.45 (0.30), residues: 293 loop : 0.14 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 218 TYR 0.017 0.001 TYR H 190 PHE 0.011 0.001 PHE A 292 TRP 0.016 0.001 TRP A 169 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8205) covalent geometry : angle 0.48946 (11191) SS BOND : bond 0.00438 ( 5) SS BOND : angle 0.89459 ( 10) hydrogen bonds : bond 0.02890 ( 435) hydrogen bonds : angle 4.13951 ( 1212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.240 Fit side-chains REVERT: A 160 SER cc_start: 0.9117 (p) cc_final: 0.8871 (p) REVERT: B 210 LYS cc_start: 0.7249 (ptmm) cc_final: 0.6751 (pttm) REVERT: B 258 LYS cc_start: 0.8031 (ttpt) cc_final: 0.7323 (ptpp) REVERT: D 120 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.8063 (p) REVERT: D 167 MET cc_start: 0.8209 (mmt) cc_final: 0.7960 (mmp) REVERT: D 198 PHE cc_start: 0.6889 (OUTLIER) cc_final: 0.6426 (m-10) REVERT: D 218 ARG cc_start: 0.7735 (mmm-85) cc_final: 0.6972 (mtp85) REVERT: D 232 PHE cc_start: 0.7808 (m-80) cc_final: 0.7489 (t80) REVERT: D 292 VAL cc_start: 0.6227 (p) cc_final: 0.5754 (m) REVERT: H 19 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7129 (tptp) REVERT: H 82 GLN cc_start: 0.7694 (tp40) cc_final: 0.7317 (tp40) outliers start: 22 outliers final: 14 residues processed: 134 average time/residue: 0.0735 time to fit residues: 13.4484 Evaluate side-chains 132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.187947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.141509 restraints weight = 8929.431| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.72 r_work: 0.3164 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8210 Z= 0.167 Angle : 0.530 8.143 11201 Z= 0.283 Chirality : 0.043 0.154 1303 Planarity : 0.004 0.041 1440 Dihedral : 4.472 27.425 1211 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.57 % Allowed : 18.81 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.63 (0.26), residues: 1099 helix: 1.85 (0.28), residues: 372 sheet: -0.65 (0.30), residues: 284 loop : 0.07 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 218 TYR 0.017 0.001 TYR H 190 PHE 0.017 0.002 PHE A 235 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8205) covalent geometry : angle 0.52983 (11191) SS BOND : bond 0.00468 ( 5) SS BOND : angle 0.96845 ( 10) hydrogen bonds : bond 0.03227 ( 435) hydrogen bonds : angle 4.23589 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1868.10 seconds wall clock time: 32 minutes 38.31 seconds (1958.31 seconds total)