Starting phenix.real_space_refine on Wed Feb 4 01:41:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kz8_62654/02_2026/9kz8_62654.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kz8_62654/02_2026/9kz8_62654.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/9kz8_62654/02_2026/9kz8_62654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kz8_62654/02_2026/9kz8_62654.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kz8_62654/02_2026/9kz8_62654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kz8_62654/02_2026/9kz8_62654.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= 0.001 sd= 0.018 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 53 5.16 5 C 5230 2.51 5 N 1397 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8173 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2147 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1554 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2382 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 12, 'GLN:plan1': 4, 'ARG:plan': 8, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 126 Chain: "G" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 364 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1639 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 70 Classifications: {'peptide': 8} Link IDs: {'NMTRANS': 1, 'PTRANS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Classifications: {'peptide': 2} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 1} Time building chain proxies: 1.81, per 1000 atoms: 0.22 Number of scatterers: 8173 At special positions: 0 Unit cell: (86.87, 122.64, 126.473, 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 53 16.00 O 1493 8.00 N 1397 7.00 C 5230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 172 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 326.4 milliseconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 9 " Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 37.6% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'C' and resid 20 through 51 Processing helix chain 'C' and resid 58 through 82 Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 92 through 126 Proline residue: C 99 - end of helix Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 135 through 161 Proline residue: C 156 - end of helix Processing helix chain 'C' and resid 323 through 357 removed outlier: 5.200A pdb=" N VAL C 340 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Proline residue: C 341 - end of helix Processing helix chain 'C' and resid 364 through 393 Proline residue: C 385 - end of helix Processing helix chain 'C' and resid 400 through 429 removed outlier: 4.442A pdb=" N HIS C 411 " --> pdb=" O MET C 407 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N MET C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS C 422 " --> pdb=" O SER C 418 " (cutoff:3.500A) Proline residue: C 425 - end of helix Processing helix chain 'C' and resid 432 through 443 Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.573A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.615A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.877A pdb=" N LEU A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 261 removed outlier: 4.004A pdb=" N ILE A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.552A pdb=" N ALA A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.587A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.578A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.568A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.560A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.856A 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: 4.150A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.604A pdb=" N LEU A 38 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.695A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.657A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.657A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.394A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.632A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.677A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.701A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.458A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.751A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 155 through 159 removed outlier: 3.575A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 194 through 195 removed outlier: 5.619A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1239 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: 1.44 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2639 1.34 - 1.46: 1795 1.46 - 1.58: 3851 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 8355 Sorted by residual: bond pdb=" C THR C 324 " pdb=" N PRO C 325 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.36e-02 5.41e+03 7.79e-01 bond pdb=" CB ASP A 252 " pdb=" CG ASP A 252 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.07e-01 bond pdb=" CB ASN B 268 " pdb=" CG ASN B 268 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.19e-01 bond pdb=" CA GLY B 185 " pdb=" C GLY B 185 " ideal model delta sigma weight residual 1.520 1.512 0.008 1.04e-02 9.25e+03 6.00e-01 bond pdb=" CA THR C 324 " pdb=" C THR C 324 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 5.97e-01 ... (remaining 8350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 11153 1.32 - 2.65: 200 2.65 - 3.97: 31 3.97 - 5.29: 16 5.29 - 6.61: 1 Bond angle restraints: 11401 Sorted by residual: angle pdb=" N MET H 192 " pdb=" CA MET H 192 " pdb=" CB MET H 192 " ideal model delta sigma weight residual 113.65 110.34 3.31 1.47e+00 4.63e-01 5.06e+00 angle pdb=" CA GLN C 20 " pdb=" CB GLN C 20 " pdb=" CG GLN C 20 " ideal model delta sigma weight residual 114.10 118.29 -4.19 2.00e+00 2.50e-01 4.38e+00 angle pdb=" C ILE C 395 " pdb=" N THR C 396 " pdb=" CA THR C 396 " ideal model delta sigma weight residual 121.54 125.46 -3.92 1.91e+00 2.74e-01 4.21e+00 angle pdb=" CA THR C 324 " pdb=" C THR C 324 " pdb=" N PRO C 325 " ideal model delta sigma weight residual 118.44 121.66 -3.22 1.59e+00 3.96e-01 4.10e+00 angle pdb=" N THR C 324 " pdb=" CA THR C 324 " pdb=" C THR C 324 " ideal model delta sigma weight residual 109.81 113.97 -4.16 2.21e+00 2.05e-01 3.54e+00 ... (remaining 11396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4471 17.95 - 35.90: 314 35.90 - 53.84: 42 53.84 - 71.79: 6 71.79 - 89.74: 3 Dihedral angle restraints: 4836 sinusoidal: 1598 harmonic: 3238 Sorted by residual: dihedral pdb=" CB CYS C 95 " pdb=" SG CYS C 95 " pdb=" SG CYS C 172 " pdb=" CB CYS C 172 " ideal model delta sinusoidal sigma weight residual -86.00 -166.94 80.94 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CA LEU C 84 " pdb=" C LEU C 84 " pdb=" N GLN C 85 " pdb=" CA GLN C 85 " ideal model delta harmonic sigma weight residual 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CG ARG A 10 " pdb=" CD ARG A 10 " pdb=" NE ARG A 10 " pdb=" CZ ARG A 10 " ideal model delta sinusoidal sigma weight residual 180.00 137.01 42.99 2 1.50e+01 4.44e-03 9.92e+00 ... (remaining 4833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 874 0.033 - 0.066: 306 0.066 - 0.098: 105 0.098 - 0.131: 51 0.131 - 0.164: 2 Chirality restraints: 1338 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA THR C 324 " pdb=" N THR C 324 " pdb=" C THR C 324 " pdb=" CB THR C 324 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1335 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.47e+00 pdb=" N PRO B 236 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 335 " -0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00 pdb=" C VAL C 335 " 0.021 2.00e-02 2.50e+03 pdb=" O VAL C 335 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL C 336 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 75 " 0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO C 76 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " 0.015 5.00e-02 4.00e+02 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1094 2.76 - 3.29: 7751 3.29 - 3.83: 13099 3.83 - 4.36: 14378 4.36 - 4.90: 26375 Nonbonded interactions: 62697 Sorted by model distance: nonbonded pdb=" OD2 ASP B 212 " pdb=" NH1 ARG B 219 " model vdw 2.219 3.120 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.260 3.040 nonbonded pdb=" OE2 GLU A 14 " pdb=" OG SER H 52 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.280 3.040 ... (remaining 62692 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: 1.650 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.900 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 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 : 0.002 0.099 8359 Z= 0.149 Angle : 0.474 6.614 11407 Z= 0.256 Chirality : 0.041 0.164 1338 Planarity : 0.003 0.030 1450 Dihedral : 12.344 89.741 2733 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.27), residues: 1095 helix: 2.22 (0.27), residues: 382 sheet: -0.01 (0.32), residues: 286 loop : -0.56 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.011 0.001 TYR C 174 PHE 0.011 0.001 PHE B 199 TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 8355) covalent geometry : angle 0.47431 (11401) SS BOND : bond 0.00062 ( 3) SS BOND : angle 0.25535 ( 6) hydrogen bonds : bond 0.17349 ( 428) hydrogen bonds : angle 6.61418 ( 1239) Misc. bond : bond 0.09935 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.189 Fit side-chains REVERT: C 30 LEU cc_start: 0.8118 (mt) cc_final: 0.7821 (mt) REVERT: C 52 MET cc_start: 0.6610 (mtt) cc_final: 0.6405 (mtt) REVERT: C 61 PHE cc_start: 0.6684 (m-80) cc_final: 0.6461 (m-80) REVERT: C 93 PHE cc_start: 0.6914 (t80) cc_final: 0.6661 (t80) REVERT: C 117 SER cc_start: 0.8667 (t) cc_final: 0.8198 (p) REVERT: C 119 ASP cc_start: 0.7227 (t70) cc_final: 0.6817 (t0) REVERT: C 381 ILE cc_start: 0.7463 (tp) cc_final: 0.7227 (tt) REVERT: C 392 LEU cc_start: 0.7315 (mt) cc_final: 0.7055 (mp) REVERT: C 407 MET cc_start: 0.7379 (mtt) cc_final: 0.7177 (mtm) REVERT: A 195 LEU cc_start: 0.7951 (mt) cc_final: 0.7604 (mt) REVERT: A 256 ASN cc_start: 0.8227 (m-40) cc_final: 0.7955 (m110) REVERT: A 323 MET cc_start: 0.7725 (mmt) cc_final: 0.7470 (mmm) REVERT: A 333 GLN cc_start: 0.7607 (tp40) cc_final: 0.7017 (mm-40) REVERT: A 341 ASP cc_start: 0.7259 (t0) cc_final: 0.7041 (t0) REVERT: B 63 TRP cc_start: 0.8370 (m100) cc_final: 0.8130 (m100) REVERT: B 137 ARG cc_start: 0.7980 (tpp80) cc_final: 0.7768 (tpp-160) REVERT: B 333 ASP cc_start: 0.7491 (p0) cc_final: 0.7283 (p0) REVERT: H 23 SER cc_start: 0.7823 (t) cc_final: 0.7270 (p) REVERT: H 39 GLN cc_start: 0.8038 (tt0) cc_final: 0.7789 (tt0) REVERT: H 145 SER cc_start: 0.8293 (m) cc_final: 0.8030 (t) REVERT: H 195 LEU cc_start: 0.7662 (tp) cc_final: 0.7389 (tp) REVERT: H 215 THR cc_start: 0.7692 (t) cc_final: 0.7492 (p) REVERT: H 235 TYR cc_start: 0.7859 (m-80) cc_final: 0.7398 (m-80) REVERT: D 6 MET cc_start: 0.7375 (mmp) cc_final: 0.7146 (mmp) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.0800 time to fit residues: 32.5237 Evaluate side-chains 247 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN C 133 HIS C 175 ASN A 214 HIS A 305 GLN B 176 GLN B 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.112630 restraints weight = 13305.636| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.36 r_work: 0.3315 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8359 Z= 0.214 Angle : 0.593 7.038 11407 Z= 0.319 Chirality : 0.046 0.190 1338 Planarity : 0.004 0.032 1450 Dihedral : 4.192 43.133 1187 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.93 % Allowed : 13.71 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.26), residues: 1095 helix: 1.93 (0.27), residues: 387 sheet: -0.38 (0.31), residues: 281 loop : -0.60 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 198 TYR 0.015 0.002 TYR H 190 PHE 0.021 0.002 PHE C 354 TRP 0.020 0.003 TRP B 211 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 8355) covalent geometry : angle 0.59261 (11401) SS BOND : bond 0.00288 ( 3) SS BOND : angle 0.90951 ( 6) hydrogen bonds : bond 0.04890 ( 428) hydrogen bonds : angle 4.96640 ( 1239) Misc. bond : bond 0.00133 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 0.286 Fit side-chains REVERT: C 30 LEU cc_start: 0.8517 (mt) cc_final: 0.8220 (mt) REVERT: C 52 MET cc_start: 0.8203 (mtt) cc_final: 0.7827 (mtt) REVERT: C 61 PHE cc_start: 0.7458 (m-80) cc_final: 0.7242 (m-80) REVERT: C 117 SER cc_start: 0.8716 (t) cc_final: 0.8284 (p) REVERT: C 119 ASP cc_start: 0.7815 (t70) cc_final: 0.7438 (t70) REVERT: C 153 MET cc_start: 0.8384 (tpp) cc_final: 0.7911 (tpp) REVERT: C 345 MET cc_start: 0.8408 (mtp) cc_final: 0.8061 (ttm) REVERT: C 381 ILE cc_start: 0.7913 (tp) cc_final: 0.7676 (tt) REVERT: A 195 LEU cc_start: 0.8288 (mt) cc_final: 0.8025 (mt) REVERT: A 246 GLU cc_start: 0.6782 (pm20) cc_final: 0.6256 (pm20) REVERT: A 253 SER cc_start: 0.8624 (t) cc_final: 0.8332 (p) REVERT: A 256 ASN cc_start: 0.8596 (m-40) cc_final: 0.8281 (m110) REVERT: A 307 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7679 (mp10) REVERT: A 323 MET cc_start: 0.8362 (mmt) cc_final: 0.8135 (mmm) REVERT: A 330 ASN cc_start: 0.7943 (m-40) cc_final: 0.7680 (t0) REVERT: B 32 GLN cc_start: 0.7037 (mt0) cc_final: 0.6789 (mt0) REVERT: B 48 ARG cc_start: 0.8554 (mmt180) cc_final: 0.8307 (mmt-90) REVERT: B 211 TRP cc_start: 0.8413 (m100) cc_final: 0.8103 (m100) REVERT: B 298 ASP cc_start: 0.8116 (t0) cc_final: 0.7913 (t70) REVERT: B 317 CYS cc_start: 0.7842 (p) cc_final: 0.7372 (p) REVERT: B 333 ASP cc_start: 0.8226 (p0) cc_final: 0.7985 (p0) REVERT: H 23 SER cc_start: 0.8006 (t) cc_final: 0.7488 (p) REVERT: H 39 GLN cc_start: 0.8532 (tt0) cc_final: 0.8238 (tt0) REVERT: H 103 TYR cc_start: 0.8238 (t80) cc_final: 0.8014 (t80) REVERT: H 145 SER cc_start: 0.8407 (m) cc_final: 0.8136 (t) REVERT: H 195 LEU cc_start: 0.8238 (tp) cc_final: 0.7979 (tp) REVERT: H 212 PHE cc_start: 0.8296 (m-80) cc_final: 0.7884 (m-80) REVERT: H 215 THR cc_start: 0.8062 (t) cc_final: 0.7840 (p) outliers start: 31 outliers final: 18 residues processed: 273 average time/residue: 0.0773 time to fit residues: 29.2600 Evaluate side-chains 265 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 199 VAL 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 29 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 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 214 HIS A 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.112861 restraints weight = 13317.169| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.34 r_work: 0.3319 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8359 Z= 0.184 Angle : 0.560 7.709 11407 Z= 0.298 Chirality : 0.045 0.259 1338 Planarity : 0.004 0.032 1450 Dihedral : 4.161 37.732 1187 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.57 % Allowed : 17.39 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.26), residues: 1095 helix: 1.84 (0.27), residues: 387 sheet: -0.39 (0.31), residues: 279 loop : -0.57 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 198 TYR 0.013 0.001 TYR H 190 PHE 0.019 0.002 PHE B 199 TRP 0.015 0.002 TRP B 211 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 8355) covalent geometry : angle 0.55947 (11401) SS BOND : bond 0.00242 ( 3) SS BOND : angle 0.96496 ( 6) hydrogen bonds : bond 0.04525 ( 428) hydrogen bonds : angle 4.76427 ( 1239) Misc. bond : bond 0.00078 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 0.339 Fit side-chains REVERT: C 52 MET cc_start: 0.8172 (mtt) cc_final: 0.7804 (mtt) REVERT: C 93 PHE cc_start: 0.7613 (t80) cc_final: 0.7262 (t80) REVERT: C 110 VAL cc_start: 0.8244 (p) cc_final: 0.7892 (t) REVERT: C 117 SER cc_start: 0.8676 (t) cc_final: 0.8264 (p) REVERT: C 119 ASP cc_start: 0.7848 (t70) cc_final: 0.7439 (t0) REVERT: C 148 VAL cc_start: 0.8391 (t) cc_final: 0.8188 (p) REVERT: C 153 MET cc_start: 0.8415 (tpp) cc_final: 0.7979 (tpp) REVERT: C 345 MET cc_start: 0.8422 (mtp) cc_final: 0.8084 (ttm) REVERT: C 381 ILE cc_start: 0.7938 (tp) cc_final: 0.7710 (tt) REVERT: A 202 VAL cc_start: 0.8838 (p) cc_final: 0.8412 (t) REVERT: A 253 SER cc_start: 0.8605 (t) cc_final: 0.8315 (p) REVERT: A 256 ASN cc_start: 0.8683 (m-40) cc_final: 0.8355 (m110) REVERT: A 307 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7656 (mp10) REVERT: A 323 MET cc_start: 0.8314 (mmt) cc_final: 0.8087 (mmm) REVERT: B 32 GLN cc_start: 0.7083 (mt0) cc_final: 0.6819 (mt0) REVERT: B 211 TRP cc_start: 0.8455 (m100) cc_final: 0.8140 (m100) REVERT: B 298 ASP cc_start: 0.8141 (t0) cc_final: 0.7921 (t70) REVERT: B 307 VAL cc_start: 0.8616 (t) cc_final: 0.8327 (p) REVERT: B 317 CYS cc_start: 0.7744 (p) cc_final: 0.7268 (p) REVERT: B 333 ASP cc_start: 0.8195 (p0) cc_final: 0.7931 (p0) REVERT: H 23 SER cc_start: 0.8105 (t) cc_final: 0.7702 (p) REVERT: H 90 ASP cc_start: 0.8311 (m-30) cc_final: 0.8109 (m-30) REVERT: H 178 LEU cc_start: 0.8747 (tp) cc_final: 0.8547 (tt) REVERT: H 195 LEU cc_start: 0.8242 (tp) cc_final: 0.8002 (tp) REVERT: H 212 PHE cc_start: 0.8322 (m-80) cc_final: 0.7953 (m-80) outliers start: 36 outliers final: 28 residues processed: 266 average time/residue: 0.0781 time to fit residues: 28.6926 Evaluate side-chains 277 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 248 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 199 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 99 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.130640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.112711 restraints weight = 13504.761| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.38 r_work: 0.3314 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8359 Z= 0.176 Angle : 0.534 6.306 11407 Z= 0.287 Chirality : 0.044 0.190 1338 Planarity : 0.004 0.035 1450 Dihedral : 4.127 34.301 1187 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.20 % Allowed : 18.53 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.26), residues: 1095 helix: 1.93 (0.27), residues: 387 sheet: -0.43 (0.31), residues: 281 loop : -0.52 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 198 TYR 0.015 0.001 TYR A 291 PHE 0.020 0.002 PHE C 354 TRP 0.013 0.002 TRP B 211 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8355) covalent geometry : angle 0.53397 (11401) SS BOND : bond 0.00255 ( 3) SS BOND : angle 0.85442 ( 6) hydrogen bonds : bond 0.04360 ( 428) hydrogen bonds : angle 4.62734 ( 1239) Misc. bond : bond 0.00081 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 0.349 Fit side-chains REVERT: C 52 MET cc_start: 0.8233 (mtt) cc_final: 0.7869 (mtt) REVERT: C 61 PHE cc_start: 0.7375 (m-80) cc_final: 0.7169 (m-80) REVERT: C 93 PHE cc_start: 0.7626 (t80) cc_final: 0.7249 (t80) REVERT: C 109 SER cc_start: 0.8228 (p) cc_final: 0.7989 (t) REVERT: C 110 VAL cc_start: 0.8257 (p) cc_final: 0.8013 (t) REVERT: C 117 SER cc_start: 0.8680 (t) cc_final: 0.8268 (p) REVERT: C 119 ASP cc_start: 0.7839 (t70) cc_final: 0.7341 (t0) REVERT: C 123 ILE cc_start: 0.8481 (mt) cc_final: 0.8243 (mt) REVERT: C 153 MET cc_start: 0.8378 (tpp) cc_final: 0.7971 (tpp) REVERT: C 345 MET cc_start: 0.8441 (mtp) cc_final: 0.8094 (ttm) REVERT: C 381 ILE cc_start: 0.7970 (tp) cc_final: 0.7697 (tt) REVERT: A 253 SER cc_start: 0.8621 (t) cc_final: 0.8339 (p) REVERT: A 256 ASN cc_start: 0.8684 (m-40) cc_final: 0.8344 (m110) REVERT: A 307 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7695 (mp10) REVERT: A 323 MET cc_start: 0.8317 (mmt) cc_final: 0.8062 (mmm) REVERT: B 32 GLN cc_start: 0.7101 (mt0) cc_final: 0.6806 (mt0) REVERT: B 211 TRP cc_start: 0.8470 (m100) cc_final: 0.8105 (m100) REVERT: B 298 ASP cc_start: 0.8163 (t0) cc_final: 0.7888 (t70) REVERT: B 307 VAL cc_start: 0.8604 (t) cc_final: 0.8328 (p) REVERT: B 317 CYS cc_start: 0.7733 (p) cc_final: 0.7223 (p) REVERT: B 333 ASP cc_start: 0.8196 (p0) cc_final: 0.7907 (p0) REVERT: H 23 SER cc_start: 0.8122 (t) cc_final: 0.7759 (p) REVERT: H 90 ASP cc_start: 0.8339 (m-30) cc_final: 0.8137 (m-30) REVERT: H 178 LEU cc_start: 0.8744 (tp) cc_final: 0.8533 (tt) REVERT: H 195 LEU cc_start: 0.8227 (tp) cc_final: 0.8007 (tp) REVERT: H 212 PHE cc_start: 0.8330 (m-80) cc_final: 0.7989 (m-80) REVERT: H 238 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7903 (t) outliers start: 41 outliers final: 33 residues processed: 265 average time/residue: 0.0804 time to fit residues: 29.5650 Evaluate side-chains 285 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 199 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 25 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 3 optimal weight: 0.0020 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS A 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.132385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.114452 restraints weight = 13365.490| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.38 r_work: 0.3341 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8359 Z= 0.122 Angle : 0.502 6.206 11407 Z= 0.266 Chirality : 0.043 0.239 1338 Planarity : 0.003 0.034 1450 Dihedral : 3.926 32.510 1187 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.70 % Allowed : 20.69 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.27), residues: 1095 helix: 2.14 (0.27), residues: 388 sheet: -0.34 (0.31), residues: 281 loop : -0.51 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.014 0.001 TYR H 190 PHE 0.012 0.001 PHE B 199 TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8355) covalent geometry : angle 0.50184 (11401) SS BOND : bond 0.00194 ( 3) SS BOND : angle 0.59417 ( 6) hydrogen bonds : bond 0.03887 ( 428) hydrogen bonds : angle 4.46075 ( 1239) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 0.259 Fit side-chains REVERT: C 52 MET cc_start: 0.8194 (mtt) cc_final: 0.7826 (mtt) REVERT: C 61 PHE cc_start: 0.7343 (m-80) cc_final: 0.7093 (m-80) REVERT: C 88 TRP cc_start: 0.6939 (t-100) cc_final: 0.6629 (t60) REVERT: C 93 PHE cc_start: 0.7602 (t80) cc_final: 0.7219 (t80) REVERT: C 110 VAL cc_start: 0.8206 (p) cc_final: 0.7844 (t) REVERT: C 117 SER cc_start: 0.8691 (t) cc_final: 0.8252 (p) REVERT: C 119 ASP cc_start: 0.7868 (t70) cc_final: 0.7533 (t0) REVERT: C 153 MET cc_start: 0.8301 (tpp) cc_final: 0.7884 (tpp) REVERT: C 345 MET cc_start: 0.8422 (mtp) cc_final: 0.8065 (ttm) REVERT: C 381 ILE cc_start: 0.7921 (tp) cc_final: 0.7661 (tt) REVERT: C 409 TRP cc_start: 0.8235 (m100) cc_final: 0.7884 (m100) REVERT: A 202 VAL cc_start: 0.8698 (p) cc_final: 0.8432 (m) REVERT: A 253 SER cc_start: 0.8588 (t) cc_final: 0.8326 (p) REVERT: A 256 ASN cc_start: 0.8627 (m-40) cc_final: 0.8270 (m110) REVERT: A 307 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7704 (mp10) REVERT: A 323 MET cc_start: 0.8258 (mmt) cc_final: 0.8027 (mtt) REVERT: B 32 GLN cc_start: 0.7426 (mt0) cc_final: 0.7124 (mt0) REVERT: B 211 TRP cc_start: 0.8496 (m100) cc_final: 0.8084 (m100) REVERT: B 298 ASP cc_start: 0.8141 (t0) cc_final: 0.7897 (t70) REVERT: B 307 VAL cc_start: 0.8566 (t) cc_final: 0.8298 (p) REVERT: B 317 CYS cc_start: 0.7715 (p) cc_final: 0.7158 (p) REVERT: B 333 ASP cc_start: 0.8156 (p0) cc_final: 0.7868 (p0) REVERT: H 23 SER cc_start: 0.8115 (t) cc_final: 0.7805 (p) REVERT: H 178 LEU cc_start: 0.8696 (tp) cc_final: 0.8493 (tt) REVERT: H 195 LEU cc_start: 0.8218 (tp) cc_final: 0.8011 (tp) REVERT: H 199 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8279 (m) REVERT: H 212 PHE cc_start: 0.8302 (m-80) cc_final: 0.8051 (m-80) REVERT: H 238 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7926 (t) outliers start: 37 outliers final: 29 residues processed: 265 average time/residue: 0.0754 time to fit residues: 27.8218 Evaluate side-chains 281 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain D residue 6 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 34 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 67 optimal weight: 0.0270 chunk 103 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.132397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.114423 restraints weight = 13237.809| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.37 r_work: 0.3340 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8359 Z= 0.125 Angle : 0.501 6.228 11407 Z= 0.266 Chirality : 0.043 0.203 1338 Planarity : 0.003 0.035 1450 Dihedral : 3.889 31.293 1187 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.82 % Allowed : 21.45 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.27), residues: 1095 helix: 2.17 (0.27), residues: 390 sheet: -0.31 (0.31), residues: 281 loop : -0.47 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.014 0.001 TYR H 190 PHE 0.022 0.001 PHE C 354 TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8355) covalent geometry : angle 0.50114 (11401) SS BOND : bond 0.00198 ( 3) SS BOND : angle 0.58342 ( 6) hydrogen bonds : bond 0.03814 ( 428) hydrogen bonds : angle 4.41014 ( 1239) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 0.231 Fit side-chains REVERT: C 52 MET cc_start: 0.8195 (mtt) cc_final: 0.7818 (mtt) REVERT: C 61 PHE cc_start: 0.7344 (m-80) cc_final: 0.7086 (m-80) REVERT: C 88 TRP cc_start: 0.6935 (t-100) cc_final: 0.6676 (t60) REVERT: C 93 PHE cc_start: 0.7604 (t80) cc_final: 0.7214 (t80) REVERT: C 109 SER cc_start: 0.8212 (p) cc_final: 0.7972 (t) REVERT: C 110 VAL cc_start: 0.8196 (p) cc_final: 0.7857 (t) REVERT: C 117 SER cc_start: 0.8686 (t) cc_final: 0.8247 (p) REVERT: C 119 ASP cc_start: 0.7879 (t70) cc_final: 0.7540 (t0) REVERT: C 153 MET cc_start: 0.8258 (tpp) cc_final: 0.7829 (tpp) REVERT: C 345 MET cc_start: 0.8424 (mtp) cc_final: 0.8083 (ttm) REVERT: C 381 ILE cc_start: 0.7941 (tp) cc_final: 0.7682 (tt) REVERT: C 409 TRP cc_start: 0.8253 (m100) cc_final: 0.7907 (m100) REVERT: A 202 VAL cc_start: 0.8689 (p) cc_final: 0.8420 (m) REVERT: A 253 SER cc_start: 0.8606 (t) cc_final: 0.8347 (p) REVERT: A 256 ASN cc_start: 0.8616 (m-40) cc_final: 0.8251 (m110) REVERT: A 291 TYR cc_start: 0.6886 (t80) cc_final: 0.6678 (t80) REVERT: A 307 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7731 (mp10) REVERT: A 323 MET cc_start: 0.8277 (mmt) cc_final: 0.8014 (mtt) REVERT: B 32 GLN cc_start: 0.7240 (mt0) cc_final: 0.6951 (mt0) REVERT: B 211 TRP cc_start: 0.8510 (m100) cc_final: 0.8023 (m100) REVERT: B 298 ASP cc_start: 0.8125 (t0) cc_final: 0.7861 (t70) REVERT: B 307 VAL cc_start: 0.8547 (t) cc_final: 0.8287 (p) REVERT: B 317 CYS cc_start: 0.7700 (p) cc_final: 0.7134 (p) REVERT: B 333 ASP cc_start: 0.8169 (p0) cc_final: 0.7885 (p0) REVERT: H 23 SER cc_start: 0.8077 (t) cc_final: 0.7786 (p) REVERT: H 39 GLN cc_start: 0.8511 (tt0) cc_final: 0.8184 (tt0) REVERT: H 178 LEU cc_start: 0.8612 (tp) cc_final: 0.8404 (tt) REVERT: H 199 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8252 (m) REVERT: H 212 PHE cc_start: 0.8293 (m-80) cc_final: 0.8083 (m-80) REVERT: H 238 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7946 (t) outliers start: 38 outliers final: 29 residues processed: 266 average time/residue: 0.0719 time to fit residues: 26.6983 Evaluate side-chains 285 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain D residue 6 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 6 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112055 restraints weight = 13400.085| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.35 r_work: 0.3306 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8359 Z= 0.211 Angle : 0.569 6.471 11407 Z= 0.303 Chirality : 0.045 0.208 1338 Planarity : 0.004 0.039 1450 Dihedral : 4.177 31.613 1187 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 5.20 % Allowed : 21.83 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.27), residues: 1095 helix: 1.96 (0.27), residues: 390 sheet: -0.41 (0.31), residues: 280 loop : -0.57 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 198 TYR 0.011 0.002 TYR H 103 PHE 0.019 0.002 PHE B 199 TRP 0.021 0.002 TRP B 332 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 8355) covalent geometry : angle 0.56871 (11401) SS BOND : bond 0.00314 ( 3) SS BOND : angle 0.91247 ( 6) hydrogen bonds : bond 0.04556 ( 428) hydrogen bonds : angle 4.58487 ( 1239) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 246 time to evaluate : 0.281 Fit side-chains REVERT: C 30 LEU cc_start: 0.8611 (mt) cc_final: 0.8106 (mt) REVERT: C 52 MET cc_start: 0.8208 (mtt) cc_final: 0.7840 (mtt) REVERT: C 61 PHE cc_start: 0.7521 (m-80) cc_final: 0.7302 (m-80) REVERT: C 88 TRP cc_start: 0.7081 (t-100) cc_final: 0.6809 (t60) REVERT: C 93 PHE cc_start: 0.7611 (t80) cc_final: 0.7209 (t80) REVERT: C 109 SER cc_start: 0.8334 (p) cc_final: 0.8100 (t) REVERT: C 110 VAL cc_start: 0.8279 (p) cc_final: 0.8059 (t) REVERT: C 117 SER cc_start: 0.8694 (t) cc_final: 0.8298 (p) REVERT: C 119 ASP cc_start: 0.7856 (t70) cc_final: 0.7536 (t0) REVERT: C 148 VAL cc_start: 0.8364 (t) cc_final: 0.8132 (p) REVERT: C 153 MET cc_start: 0.8382 (tpp) cc_final: 0.7945 (tpp) REVERT: C 345 MET cc_start: 0.8476 (mtp) cc_final: 0.8134 (ttm) REVERT: C 381 ILE cc_start: 0.7940 (tp) cc_final: 0.7671 (tt) REVERT: C 409 TRP cc_start: 0.8396 (m100) cc_final: 0.8102 (m100) REVERT: A 202 VAL cc_start: 0.8766 (p) cc_final: 0.8472 (m) REVERT: A 253 SER cc_start: 0.8631 (t) cc_final: 0.8356 (p) REVERT: A 256 ASN cc_start: 0.8742 (m-40) cc_final: 0.8394 (m110) REVERT: A 258 LYS cc_start: 0.8619 (ptpt) cc_final: 0.8401 (ptpt) REVERT: A 307 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7736 (mp10) REVERT: A 323 MET cc_start: 0.8306 (mmt) cc_final: 0.8070 (mtt) REVERT: B 32 GLN cc_start: 0.7426 (mt0) cc_final: 0.7059 (mt0) REVERT: B 211 TRP cc_start: 0.8529 (m100) cc_final: 0.8112 (m100) REVERT: B 307 VAL cc_start: 0.8590 (t) cc_final: 0.8322 (p) REVERT: B 317 CYS cc_start: 0.7685 (p) cc_final: 0.7154 (p) REVERT: B 333 ASP cc_start: 0.8274 (p0) cc_final: 0.7944 (p0) REVERT: H 23 SER cc_start: 0.8099 (t) cc_final: 0.7769 (p) REVERT: H 39 GLN cc_start: 0.8482 (tt0) cc_final: 0.8184 (tt0) REVERT: H 212 PHE cc_start: 0.8351 (m-80) cc_final: 0.8101 (m-80) outliers start: 41 outliers final: 30 residues processed: 258 average time/residue: 0.0731 time to fit residues: 26.1302 Evaluate side-chains 271 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 199 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.130263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.112423 restraints weight = 13332.723| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.36 r_work: 0.3315 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 8359 Z= 0.184 Angle : 0.559 6.710 11407 Z= 0.296 Chirality : 0.044 0.187 1338 Planarity : 0.004 0.036 1450 Dihedral : 4.198 31.244 1187 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.06 % Allowed : 23.98 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.27), residues: 1095 helix: 2.00 (0.26), residues: 390 sheet: -0.45 (0.31), residues: 280 loop : -0.60 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.012 0.001 TYR H 190 PHE 0.023 0.002 PHE C 354 TRP 0.012 0.002 TRP B 332 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 8355) covalent geometry : angle 0.55897 (11401) SS BOND : bond 0.00203 ( 3) SS BOND : angle 0.74624 ( 6) hydrogen bonds : bond 0.04348 ( 428) hydrogen bonds : angle 4.58714 ( 1239) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.294 Fit side-chains REVERT: C 30 LEU cc_start: 0.8610 (mt) cc_final: 0.8116 (mt) REVERT: C 52 MET cc_start: 0.8202 (mtt) cc_final: 0.7827 (mtt) REVERT: C 61 PHE cc_start: 0.7509 (m-80) cc_final: 0.7292 (m-80) REVERT: C 93 PHE cc_start: 0.7638 (t80) cc_final: 0.7241 (t80) REVERT: C 109 SER cc_start: 0.8335 (p) cc_final: 0.8116 (t) REVERT: C 110 VAL cc_start: 0.8261 (p) cc_final: 0.8039 (t) REVERT: C 117 SER cc_start: 0.8699 (t) cc_final: 0.8298 (p) REVERT: C 119 ASP cc_start: 0.7864 (t70) cc_final: 0.7549 (t0) REVERT: C 153 MET cc_start: 0.8388 (tpp) cc_final: 0.7956 (tpp) REVERT: C 345 MET cc_start: 0.8458 (mtp) cc_final: 0.8116 (ttm) REVERT: C 381 ILE cc_start: 0.7917 (tp) cc_final: 0.7658 (tt) REVERT: C 409 TRP cc_start: 0.8414 (m100) cc_final: 0.8105 (m100) REVERT: A 202 VAL cc_start: 0.8723 (p) cc_final: 0.8442 (m) REVERT: A 253 SER cc_start: 0.8620 (t) cc_final: 0.8349 (p) REVERT: A 256 ASN cc_start: 0.8682 (m-40) cc_final: 0.8339 (m110) REVERT: A 258 LYS cc_start: 0.8641 (ptpt) cc_final: 0.8419 (ptpt) REVERT: A 307 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7709 (mp10) REVERT: A 323 MET cc_start: 0.8283 (mmt) cc_final: 0.8029 (mtt) REVERT: B 32 GLN cc_start: 0.7265 (mt0) cc_final: 0.6926 (mt0) REVERT: B 211 TRP cc_start: 0.8520 (m100) cc_final: 0.8103 (m100) REVERT: B 298 ASP cc_start: 0.8149 (t0) cc_final: 0.7885 (t70) REVERT: B 307 VAL cc_start: 0.8572 (t) cc_final: 0.8299 (p) REVERT: B 317 CYS cc_start: 0.7710 (p) cc_final: 0.7193 (p) REVERT: B 333 ASP cc_start: 0.8277 (p0) cc_final: 0.7942 (p0) REVERT: H 23 SER cc_start: 0.8082 (t) cc_final: 0.7759 (p) REVERT: H 39 GLN cc_start: 0.8455 (tt0) cc_final: 0.8166 (tt0) REVERT: H 199 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8187 (m) REVERT: H 212 PHE cc_start: 0.8347 (m-80) cc_final: 0.8108 (m-80) outliers start: 32 outliers final: 28 residues processed: 242 average time/residue: 0.0758 time to fit residues: 25.0603 Evaluate side-chains 257 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain D residue 6 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 74 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.131135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113260 restraints weight = 13289.886| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.38 r_work: 0.3322 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8359 Z= 0.162 Angle : 0.547 7.065 11407 Z= 0.287 Chirality : 0.044 0.184 1338 Planarity : 0.004 0.035 1450 Dihedral : 4.124 30.458 1187 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.19 % Allowed : 23.98 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.27), residues: 1095 helix: 2.07 (0.26), residues: 390 sheet: -0.46 (0.31), residues: 289 loop : -0.55 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.012 0.001 TYR H 190 PHE 0.028 0.002 PHE C 354 TRP 0.010 0.001 TRP A 212 HIS 0.003 0.001 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8355) covalent geometry : angle 0.54672 (11401) SS BOND : bond 0.00280 ( 3) SS BOND : angle 0.69206 ( 6) hydrogen bonds : bond 0.04186 ( 428) hydrogen bonds : angle 4.54171 ( 1239) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.193 Fit side-chains REVERT: C 30 LEU cc_start: 0.8636 (mt) cc_final: 0.8102 (mt) REVERT: C 52 MET cc_start: 0.8226 (mtt) cc_final: 0.7851 (mtt) REVERT: C 61 PHE cc_start: 0.7360 (m-80) cc_final: 0.7141 (m-80) REVERT: C 93 PHE cc_start: 0.7651 (t80) cc_final: 0.7270 (t80) REVERT: C 109 SER cc_start: 0.8223 (p) cc_final: 0.8014 (t) REVERT: C 110 VAL cc_start: 0.8243 (p) cc_final: 0.8016 (t) REVERT: C 117 SER cc_start: 0.8718 (t) cc_final: 0.8310 (p) REVERT: C 119 ASP cc_start: 0.7864 (t70) cc_final: 0.7556 (t0) REVERT: C 153 MET cc_start: 0.8374 (tpp) cc_final: 0.7916 (tpp) REVERT: C 345 MET cc_start: 0.8436 (mtp) cc_final: 0.8120 (ttm) REVERT: C 381 ILE cc_start: 0.7966 (tp) cc_final: 0.7694 (tt) REVERT: C 409 TRP cc_start: 0.8380 (m100) cc_final: 0.8084 (m100) REVERT: A 202 VAL cc_start: 0.8722 (p) cc_final: 0.8440 (m) REVERT: A 246 GLU cc_start: 0.6788 (pm20) cc_final: 0.6535 (pm20) REVERT: A 253 SER cc_start: 0.8617 (t) cc_final: 0.8353 (p) REVERT: A 256 ASN cc_start: 0.8672 (m-40) cc_final: 0.8315 (m110) REVERT: A 307 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7717 (mp10) REVERT: A 323 MET cc_start: 0.8243 (mmt) cc_final: 0.8001 (mtt) REVERT: A 340 THR cc_start: 0.8471 (p) cc_final: 0.8143 (p) REVERT: B 32 GLN cc_start: 0.7206 (mt0) cc_final: 0.6859 (mt0) REVERT: B 211 TRP cc_start: 0.8504 (m100) cc_final: 0.8067 (m100) REVERT: B 284 LEU cc_start: 0.8727 (mt) cc_final: 0.8526 (mp) REVERT: B 298 ASP cc_start: 0.8153 (t0) cc_final: 0.7882 (t70) REVERT: B 307 VAL cc_start: 0.8560 (t) cc_final: 0.8300 (p) REVERT: B 317 CYS cc_start: 0.7683 (p) cc_final: 0.7188 (p) REVERT: B 333 ASP cc_start: 0.8267 (p0) cc_final: 0.7982 (p0) REVERT: H 23 SER cc_start: 0.8052 (t) cc_final: 0.7754 (p) REVERT: H 39 GLN cc_start: 0.8474 (tt0) cc_final: 0.8179 (tt0) REVERT: H 199 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8174 (m) REVERT: H 212 PHE cc_start: 0.8347 (m-80) cc_final: 0.8123 (m-80) outliers start: 33 outliers final: 28 residues processed: 250 average time/residue: 0.0650 time to fit residues: 22.5345 Evaluate side-chains 268 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 229 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 33 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.130923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.113040 restraints weight = 13283.102| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.37 r_work: 0.3318 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8359 Z= 0.168 Angle : 0.558 8.309 11407 Z= 0.292 Chirality : 0.044 0.191 1338 Planarity : 0.004 0.036 1450 Dihedral : 4.167 30.798 1187 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.19 % Allowed : 23.98 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.27), residues: 1095 helix: 2.10 (0.27), residues: 389 sheet: -0.49 (0.30), residues: 288 loop : -0.57 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 191 TYR 0.012 0.001 TYR H 190 PHE 0.026 0.002 PHE C 354 TRP 0.010 0.001 TRP A 212 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8355) covalent geometry : angle 0.55820 (11401) SS BOND : bond 0.00223 ( 3) SS BOND : angle 0.69203 ( 6) hydrogen bonds : bond 0.04243 ( 428) hydrogen bonds : angle 4.54552 ( 1239) Misc. bond : bond 0.00003 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 0.293 Fit side-chains REVERT: C 30 LEU cc_start: 0.8648 (mt) cc_final: 0.8111 (mt) REVERT: C 52 MET cc_start: 0.8236 (mtt) cc_final: 0.7874 (mtt) REVERT: C 61 PHE cc_start: 0.7513 (m-80) cc_final: 0.7291 (m-80) REVERT: C 93 PHE cc_start: 0.7657 (t80) cc_final: 0.7284 (t80) REVERT: C 109 SER cc_start: 0.8367 (p) cc_final: 0.8156 (t) REVERT: C 110 VAL cc_start: 0.8249 (p) cc_final: 0.8022 (t) REVERT: C 117 SER cc_start: 0.8710 (t) cc_final: 0.8312 (p) REVERT: C 119 ASP cc_start: 0.7898 (t70) cc_final: 0.7590 (t0) REVERT: C 153 MET cc_start: 0.8358 (tpp) cc_final: 0.7897 (tpp) REVERT: C 345 MET cc_start: 0.8467 (mtp) cc_final: 0.8152 (ttm) REVERT: C 381 ILE cc_start: 0.7954 (tp) cc_final: 0.7696 (tt) REVERT: C 409 TRP cc_start: 0.8393 (m100) cc_final: 0.8086 (m100) REVERT: A 202 VAL cc_start: 0.8727 (p) cc_final: 0.8461 (m) REVERT: A 253 SER cc_start: 0.8601 (t) cc_final: 0.8341 (p) REVERT: A 256 ASN cc_start: 0.8676 (m-40) cc_final: 0.8318 (m110) REVERT: A 323 MET cc_start: 0.8229 (mmt) cc_final: 0.7984 (mtt) REVERT: A 340 THR cc_start: 0.8406 (p) cc_final: 0.8033 (p) REVERT: B 32 GLN cc_start: 0.7204 (mt0) cc_final: 0.6871 (mt0) REVERT: B 211 TRP cc_start: 0.8499 (m100) cc_final: 0.8073 (m100) REVERT: B 284 LEU cc_start: 0.8738 (mt) cc_final: 0.8522 (mp) REVERT: B 307 VAL cc_start: 0.8566 (t) cc_final: 0.8287 (p) REVERT: B 317 CYS cc_start: 0.7672 (p) cc_final: 0.7205 (p) REVERT: B 333 ASP cc_start: 0.8285 (p0) cc_final: 0.8010 (p0) REVERT: H 23 SER cc_start: 0.8019 (t) cc_final: 0.7748 (p) REVERT: H 39 GLN cc_start: 0.8471 (tt0) cc_final: 0.8186 (tt0) REVERT: H 103 TYR cc_start: 0.7873 (t80) cc_final: 0.7668 (t80) REVERT: H 199 VAL cc_start: 0.8478 (OUTLIER) cc_final: 0.8136 (m) REVERT: H 212 PHE cc_start: 0.8352 (m-80) cc_final: 0.8133 (m-80) outliers start: 33 outliers final: 30 residues processed: 247 average time/residue: 0.0723 time to fit residues: 24.8390 Evaluate side-chains 265 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 229 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 98 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 74 optimal weight: 0.0870 chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.131188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113323 restraints weight = 13279.262| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.36 r_work: 0.3323 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8359 Z= 0.152 Angle : 0.542 7.174 11407 Z= 0.284 Chirality : 0.043 0.183 1338 Planarity : 0.004 0.035 1450 Dihedral : 4.123 30.755 1187 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.31 % Allowed : 23.98 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.27), residues: 1095 helix: 2.15 (0.27), residues: 389 sheet: -0.44 (0.31), residues: 289 loop : -0.57 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 191 TYR 0.012 0.001 TYR H 190 PHE 0.025 0.002 PHE C 354 TRP 0.010 0.001 TRP A 212 HIS 0.003 0.001 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8355) covalent geometry : angle 0.54151 (11401) SS BOND : bond 0.00243 ( 3) SS BOND : angle 0.64176 ( 6) hydrogen bonds : bond 0.04109 ( 428) hydrogen bonds : angle 4.51593 ( 1239) Misc. bond : bond 0.00005 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2009.05 seconds wall clock time: 35 minutes 2.27 seconds (2102.27 seconds total)