Starting phenix.real_space_refine on Wed Aug 5 05:49:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vy7_43647/08_2026/8vy7_43647.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vy7_43647/08_2026/8vy7_43647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vy7_43647/08_2026/8vy7_43647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vy7_43647/08_2026/8vy7_43647.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vy7_43647/08_2026/8vy7_43647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vy7_43647/08_2026/8vy7_43647.map" } resolution = 2.68 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= 0.021 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: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 5659 2.51 5 N 1488 2.21 5 O 1601 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8811 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1753 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2564 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 401 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1743 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "R" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2299 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'A1AEI': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.41, per 1000 atoms: 0.16 Number of scatterers: 8811 At special positions: 0 Unit cell: (90.228, 120.888, 134.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 F 3 9.00 O 1601 8.00 N 1488 7.00 C 5659 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 238.8 milliseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 39.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.852A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.585A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.647A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.557A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.739A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 53 through 56 removed outlier: 4.366A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.658A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 37 Processing helix chain 'R' and resid 42 through 72 Processing helix chain 'R' and resid 72 through 77 Processing helix chain 'R' and resid 78 through 112 Processing helix chain 'R' and resid 116 through 124 Processing helix chain 'R' and resid 125 through 137 Processing helix chain 'R' and resid 137 through 158 removed outlier: 3.606A pdb=" N LEU R 141 " --> pdb=" O THR R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 213 removed outlier: 4.214A pdb=" N LEU R 181 " --> pdb=" O SER R 177 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE R 189 " --> pdb=" O VAL R 185 " (cutoff:3.500A) Proline residue: R 190 - end of helix Processing helix chain 'R' and resid 228 through 257 removed outlier: 4.386A pdb=" N SER R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU R 239 " --> pdb=" O THR R 235 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER R 246 " --> pdb=" O ILE R 242 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU R 257 " --> pdb=" O THR R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 270 removed outlier: 3.751A pdb=" N LEU R 264 " --> pdb=" O ASN R 260 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET R 270 " --> pdb=" O GLN R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 282 removed outlier: 4.624A pdb=" N SER R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS R 278 " --> pdb=" O SER R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 302 removed outlier: 3.791A pdb=" N ARG R 299 " --> pdb=" O LEU R 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.545A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.705A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.695A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.778A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.621A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.744A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.666A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.628A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.722A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.722A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.911A pdb=" N ALA D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 135 through 136 removed outlier: 6.704A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1338 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: 1.03 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2778 1.34 - 1.46: 1822 1.46 - 1.57: 4307 1.57 - 1.69: 2 1.69 - 1.81: 90 Bond restraints: 8999 Sorted by residual: bond pdb=" C10 A1AEI R 501 " pdb=" N11 A1AEI R 501 " ideal model delta sigma weight residual 1.364 1.459 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C13 A1AEI R 501 " pdb=" C14 A1AEI R 501 " ideal model delta sigma weight residual 1.461 1.529 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" N16 A1AEI R 501 " pdb=" N17 A1AEI R 501 " ideal model delta sigma weight residual 1.275 1.333 -0.058 2.00e-02 2.50e+03 8.56e+00 bond pdb=" C16 CLR R 502 " pdb=" C17 CLR R 502 " ideal model delta sigma weight residual 1.554 1.607 -0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" C23 CLR R 502 " pdb=" C24 CLR R 502 " ideal model delta sigma weight residual 1.525 1.574 -0.049 2.00e-02 2.50e+03 5.94e+00 ... (remaining 8994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 11987 2.23 - 4.45: 171 4.45 - 6.68: 29 6.68 - 8.90: 11 8.90 - 11.13: 2 Bond angle restraints: 12200 Sorted by residual: angle pdb=" CA LEU A 227 " pdb=" CB LEU A 227 " pdb=" CG LEU A 227 " ideal model delta sigma weight residual 116.30 127.43 -11.13 3.50e+00 8.16e-02 1.01e+01 angle pdb=" N PRO D 224 " pdb=" CA PRO D 224 " pdb=" C PRO D 224 " ideal model delta sigma weight residual 112.10 120.32 -8.22 2.60e+00 1.48e-01 9.99e+00 angle pdb=" CA TYR D 178 " pdb=" CB TYR D 178 " pdb=" CG TYR D 178 " ideal model delta sigma weight residual 113.90 119.48 -5.58 1.80e+00 3.09e-01 9.62e+00 angle pdb=" C22 CLR R 502 " pdb=" C23 CLR R 502 " pdb=" C24 CLR R 502 " ideal model delta sigma weight residual 111.95 103.38 8.57 3.00e+00 1.11e-01 8.16e+00 angle pdb=" CA LEU R 51 " pdb=" CB LEU R 51 " pdb=" CG LEU R 51 " ideal model delta sigma weight residual 116.30 126.28 -9.98 3.50e+00 8.16e-02 8.14e+00 ... (remaining 12195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 4972 22.47 - 44.95: 332 44.95 - 67.42: 23 67.42 - 89.90: 4 89.90 - 112.37: 3 Dihedral angle restraints: 5334 sinusoidal: 2046 harmonic: 3288 Sorted by residual: dihedral pdb=" CA LYS R 217 " pdb=" C LYS R 217 " pdb=" N ILE R 218 " pdb=" CA ILE R 218 " ideal model delta harmonic sigma weight residual 180.00 -148.99 -31.01 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 5331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1109 0.055 - 0.109: 240 0.109 - 0.164: 53 0.164 - 0.218: 6 0.218 - 0.273: 2 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CB THR R 224 " pdb=" CA THR R 224 " pdb=" OG1 THR R 224 " pdb=" CG2 THR R 224 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C17 CLR R 502 " pdb=" C13 CLR R 502 " pdb=" C16 CLR R 502 " pdb=" C20 CLR R 502 " both_signs ideal model delta sigma weight residual False 2.55 2.78 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB VAL A 233 " pdb=" CA VAL A 233 " pdb=" CG1 VAL A 233 " pdb=" CG2 VAL A 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1407 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 90 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.44e+00 pdb=" C THR R 90 " 0.032 2.00e-02 2.50e+03 pdb=" O THR R 90 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL R 91 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO B 194 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 240 " 0.020 2.00e-02 2.50e+03 1.29e-02 3.34e+00 pdb=" CG TYR R 240 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR R 240 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR R 240 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR R 240 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 240 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR R 240 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 240 " 0.006 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1779 2.78 - 3.31: 7653 3.31 - 3.84: 15003 3.84 - 4.37: 17000 4.37 - 4.90: 30633 Nonbonded interactions: 72068 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.245 3.040 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.287 3.040 nonbonded pdb=" OE2 GLU A 14 " pdb=" OG1 THR D 57 " model vdw 2.289 3.040 nonbonded pdb=" O LEU R 133 " pdb=" OG1 THR R 137 " model vdw 2.293 3.040 nonbonded pdb=" O ASN R 21 " pdb=" OG SER R 25 " model vdw 2.294 3.040 ... (remaining 72063 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: 1.920 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.480 Find NCS groups from input model: 0.050 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:7.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 9000 Z= 0.240 Angle : 0.708 11.125 12202 Z= 0.357 Chirality : 0.049 0.273 1410 Planarity : 0.004 0.046 1513 Dihedral : 14.098 112.369 3205 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.24), residues: 1120 helix: 0.36 (0.22), residues: 414 sheet: 0.59 (0.32), residues: 286 loop : -1.15 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 67 TYR 0.030 0.002 TYR R 240 PHE 0.020 0.002 PHE A 267 TRP 0.021 0.002 TRP R 297 HIS 0.005 0.001 HIS R 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.24 ( 8999) covalent geometry : angle 0.70833 / 0.36 (12200) SS BOND : bond 0.00064 / 0.03 ( 1) SS BOND : angle 0.28220 / 0.15 ( 2) hydrogen bonds : bond 0.15993 / 10.57 ( 467) hydrogen bonds : angle 6.11056 / 4.16 ( 1338) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.197 Fit side-chains REVERT: A 26 ASP cc_start: 0.7783 (m-30) cc_final: 0.7396 (m-30) REVERT: A 240 MET cc_start: 0.4803 (pmm) cc_final: 0.4514 (pmm) REVERT: B 170 ASP cc_start: 0.7977 (t70) cc_final: 0.7591 (t0) REVERT: B 191 SER cc_start: 0.8600 (t) cc_final: 0.8381 (p) REVERT: D 144 SER cc_start: 0.8624 (m) cc_final: 0.8215 (t) REVERT: R 16 GLU cc_start: 0.7587 (pt0) cc_final: 0.7328 (pt0) REVERT: R 19 ILE cc_start: 0.8249 (mm) cc_final: 0.8025 (tp) REVERT: R 87 ASN cc_start: 0.8530 (m-40) cc_final: 0.8285 (m-40) REVERT: R 95 PHE cc_start: 0.7876 (m-10) cc_final: 0.7538 (m-80) REVERT: R 301 MET cc_start: 0.4282 (tpt) cc_final: 0.3935 (tpt) outliers start: 0 outliers final: 1 residues processed: 230 average time/residue: 0.3538 time to fit residues: 87.9028 Evaluate side-chains 202 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 261 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 97 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.4832 > 50:) chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.127871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.111750 restraints weight = 13040.274| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.75 r_work: 0.3408 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9000 Z= 0.158 Angle : 0.558 10.389 12202 Z= 0.290 Chirality : 0.041 0.150 1410 Planarity : 0.004 0.037 1513 Dihedral : 5.217 58.871 1288 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.60 % Allowed : 10.77 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.64 (0.25), residues: 1120 helix: 1.77 (0.24), residues: 416 sheet: 0.61 (0.30), residues: 280 loop : -1.08 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.018 0.001 TYR D 178 PHE 0.024 0.001 PHE R 82 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 8999) covalent geometry : angle 0.55773 / 0.29 (12200) SS BOND : bond 0.00450 / 0.24 ( 1) SS BOND : angle 0.47595 / 0.25 ( 2) hydrogen bonds : bond 0.04247 / 2.81 ( 467) hydrogen bonds : angle 4.44343 / 3.09 ( 1338) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.276 Fit side-chains REVERT: A 26 ASP cc_start: 0.7944 (m-30) cc_final: 0.7590 (m-30) REVERT: A 240 MET cc_start: 0.5128 (pmm) cc_final: 0.4843 (pmm) REVERT: A 312 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8213 (mttm) REVERT: A 345 LYS cc_start: 0.8303 (mmtt) cc_final: 0.8063 (mttp) REVERT: B 52 ARG cc_start: 0.8374 (mtm-85) cc_final: 0.8060 (mtt-85) REVERT: B 217 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.8066 (pmm) REVERT: B 219 ARG cc_start: 0.8406 (mtt-85) cc_final: 0.8192 (mtp85) REVERT: D 67 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8163 (ptm160) REVERT: D 144 SER cc_start: 0.8638 (m) cc_final: 0.8307 (t) REVERT: D 226 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8411 (p) REVERT: R 19 ILE cc_start: 0.8238 (mm) cc_final: 0.8020 (tp) REVERT: R 24 ASN cc_start: 0.7724 (m-40) cc_final: 0.7457 (m-40) REVERT: R 31 ASN cc_start: 0.7273 (m110) cc_final: 0.6993 (m110) REVERT: R 87 ASN cc_start: 0.8434 (m-40) cc_final: 0.8230 (m-40) REVERT: R 95 PHE cc_start: 0.7970 (m-10) cc_final: 0.7663 (m-80) REVERT: R 116 ASN cc_start: 0.7742 (t0) cc_final: 0.7470 (t0) REVERT: R 144 ASN cc_start: 0.8461 (t0) cc_final: 0.8203 (t0) REVERT: R 212 MET cc_start: 0.8311 (mmm) cc_final: 0.8074 (mmm) REVERT: R 301 MET cc_start: 0.4545 (tpt) cc_final: 0.4184 (tpt) outliers start: 15 outliers final: 3 residues processed: 204 average time/residue: 0.3819 time to fit residues: 84.8124 Evaluate side-chains 197 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 190 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain R residue 188 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 14 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.111024 restraints weight = 12983.884| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.74 r_work: 0.3397 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9000 Z= 0.176 Angle : 0.548 9.384 12202 Z= 0.286 Chirality : 0.043 0.209 1410 Planarity : 0.003 0.035 1513 Dihedral : 5.084 55.875 1286 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.67 % Allowed : 14.07 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.90 (0.25), residues: 1120 helix: 2.14 (0.25), residues: 417 sheet: 0.60 (0.30), residues: 281 loop : -1.00 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.022 0.001 TYR D 178 PHE 0.025 0.002 PHE R 26 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS R 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 8999) covalent geometry : angle 0.54843 / 0.29 (12200) SS BOND : bond 0.00414 / 0.22 ( 1) SS BOND : angle 0.52799 / 0.28 ( 2) hydrogen bonds : bond 0.04115 / 2.73 ( 467) hydrogen bonds : angle 4.26913 / 2.97 ( 1338) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.330 Fit side-chains REVERT: A 26 ASP cc_start: 0.7925 (m-30) cc_final: 0.7568 (m-30) REVERT: A 240 MET cc_start: 0.5063 (pmm) cc_final: 0.4781 (pmm) REVERT: A 312 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8229 (mttm) REVERT: B 52 ARG cc_start: 0.8377 (mtm-85) cc_final: 0.8106 (mtt-85) REVERT: B 136 SER cc_start: 0.8435 (m) cc_final: 0.8196 (p) REVERT: B 170 ASP cc_start: 0.8033 (t70) cc_final: 0.7629 (t0) REVERT: B 219 ARG cc_start: 0.8385 (mtt-85) cc_final: 0.8164 (mtp85) REVERT: D 144 SER cc_start: 0.8613 (m) cc_final: 0.8298 (t) REVERT: D 226 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8398 (p) REVERT: R 31 ASN cc_start: 0.7384 (m110) cc_final: 0.7061 (m110) REVERT: R 95 PHE cc_start: 0.7979 (m-10) cc_final: 0.7677 (m-80) REVERT: R 212 MET cc_start: 0.8279 (mmm) cc_final: 0.8032 (mmm) REVERT: R 247 PHE cc_start: 0.6245 (OUTLIER) cc_final: 0.5983 (m-10) REVERT: R 301 MET cc_start: 0.4550 (tpt) cc_final: 0.4207 (tpt) outliers start: 25 outliers final: 9 residues processed: 207 average time/residue: 0.3896 time to fit residues: 87.3652 Evaluate side-chains 199 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 247 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 0.0270 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.127420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.111165 restraints weight = 13140.630| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.76 r_work: 0.3397 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9000 Z= 0.151 Angle : 0.529 8.792 12202 Z= 0.276 Chirality : 0.042 0.152 1410 Planarity : 0.003 0.033 1513 Dihedral : 5.001 55.526 1286 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.13 % Allowed : 15.99 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.25), residues: 1120 helix: 2.29 (0.25), residues: 417 sheet: 0.66 (0.30), residues: 279 loop : -1.02 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.021 0.001 TYR D 178 PHE 0.018 0.001 PHE R 26 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 8999) covalent geometry : angle 0.52941 / 0.28 (12200) SS BOND : bond 0.00376 / 0.20 ( 1) SS BOND : angle 0.50453 / 0.27 ( 2) hydrogen bonds : bond 0.03854 / 2.55 ( 467) hydrogen bonds : angle 4.16540 / 2.91 ( 1338) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.274 Fit side-chains REVERT: A 26 ASP cc_start: 0.7942 (m-30) cc_final: 0.7583 (m-30) REVERT: A 240 MET cc_start: 0.5047 (pmm) cc_final: 0.4764 (pmm) REVERT: B 136 SER cc_start: 0.8427 (m) cc_final: 0.8227 (p) REVERT: B 219 ARG cc_start: 0.8342 (mtt-85) cc_final: 0.8123 (mtp85) REVERT: D 144 SER cc_start: 0.8600 (m) cc_final: 0.8303 (t) REVERT: R 19 ILE cc_start: 0.8295 (mt) cc_final: 0.8004 (tp) REVERT: R 31 ASN cc_start: 0.7365 (m110) cc_final: 0.7035 (m110) REVERT: R 95 PHE cc_start: 0.7986 (m-10) cc_final: 0.7678 (m-80) REVERT: R 247 PHE cc_start: 0.6402 (OUTLIER) cc_final: 0.6156 (m-10) REVERT: R 301 MET cc_start: 0.4546 (tpt) cc_final: 0.4204 (tpt) outliers start: 20 outliers final: 10 residues processed: 201 average time/residue: 0.3742 time to fit residues: 81.1162 Evaluate side-chains 199 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 247 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 5 optimal weight: 0.0370 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.127742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.111502 restraints weight = 13007.325| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.74 r_work: 0.3405 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9000 Z= 0.129 Angle : 0.512 8.811 12202 Z= 0.267 Chirality : 0.041 0.138 1410 Planarity : 0.003 0.032 1513 Dihedral : 4.916 56.646 1286 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.92 % Allowed : 17.48 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.25), residues: 1120 helix: 2.38 (0.25), residues: 420 sheet: 0.69 (0.30), residues: 277 loop : -1.01 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.020 0.001 TYR D 178 PHE 0.016 0.001 PHE R 82 TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS R 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 8999) covalent geometry : angle 0.51192 / 0.27 (12200) SS BOND : bond 0.00362 / 0.19 ( 1) SS BOND : angle 0.48356 / 0.26 ( 2) hydrogen bonds : bond 0.03652 / 2.42 ( 467) hydrogen bonds : angle 4.09760 / 2.88 ( 1338) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.333 Fit side-chains REVERT: A 8 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7462 (mt-10) REVERT: A 26 ASP cc_start: 0.7930 (m-30) cc_final: 0.7570 (m-30) REVERT: A 240 MET cc_start: 0.5030 (pmm) cc_final: 0.4753 (pmm) REVERT: A 312 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8166 (mptm) REVERT: B 150 ARG cc_start: 0.8841 (mmt-90) cc_final: 0.8625 (mmt-90) REVERT: B 219 ARG cc_start: 0.8336 (mtt-85) cc_final: 0.8124 (mtp85) REVERT: D 144 SER cc_start: 0.8574 (m) cc_final: 0.8283 (t) REVERT: D 226 THR cc_start: 0.8620 (m) cc_final: 0.8333 (p) REVERT: R 19 ILE cc_start: 0.8271 (mt) cc_final: 0.7978 (tp) REVERT: R 95 PHE cc_start: 0.7966 (m-10) cc_final: 0.7673 (m-80) REVERT: R 120 LEU cc_start: 0.8591 (mp) cc_final: 0.8325 (mm) REVERT: R 212 MET cc_start: 0.8225 (mmm) cc_final: 0.8025 (mtm) REVERT: R 247 PHE cc_start: 0.6422 (OUTLIER) cc_final: 0.6213 (m-10) REVERT: R 301 MET cc_start: 0.4533 (tpt) cc_final: 0.4203 (tpt) outliers start: 18 outliers final: 8 residues processed: 186 average time/residue: 0.3869 time to fit residues: 77.8476 Evaluate side-chains 185 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 247 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 12 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 78 optimal weight: 0.0270 chunk 36 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.127636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.111370 restraints weight = 13040.268| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.74 r_work: 0.3402 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9000 Z= 0.138 Angle : 0.518 9.159 12202 Z= 0.269 Chirality : 0.041 0.142 1410 Planarity : 0.003 0.032 1513 Dihedral : 4.924 56.551 1286 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.13 % Allowed : 18.12 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.25), residues: 1120 helix: 2.44 (0.25), residues: 420 sheet: 0.76 (0.31), residues: 271 loop : -1.02 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.020 0.001 TYR D 178 PHE 0.016 0.001 PHE R 82 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 8999) covalent geometry : angle 0.51795 / 0.27 (12200) SS BOND : bond 0.00351 / 0.18 ( 1) SS BOND : angle 0.46420 / 0.25 ( 2) hydrogen bonds : bond 0.03657 / 2.42 ( 467) hydrogen bonds : angle 4.07433 / 2.87 ( 1338) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.214 Fit side-chains REVERT: A 8 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: A 26 ASP cc_start: 0.7937 (m-30) cc_final: 0.7568 (m-30) REVERT: A 240 MET cc_start: 0.5065 (pmm) cc_final: 0.4786 (pmm) REVERT: A 312 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8175 (mptm) REVERT: B 52 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8062 (mtt-85) REVERT: B 76 ASP cc_start: 0.8106 (p0) cc_final: 0.7879 (p0) REVERT: B 254 ASP cc_start: 0.7802 (t70) cc_final: 0.7529 (t70) REVERT: D 144 SER cc_start: 0.8573 (m) cc_final: 0.8281 (t) REVERT: D 226 THR cc_start: 0.8621 (m) cc_final: 0.8336 (p) REVERT: R 19 ILE cc_start: 0.8262 (mt) cc_final: 0.7969 (tp) REVERT: R 95 PHE cc_start: 0.7958 (m-10) cc_final: 0.7655 (m-80) REVERT: R 120 LEU cc_start: 0.8599 (mp) cc_final: 0.8328 (mm) REVERT: R 301 MET cc_start: 0.4536 (tpt) cc_final: 0.4218 (tpt) outliers start: 20 outliers final: 11 residues processed: 189 average time/residue: 0.3641 time to fit residues: 74.8033 Evaluate side-chains 192 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 188 PHE Chi-restraints excluded: chain R residue 204 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 0.9980 chunk 73 optimal weight: 0.0270 chunk 74 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.127933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.111684 restraints weight = 13048.692| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.74 r_work: 0.3409 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9000 Z= 0.135 Angle : 0.523 9.098 12202 Z= 0.271 Chirality : 0.042 0.198 1410 Planarity : 0.003 0.031 1513 Dihedral : 4.868 56.294 1286 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.60 % Allowed : 19.40 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.25), residues: 1120 helix: 2.51 (0.25), residues: 420 sheet: 0.76 (0.31), residues: 271 loop : -0.99 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.020 0.001 TYR D 178 PHE 0.024 0.001 PHE R 72 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 8999) covalent geometry : angle 0.52266 / 0.27 (12200) SS BOND : bond 0.00346 / 0.18 ( 1) SS BOND : angle 0.45438 / 0.25 ( 2) hydrogen bonds : bond 0.03601 / 2.37 ( 467) hydrogen bonds : angle 4.06810 / 2.88 ( 1338) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.206 Fit side-chains REVERT: A 8 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: A 26 ASP cc_start: 0.7930 (m-30) cc_final: 0.7568 (m-30) REVERT: A 240 MET cc_start: 0.5047 (pmm) cc_final: 0.4770 (pmm) REVERT: B 52 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.8080 (mtt-85) REVERT: B 254 ASP cc_start: 0.7818 (t70) cc_final: 0.7552 (t70) REVERT: D 144 SER cc_start: 0.8558 (m) cc_final: 0.8272 (t) REVERT: D 226 THR cc_start: 0.8615 (m) cc_final: 0.8334 (p) REVERT: R 19 ILE cc_start: 0.8259 (mt) cc_final: 0.7973 (OUTLIER) REVERT: R 95 PHE cc_start: 0.7939 (m-10) cc_final: 0.7636 (m-80) REVERT: R 120 LEU cc_start: 0.8601 (mp) cc_final: 0.8331 (mm) REVERT: R 301 MET cc_start: 0.4523 (tpt) cc_final: 0.4215 (tpt) outliers start: 15 outliers final: 10 residues processed: 185 average time/residue: 0.3827 time to fit residues: 76.6296 Evaluate side-chains 190 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 188 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 78 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 66 optimal weight: 0.3980 chunk 3 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.128163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.111989 restraints weight = 12985.073| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.73 r_work: 0.3412 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9000 Z= 0.126 Angle : 0.527 9.300 12202 Z= 0.272 Chirality : 0.041 0.193 1410 Planarity : 0.003 0.031 1513 Dihedral : 4.831 57.153 1286 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.39 % Allowed : 20.04 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.25), residues: 1120 helix: 2.57 (0.25), residues: 420 sheet: 0.80 (0.31), residues: 269 loop : -1.00 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.019 0.001 TYR D 178 PHE 0.015 0.001 PHE R 82 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 8999) covalent geometry : angle 0.52731 / 0.27 (12200) SS BOND : bond 0.00347 / 0.18 ( 1) SS BOND : angle 0.45206 / 0.25 ( 2) hydrogen bonds : bond 0.03525 / 2.33 ( 467) hydrogen bonds : angle 4.04791 / 2.87 ( 1338) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: A 26 ASP cc_start: 0.7922 (m-30) cc_final: 0.7553 (m-30) REVERT: A 240 MET cc_start: 0.5023 (pmm) cc_final: 0.4736 (pmm) REVERT: A 312 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8185 (mptm) REVERT: A 345 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7970 (mttp) REVERT: B 52 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.8086 (mtt-85) REVERT: B 197 ARG cc_start: 0.7827 (mtt-85) cc_final: 0.7518 (mtt-85) REVERT: B 254 ASP cc_start: 0.7801 (t70) cc_final: 0.7535 (t70) REVERT: D 144 SER cc_start: 0.8545 (m) cc_final: 0.8272 (t) REVERT: D 226 THR cc_start: 0.8625 (m) cc_final: 0.8341 (p) REVERT: R 19 ILE cc_start: 0.8271 (mt) cc_final: 0.7977 (OUTLIER) REVERT: R 95 PHE cc_start: 0.7930 (m-10) cc_final: 0.7663 (m-80) REVERT: R 120 LEU cc_start: 0.8610 (mp) cc_final: 0.8341 (mm) REVERT: R 301 MET cc_start: 0.4508 (tpt) cc_final: 0.4192 (tpt) outliers start: 13 outliers final: 8 residues processed: 189 average time/residue: 0.3662 time to fit residues: 75.2328 Evaluate side-chains 190 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 182 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 204 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.127576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.111396 restraints weight = 12944.331| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.73 r_work: 0.3402 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9000 Z= 0.158 Angle : 0.546 10.227 12202 Z= 0.280 Chirality : 0.042 0.191 1410 Planarity : 0.003 0.032 1513 Dihedral : 4.885 56.218 1286 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.39 % Allowed : 20.68 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.25), residues: 1120 helix: 2.54 (0.25), residues: 420 sheet: 0.74 (0.31), residues: 270 loop : -1.00 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.022 0.002 TYR D 178 PHE 0.024 0.001 PHE R 72 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 8999) covalent geometry : angle 0.54587 / 0.28 (12200) SS BOND : bond 0.00398 / 0.21 ( 1) SS BOND : angle 0.50841 / 0.28 ( 2) hydrogen bonds : bond 0.03709 / 2.45 ( 467) hydrogen bonds : angle 4.10358 / 2.91 ( 1338) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: A 26 ASP cc_start: 0.7895 (m-30) cc_final: 0.7530 (m-30) REVERT: A 240 MET cc_start: 0.5128 (pmm) cc_final: 0.4810 (pmm) REVERT: A 312 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8195 (mptm) REVERT: B 52 ARG cc_start: 0.8414 (mtm-85) cc_final: 0.8091 (mtt-85) REVERT: B 197 ARG cc_start: 0.7870 (mtt-85) cc_final: 0.7558 (mtt-85) REVERT: B 254 ASP cc_start: 0.7832 (t70) cc_final: 0.7548 (t70) REVERT: D 144 SER cc_start: 0.8549 (m) cc_final: 0.8289 (t) REVERT: R 19 ILE cc_start: 0.8263 (mt) cc_final: 0.7978 (tp) REVERT: R 95 PHE cc_start: 0.7946 (m-10) cc_final: 0.7638 (m-80) REVERT: R 120 LEU cc_start: 0.8627 (mp) cc_final: 0.8336 (mm) REVERT: R 301 MET cc_start: 0.4478 (tpt) cc_final: 0.4174 (tpt) outliers start: 13 outliers final: 7 residues processed: 194 average time/residue: 0.3495 time to fit residues: 73.5370 Evaluate side-chains 199 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 27 optimal weight: 0.0770 chunk 21 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 32 optimal weight: 0.0770 chunk 107 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 76 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.128681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.112529 restraints weight = 13018.086| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.74 r_work: 0.3425 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9000 Z= 0.111 Angle : 0.528 9.655 12202 Z= 0.271 Chirality : 0.040 0.188 1410 Planarity : 0.003 0.038 1513 Dihedral : 4.800 58.852 1286 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.07 % Allowed : 20.90 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.26), residues: 1120 helix: 2.71 (0.25), residues: 420 sheet: 0.80 (0.31), residues: 268 loop : -0.99 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 83 TYR 0.017 0.001 TYR D 178 PHE 0.014 0.001 PHE R 82 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 8999) covalent geometry : angle 0.52836 / 0.27 (12200) SS BOND : bond 0.00418 / 0.22 ( 1) SS BOND : angle 0.64641 / 0.36 ( 2) hydrogen bonds : bond 0.03391 / 2.24 ( 467) hydrogen bonds : angle 4.02720 / 2.85 ( 1338) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.263 Fit side-chains REVERT: A 8 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: A 26 ASP cc_start: 0.7914 (m-30) cc_final: 0.7551 (m-30) REVERT: A 240 MET cc_start: 0.5098 (pmm) cc_final: 0.4762 (pmm) REVERT: A 312 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8165 (mptm) REVERT: A 345 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7956 (mttp) REVERT: B 52 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.8071 (mtt-85) REVERT: B 197 ARG cc_start: 0.7827 (mtt-85) cc_final: 0.7224 (mtt-85) REVERT: B 214 ARG cc_start: 0.8594 (mpt-90) cc_final: 0.8063 (mpp-170) REVERT: B 254 ASP cc_start: 0.7800 (t70) cc_final: 0.7535 (t70) REVERT: D 144 SER cc_start: 0.8531 (m) cc_final: 0.8266 (t) REVERT: D 226 THR cc_start: 0.8618 (m) cc_final: 0.8336 (p) REVERT: R 19 ILE cc_start: 0.8252 (mt) cc_final: 0.7965 (tp) REVERT: R 95 PHE cc_start: 0.7924 (m-10) cc_final: 0.7654 (m-80) REVERT: R 120 LEU cc_start: 0.8610 (mp) cc_final: 0.8329 (mm) REVERT: R 301 MET cc_start: 0.4445 (tpt) cc_final: 0.4151 (tpt) outliers start: 10 outliers final: 6 residues processed: 188 average time/residue: 0.3548 time to fit residues: 72.7157 Evaluate side-chains 190 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 183 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 94 optimal weight: 0.3980 chunk 85 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.127664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.111527 restraints weight = 12932.346| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.74 r_work: 0.3404 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9000 Z= 0.159 Angle : 0.570 10.861 12202 Z= 0.289 Chirality : 0.042 0.185 1410 Planarity : 0.003 0.039 1513 Dihedral : 4.882 56.340 1286 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.17 % Allowed : 21.00 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.26), residues: 1120 helix: 2.60 (0.25), residues: 420 sheet: 0.77 (0.31), residues: 269 loop : -0.98 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 83 TYR 0.022 0.001 TYR D 178 PHE 0.022 0.001 PHE R 72 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 8999) covalent geometry : angle 0.56959 / 0.29 (12200) SS BOND : bond 0.00445 / 0.23 ( 1) SS BOND : angle 0.64105 / 0.35 ( 2) hydrogen bonds : bond 0.03677 / 2.42 ( 467) hydrogen bonds : angle 4.08295 / 2.89 ( 1338) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2935.89 seconds wall clock time: 50 minutes 23.98 seconds (3023.98 seconds total)