Starting phenix.real_space_refine on Thu Jul 2 12:31:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8feg_29026/07_2026/8feg_29026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8feg_29026/07_2026/8feg_29026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8feg_29026/07_2026/8feg_29026.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8feg_29026/07_2026/8feg_29026.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8feg_29026/07_2026/8feg_29026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8feg_29026/07_2026/8feg_29026.map" model { file = "/net/cci-nas-00/data/ceres_data/8feg_29026/07_2026/8feg_29026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8feg_29026/07_2026/8feg_29026.cif" } resolution = 2.54 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5453 2.51 5 N 1418 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8539 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1507 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 193} Chain breaks: 3 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'GLU:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2600 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "F" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2129 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain breaks: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'ACE': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 1} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 39 Classifications: {'peptide': 5} Link IDs: {'CIS': 3, 'TRANS': 1} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'XT9': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DPN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.30, per 1000 atoms: 0.15 Number of scatterers: 8539 At special positions: 0 Unit cell: (88.88, 123.2, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1604 8.00 N 1418 7.00 C 5453 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 217 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 210 " 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=2, symmetry=0 Links applied TRANS " DTY A 4 " - " ALA A 3 " " DPN A 9 " - " THR A 8 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 339.1 milliseconds 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTY A 4 " pdb=" CB DTH A 5 " pdb=" CB DPN A 9 " Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 37.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.857A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE C 215 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 231 Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.633A pdb=" N ALA C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.659A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 4.008A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 329 through 351 removed outlier: 4.273A pdb=" N VAL C 335 " --> pdb=" O ASN C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 26 Processing helix chain 'D' and resid 29 through 34 removed outlier: 3.528A pdb=" N ILE D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'E' and resid 9 through 18 Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 45 through 48 removed outlier: 3.563A pdb=" N ASP E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 45 through 48' Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 53 through 56 removed outlier: 4.230A pdb=" N GLY F 56 " --> pdb=" O SER F 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 53 through 56' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.865A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 212 removed outlier: 3.514A pdb=" N ASP F 211 " --> pdb=" O GLU F 208 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL F 212 " --> pdb=" O ALA F 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 208 through 212' Processing helix chain 'B' and resid 60 through 87 removed outlier: 3.512A pdb=" N ALA B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 110 Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.993A pdb=" N MET B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 162 Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.861A pdb=" N LEU B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 195 removed outlier: 4.483A pdb=" N VAL B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 235 Processing helix chain 'B' and resid 235 through 254 Processing helix chain 'B' and resid 255 through 260 removed outlier: 7.257A pdb=" N LEU B 258 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 259 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 299 removed outlier: 3.774A pdb=" N LEU B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 306 through 324 removed outlier: 4.399A pdb=" N TYR B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 323 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 Processing sheet with id=AA1, first strand: chain 'C' and resid 185 through 190 removed outlier: 3.642A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 51 removed outlier: 5.547A pdb=" N THR D 47 " --> pdb=" O ASN D 340 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN D 340 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG D 49 " --> pdb=" O ILE D 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 63 removed outlier: 4.514A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 73 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASP D 83 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS D 89 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.728A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY D 116 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE D 120 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 151 removed outlier: 4.221A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.850A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.538A pdb=" N CYS D 250 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR D 263 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU D 252 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN D 259 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 275 through 278 removed outlier: 3.819A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.748A pdb=" N MET F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'F' and resid 135 through 136 removed outlier: 3.563A pdb=" N GLU F 234 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP F 164 " --> pdb=" O LEU F 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 199 through 201 444 hydrogen bonds defined for protein. 1260 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: 0.86 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1382 1.31 - 1.44: 2390 1.44 - 1.57: 4841 1.57 - 1.70: 4 1.70 - 1.83: 94 Bond restraints: 8711 Sorted by residual: bond pdb=" C36 XT9 A 101 " pdb=" N40 XT9 A 101 " ideal model delta sigma weight residual 1.493 1.248 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C CYS A 7 " pdb=" N THR A 8 " ideal model delta sigma weight residual 1.329 1.491 -0.162 1.40e-02 5.10e+03 1.34e+02 bond pdb=" C DTH A 5 " pdb=" N THR A 6 " ideal model delta sigma weight residual 1.329 1.488 -0.159 1.40e-02 5.10e+03 1.29e+02 bond pdb=" C37 XT9 A 101 " pdb=" C45 XT9 A 101 " ideal model delta sigma weight residual 1.507 1.716 -0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C DTY A 4 " pdb=" N DTH A 5 " ideal model delta sigma weight residual 1.329 1.476 -0.147 1.40e-02 5.10e+03 1.10e+02 ... (remaining 8706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 11579 2.69 - 5.39: 206 5.39 - 8.08: 38 8.08 - 10.78: 3 10.78 - 13.47: 5 Bond angle restraints: 11831 Sorted by residual: angle pdb=" C PRO B 59 " pdb=" N VAL B 60 " pdb=" CA VAL B 60 " ideal model delta sigma weight residual 122.09 110.85 11.24 1.49e+00 4.50e-01 5.70e+01 angle pdb=" N LYS B 338 " pdb=" CA LYS B 338 " pdb=" C LYS B 338 " ideal model delta sigma weight residual 113.21 105.23 7.98 1.15e+00 7.56e-01 4.81e+01 angle pdb=" N VAL C 201 " pdb=" CA VAL C 201 " pdb=" C VAL C 201 " ideal model delta sigma weight residual 113.71 108.29 5.42 9.50e-01 1.11e+00 3.26e+01 angle pdb=" CA CYS A 7 " pdb=" C CYS A 7 " pdb=" N THR A 8 " ideal model delta sigma weight residual 116.20 125.78 -9.58 2.00e+00 2.50e-01 2.29e+01 angle pdb=" N THR B 302 " pdb=" CA THR B 302 " pdb=" C THR B 302 " ideal model delta sigma weight residual 110.80 100.92 9.88 2.13e+00 2.20e-01 2.15e+01 ... (remaining 11826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 4634 17.40 - 34.80: 425 34.80 - 52.20: 97 52.20 - 69.60: 20 69.60 - 87.00: 5 Dihedral angle restraints: 5181 sinusoidal: 1968 harmonic: 3213 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 210 " pdb=" CB CYS B 210 " ideal model delta sinusoidal sigma weight residual 93.00 133.89 -40.89 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CA GLY D 306 " pdb=" C GLY D 306 " pdb=" N VAL D 307 " pdb=" CA VAL D 307 " ideal model delta harmonic sigma weight residual -180.00 -159.96 -20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA PHE F 32 " pdb=" C PHE F 32 " pdb=" N GLY F 33 " pdb=" CA GLY F 33 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 5178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.027: 1380 1.027 - 2.055: 0 2.055 - 3.082: 0 3.082 - 4.110: 0 4.110 - 5.137: 3 Chirality restraints: 1383 Sorted by residual: chirality pdb=" CA DTH A 5 " pdb=" N DTH A 5 " pdb=" C DTH A 5 " pdb=" CB DTH A 5 " both_signs ideal model delta sigma weight residual False 2.53 -2.61 5.14 2.00e-01 2.50e+01 6.60e+02 chirality pdb=" CA DTY A 4 " pdb=" N DTY A 4 " pdb=" C DTY A 4 " pdb=" CB DTY A 4 " both_signs ideal model delta sigma weight residual False 2.51 -2.62 5.13 2.00e-01 2.50e+01 6.59e+02 chirality pdb=" CB DTH A 5 " pdb=" CA DTH A 5 " pdb=" OG1 DTH A 5 " pdb=" CG2 DTH A 5 " both_signs ideal model delta sigma weight residual False 2.55 -2.53 5.08 2.00e-01 2.50e+01 6.46e+02 ... (remaining 1380 not shown) Planarity restraints: 1480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 332 " 0.031 2.00e-02 2.50e+03 2.74e-02 1.88e+01 pdb=" CG TRP D 332 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP D 332 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP D 332 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP D 332 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 332 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 332 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 332 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 332 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 332 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 299 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C LEU B 299 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU B 299 " -0.023 2.00e-02 2.50e+03 pdb=" N GLY B 300 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 83 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.01e+01 pdb=" C VAL B 83 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL B 83 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE B 84 " 0.018 2.00e-02 2.50e+03 ... (remaining 1477 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1015 2.75 - 3.29: 7979 3.29 - 3.83: 14524 3.83 - 4.36: 16716 4.36 - 4.90: 29237 Nonbonded interactions: 69471 Sorted by model distance: nonbonded pdb=" CG1 VAL B 69 " pdb=" SG CYS B 324 " model vdw 2.217 3.820 nonbonded pdb=" OG SER D 331 " pdb=" OD1 ASP D 333 " model vdw 2.245 3.040 nonbonded pdb=" OG1 THR D 128 " pdb=" O GLU D 130 " model vdw 2.263 3.040 nonbonded pdb=" OE2 GLU C 8 " pdb=" OH TYR F 163 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR D 85 " pdb=" OE1 GLU E 58 " model vdw 2.291 3.040 ... (remaining 69466 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: 1.480 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.450 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:5.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 : 0.009 0.245 8717 Z= 0.529 Angle : 0.912 13.471 11841 Z= 0.499 Chirality : 0.245 5.137 1383 Planarity : 0.006 0.065 1478 Dihedral : 14.313 87.003 3093 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 1.11 % Allowed : 5.00 % Favored : 93.88 % Rotamer: Outliers : 1.52 % Allowed : 1.31 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.96 (0.24), residues: 1079 helix: 0.26 (0.25), residues: 359 sheet: -0.13 (0.30), residues: 269 loop : -1.64 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 314 TYR 0.020 0.002 TYR F 178 PHE 0.029 0.002 PHE F 200 TRP 0.072 0.003 TRP D 332 HIS 0.006 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00870 / 0.48 ( 8711) covalent geometry : angle 0.90734 / 0.50 (11831) SS BOND : bond 0.00479 / 0.25 ( 2) SS BOND : angle 1.72072 / 0.91 ( 4) hydrogen bonds : bond 0.13742 / 8.86 ( 444) hydrogen bonds : angle 6.48069 / 4.66 ( 1260) Misc. bond : bond 0.07813 / 3.85 ( 2) link_TRANS : bond 0.16520 / 8.22 ( 2) link_TRANS : angle 3.83266 / 1.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: B 302 THR cc_start: 0.7425 (OUTLIER) cc_final: 0.7070 (m) REVERT: B 305 SER cc_start: 0.8180 (m) cc_final: 0.7736 (p) outliers start: 14 outliers final: 9 residues processed: 184 average time/residue: 0.3763 time to fit residues: 74.5104 Evaluate side-chains 171 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0040 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 overall best weight: 0.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 313 ASN F 130 GLN B 115 GLN B 304 HIS B 322 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.169338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.140192 restraints weight = 11934.065| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.93 r_work: 0.3701 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8717 Z= 0.122 Angle : 0.624 13.322 11841 Z= 0.316 Chirality : 0.052 1.034 1383 Planarity : 0.004 0.055 1478 Dihedral : 8.080 58.328 1264 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.18 % Allowed : 11.75 % Favored : 86.07 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.13 (0.25), residues: 1079 helix: 1.44 (0.27), residues: 362 sheet: -0.20 (0.30), residues: 263 loop : -1.26 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 219 TYR 0.015 0.001 TYR B 140 PHE 0.023 0.001 PHE B 293 TRP 0.024 0.002 TRP D 332 HIS 0.003 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 8711) covalent geometry : angle 0.62224 / 0.32 (11831) SS BOND : bond 0.00422 / 0.21 ( 2) SS BOND : angle 0.94354 / 0.47 ( 4) hydrogen bonds : bond 0.04101 / 2.70 ( 444) hydrogen bonds : angle 4.87337 / 3.44 ( 1260) Misc. bond : bond 0.00018 / 0.01 ( 2) link_TRANS : bond 0.01088 / 0.57 ( 2) link_TRANS : angle 2.03421 / 0.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.284 Fit side-chains REVERT: D 219 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7757 (ttm-80) REVERT: D 325 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7689 (mtp) REVERT: B 81 MET cc_start: 0.4952 (mpp) cc_final: 0.4713 (mpp) REVERT: B 305 SER cc_start: 0.8143 (m) cc_final: 0.7310 (p) REVERT: A 2 TYR cc_start: 0.1704 (OUTLIER) cc_final: 0.0523 (t80) outliers start: 20 outliers final: 13 residues processed: 178 average time/residue: 0.3341 time to fit residues: 64.5824 Evaluate side-chains 179 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 304 HIS Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 0.0270 chunk 52 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 88 ASN D 110 ASN D 125 ASN D 239 ASN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 ASN D 295 ASN D 313 ASN D 340 ASN B 304 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.167272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.137813 restraints weight = 11821.489| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.93 r_work: 0.3672 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8717 Z= 0.143 Angle : 0.602 11.398 11841 Z= 0.306 Chirality : 0.050 0.869 1383 Planarity : 0.004 0.051 1478 Dihedral : 7.832 59.502 1262 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.83 % Allowed : 14.58 % Favored : 82.59 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.19 (0.25), residues: 1079 helix: 1.87 (0.28), residues: 364 sheet: -0.13 (0.30), residues: 267 loop : -1.18 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 314 TYR 0.015 0.001 TYR F 178 PHE 0.012 0.001 PHE B 231 TRP 0.014 0.001 TRP D 169 HIS 0.009 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 8711) covalent geometry : angle 0.60005 / 0.31 (11831) SS BOND : bond 0.00482 / 0.25 ( 2) SS BOND : angle 1.26445 / 0.64 ( 4) hydrogen bonds : bond 0.04156 / 2.76 ( 444) hydrogen bonds : angle 4.65395 / 3.29 ( 1260) Misc. bond : bond 0.00097 / 0.05 ( 2) link_TRANS : bond 0.00614 / 0.32 ( 2) link_TRANS : angle 2.05612 / 0.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.309 Fit side-chains REVERT: D 219 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7734 (ttt-90) REVERT: B 305 SER cc_start: 0.8254 (m) cc_final: 0.7473 (p) REVERT: A 2 TYR cc_start: 0.1834 (OUTLIER) cc_final: -0.0091 (p90) outliers start: 26 outliers final: 15 residues processed: 181 average time/residue: 0.3633 time to fit residues: 70.7785 Evaluate side-chains 186 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 36 optimal weight: 0.0980 chunk 43 optimal weight: 0.0040 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 88 ASN D 110 ASN D 125 ASN D 239 ASN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 ASN D 295 ASN D 340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.166509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.136819 restraints weight = 12011.433| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.95 r_work: 0.3654 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8717 Z= 0.158 Angle : 0.616 10.879 11841 Z= 0.312 Chirality : 0.050 0.805 1383 Planarity : 0.004 0.049 1478 Dihedral : 7.524 59.397 1259 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.37 % Allowed : 16.10 % Favored : 80.52 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.26 (0.25), residues: 1079 helix: 2.00 (0.28), residues: 361 sheet: -0.14 (0.30), residues: 267 loop : -1.15 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 314 TYR 0.019 0.002 TYR B 140 PHE 0.014 0.001 PHE B 293 TRP 0.017 0.002 TRP D 332 HIS 0.003 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 8711) covalent geometry : angle 0.61375 / 0.31 (11831) SS BOND : bond 0.00500 / 0.26 ( 2) SS BOND : angle 1.34125 / 0.67 ( 4) hydrogen bonds : bond 0.04154 / 2.78 ( 444) hydrogen bonds : angle 4.59534 / 3.25 ( 1260) Misc. bond : bond 0.00073 / 0.04 ( 2) link_TRANS : bond 0.00641 / 0.34 ( 2) link_TRANS : angle 2.20751 / 0.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.312 Fit side-chains REVERT: D 217 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6717 (pmt) REVERT: D 219 ARG cc_start: 0.8090 (ttm-80) cc_final: 0.7805 (ttt-90) REVERT: D 258 ASP cc_start: 0.7593 (t0) cc_final: 0.7043 (t0) REVERT: B 257 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6590 (mtm110) REVERT: B 305 SER cc_start: 0.8335 (m) cc_final: 0.7600 (p) REVERT: A 2 TYR cc_start: 0.2448 (OUTLIER) cc_final: 0.0673 (p90) outliers start: 31 outliers final: 16 residues processed: 173 average time/residue: 0.4836 time to fit residues: 89.9417 Evaluate side-chains 173 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 304 HIS Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 45 optimal weight: 0.3980 chunk 19 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 88 optimal weight: 0.0970 chunk 40 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 ASN F 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.166197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.136669 restraints weight = 11971.944| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.94 r_work: 0.3657 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8717 Z= 0.144 Angle : 0.619 11.407 11841 Z= 0.310 Chirality : 0.049 0.767 1383 Planarity : 0.004 0.050 1478 Dihedral : 7.064 59.815 1253 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.70 % Allowed : 17.41 % Favored : 78.89 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.31 (0.25), residues: 1079 helix: 2.05 (0.28), residues: 362 sheet: -0.13 (0.30), residues: 267 loop : -1.12 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 271 TYR 0.018 0.001 TYR B 140 PHE 0.019 0.001 PHE B 293 TRP 0.020 0.002 TRP D 332 HIS 0.004 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 8711) covalent geometry : angle 0.61619 / 0.31 (11831) SS BOND : bond 0.00445 / 0.23 ( 2) SS BOND : angle 1.24841 / 0.62 ( 4) hydrogen bonds : bond 0.04009 / 2.68 ( 444) hydrogen bonds : angle 4.50321 / 3.20 ( 1260) Misc. bond : bond 0.00066 / 0.03 ( 2) link_TRANS : bond 0.00656 / 0.35 ( 2) link_TRANS : angle 2.32707 / 0.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: D 217 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6760 (pmt) REVERT: D 219 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7879 (ttt-90) REVERT: B 305 SER cc_start: 0.8340 (m) cc_final: 0.8048 (m) outliers start: 34 outliers final: 20 residues processed: 175 average time/residue: 0.4688 time to fit residues: 88.4333 Evaluate side-chains 177 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 80 optimal weight: 0.0470 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 239 ASN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 ASN F 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.165984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.136532 restraints weight = 11877.871| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.94 r_work: 0.3646 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8717 Z= 0.154 Angle : 0.620 10.314 11841 Z= 0.312 Chirality : 0.049 0.747 1383 Planarity : 0.004 0.050 1478 Dihedral : 6.927 59.411 1249 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.81 % Allowed : 17.74 % Favored : 78.45 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1079 helix: 2.06 (0.27), residues: 363 sheet: -0.14 (0.30), residues: 267 loop : -1.11 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 314 TYR 0.016 0.001 TYR F 178 PHE 0.016 0.001 PHE B 293 TRP 0.026 0.002 TRP D 332 HIS 0.003 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 8711) covalent geometry : angle 0.61797 / 0.31 (11831) SS BOND : bond 0.00490 / 0.25 ( 2) SS BOND : angle 1.30442 / 0.66 ( 4) hydrogen bonds : bond 0.04066 / 2.74 ( 444) hydrogen bonds : angle 4.50487 / 3.21 ( 1260) Misc. bond : bond 0.00046 / 0.02 ( 2) link_TRANS : bond 0.00650 / 0.34 ( 2) link_TRANS : angle 2.35253 / 0.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: D 217 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6741 (pmt) REVERT: D 219 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7874 (ttt-90) REVERT: B 305 SER cc_start: 0.8355 (m) cc_final: 0.8056 (m) REVERT: B 321 THR cc_start: 0.8381 (p) cc_final: 0.8086 (t) outliers start: 35 outliers final: 27 residues processed: 174 average time/residue: 0.4718 time to fit residues: 88.5506 Evaluate side-chains 184 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 57 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 12 optimal weight: 0.0170 chunk 76 optimal weight: 2.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 239 ASN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 ASN F 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.165472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.135933 restraints weight = 12009.656| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.93 r_work: 0.3639 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8717 Z= 0.165 Angle : 0.633 10.283 11841 Z= 0.321 Chirality : 0.050 0.739 1383 Planarity : 0.004 0.050 1478 Dihedral : 6.952 58.786 1249 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.70 % Allowed : 18.39 % Favored : 77.91 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.25), residues: 1079 helix: 1.99 (0.27), residues: 367 sheet: -0.15 (0.30), residues: 267 loop : -1.20 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.017 0.002 TYR B 140 PHE 0.025 0.001 PHE B 293 TRP 0.034 0.002 TRP D 332 HIS 0.003 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 8711) covalent geometry : angle 0.63004 / 0.32 (11831) SS BOND : bond 0.00494 / 0.26 ( 2) SS BOND : angle 1.39061 / 0.70 ( 4) hydrogen bonds : bond 0.04169 / 2.81 ( 444) hydrogen bonds : angle 4.52309 / 3.25 ( 1260) Misc. bond : bond 0.00040 / 0.02 ( 2) link_TRANS : bond 0.00656 / 0.35 ( 2) link_TRANS : angle 2.37523 / 0.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: C 243 MET cc_start: 0.6346 (mmm) cc_final: 0.5955 (mmm) REVERT: D 45 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7114 (mtt) REVERT: D 217 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6820 (pmt) REVERT: D 219 ARG cc_start: 0.8117 (ttm-80) cc_final: 0.7879 (ttt-90) REVERT: D 258 ASP cc_start: 0.7615 (t0) cc_final: 0.7066 (t0) REVERT: B 305 SER cc_start: 0.8376 (m) cc_final: 0.8082 (m) REVERT: B 321 THR cc_start: 0.8361 (p) cc_final: 0.8060 (t) outliers start: 34 outliers final: 25 residues processed: 170 average time/residue: 0.4913 time to fit residues: 89.7280 Evaluate side-chains 184 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 239 ASN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.164752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.135244 restraints weight = 11818.501| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.91 r_work: 0.3631 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8717 Z= 0.192 Angle : 0.650 10.274 11841 Z= 0.332 Chirality : 0.051 0.747 1383 Planarity : 0.004 0.050 1478 Dihedral : 7.034 57.737 1249 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.24 % Allowed : 18.17 % Favored : 77.58 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.21 (0.25), residues: 1079 helix: 1.93 (0.27), residues: 368 sheet: -0.13 (0.30), residues: 274 loop : -1.25 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 314 TYR 0.017 0.002 TYR F 178 PHE 0.027 0.002 PHE B 293 TRP 0.044 0.002 TRP D 332 HIS 0.004 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 ( 8711) covalent geometry : angle 0.64765 / 0.33 (11831) SS BOND : bond 0.00559 / 0.29 ( 2) SS BOND : angle 1.56417 / 0.78 ( 4) hydrogen bonds : bond 0.04423 / 2.99 ( 444) hydrogen bonds : angle 4.58561 / 3.31 ( 1260) Misc. bond : bond 0.00044 / 0.02 ( 2) link_TRANS : bond 0.00656 / 0.34 ( 2) link_TRANS : angle 2.36542 / 0.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: C 243 MET cc_start: 0.6333 (mmm) cc_final: 0.5985 (mmm) REVERT: D 211 TRP cc_start: 0.8703 (m100) cc_final: 0.8358 (m100) REVERT: D 217 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6829 (pmt) REVERT: D 219 ARG cc_start: 0.8128 (ttm-80) cc_final: 0.7927 (ttt-90) REVERT: D 258 ASP cc_start: 0.7629 (t0) cc_final: 0.7055 (t0) REVERT: E 37 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7718 (mp) REVERT: B 224 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7083 (tm) REVERT: B 305 SER cc_start: 0.8395 (m) cc_final: 0.8040 (m) REVERT: B 321 THR cc_start: 0.8379 (p) cc_final: 0.8063 (t) REVERT: A 2 TYR cc_start: 0.3184 (OUTLIER) cc_final: 0.2427 (t80) outliers start: 39 outliers final: 23 residues processed: 180 average time/residue: 0.4795 time to fit residues: 93.0324 Evaluate side-chains 188 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 51 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 90 optimal weight: 0.1980 chunk 2 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 230 ASN D 239 ASN F 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.167438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.138199 restraints weight = 11948.235| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.92 r_work: 0.3675 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8717 Z= 0.112 Angle : 0.608 11.367 11841 Z= 0.304 Chirality : 0.048 0.696 1383 Planarity : 0.004 0.051 1478 Dihedral : 6.713 59.300 1249 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.94 % Allowed : 19.80 % Favored : 77.26 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.36 (0.25), residues: 1079 helix: 2.10 (0.27), residues: 366 sheet: 0.01 (0.30), residues: 284 loop : -1.25 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 46 TYR 0.019 0.001 TYR B 140 PHE 0.019 0.001 PHE B 293 TRP 0.044 0.002 TRP D 332 HIS 0.003 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 8711) covalent geometry : angle 0.60497 / 0.30 (11831) SS BOND : bond 0.00373 / 0.19 ( 2) SS BOND : angle 0.91695 / 0.47 ( 4) hydrogen bonds : bond 0.03563 / 2.39 ( 444) hydrogen bonds : angle 4.38342 / 3.19 ( 1260) Misc. bond : bond 0.00007 / 0.00 ( 2) link_TRANS : bond 0.00683 / 0.36 ( 2) link_TRANS : angle 2.48726 / 0.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.315 Fit side-chains REVERT: C 243 MET cc_start: 0.6322 (mmm) cc_final: 0.5930 (mmm) REVERT: F 38 ARG cc_start: 0.8153 (ttp-170) cc_final: 0.7734 (ttp-170) REVERT: B 117 THR cc_start: 0.5975 (OUTLIER) cc_final: 0.5757 (t) REVERT: B 224 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.7024 (tm) REVERT: B 305 SER cc_start: 0.8378 (m) cc_final: 0.7994 (m) REVERT: B 321 THR cc_start: 0.8350 (p) cc_final: 0.8050 (t) REVERT: A 2 TYR cc_start: 0.3124 (OUTLIER) cc_final: 0.2244 (t80) outliers start: 27 outliers final: 11 residues processed: 173 average time/residue: 0.4762 time to fit residues: 88.8170 Evaluate side-chains 173 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.0670 chunk 60 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 239 ASN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.165621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.136043 restraints weight = 11870.684| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.92 r_work: 0.3647 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8717 Z= 0.159 Angle : 0.653 11.023 11841 Z= 0.327 Chirality : 0.050 0.714 1383 Planarity : 0.004 0.049 1478 Dihedral : 6.841 58.511 1249 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.39 % Allowed : 20.46 % Favored : 77.15 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.33 (0.26), residues: 1079 helix: 2.09 (0.27), residues: 366 sheet: -0.07 (0.30), residues: 276 loop : -1.23 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 46 TYR 0.016 0.001 TYR F 178 PHE 0.039 0.001 PHE B 293 TRP 0.057 0.002 TRP D 332 HIS 0.003 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 8711) covalent geometry : angle 0.65039 / 0.32 (11831) SS BOND : bond 0.00470 / 0.24 ( 2) SS BOND : angle 1.32912 / 0.68 ( 4) hydrogen bonds : bond 0.04063 / 2.73 ( 444) hydrogen bonds : angle 4.45869 / 3.25 ( 1260) Misc. bond : bond 0.00025 / 0.01 ( 2) link_TRANS : bond 0.00652 / 0.34 ( 2) link_TRANS : angle 2.42829 / 0.82 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.318 Fit side-chains REVERT: C 243 MET cc_start: 0.6328 (mmm) cc_final: 0.5933 (mmm) REVERT: D 314 ARG cc_start: 0.7571 (ptp-110) cc_final: 0.7345 (ptp-110) REVERT: F 38 ARG cc_start: 0.8262 (ttp-170) cc_final: 0.7883 (ttp-170) REVERT: B 117 THR cc_start: 0.5928 (OUTLIER) cc_final: 0.5713 (t) REVERT: B 224 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.7047 (tm) REVERT: B 305 SER cc_start: 0.8391 (m) cc_final: 0.8000 (m) REVERT: B 321 THR cc_start: 0.8349 (p) cc_final: 0.8052 (t) REVERT: A 2 TYR cc_start: 0.3144 (OUTLIER) cc_final: 0.2136 (t80) outliers start: 22 outliers final: 15 residues processed: 174 average time/residue: 0.4507 time to fit residues: 84.8483 Evaluate side-chains 178 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 104 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 32 GLN D 239 ASN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.164939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.135435 restraints weight = 11848.647| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.92 r_work: 0.3635 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8717 Z= 0.182 Angle : 0.677 11.383 11841 Z= 0.339 Chirality : 0.051 0.725 1383 Planarity : 0.004 0.049 1478 Dihedral : 6.940 57.728 1249 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.83 % Allowed : 20.02 % Favored : 77.15 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.25), residues: 1079 helix: 2.01 (0.27), residues: 367 sheet: -0.10 (0.31), residues: 269 loop : -1.25 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 46 TYR 0.017 0.002 TYR F 178 PHE 0.039 0.002 PHE B 293 TRP 0.059 0.002 TRP D 332 HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 8711) covalent geometry : angle 0.67425 / 0.34 (11831) SS BOND : bond 0.00511 / 0.26 ( 2) SS BOND : angle 1.46059 / 0.74 ( 4) hydrogen bonds : bond 0.04279 / 2.88 ( 444) hydrogen bonds : angle 4.53770 / 3.30 ( 1260) Misc. bond : bond 0.00032 / 0.02 ( 2) link_TRANS : bond 0.00652 / 0.34 ( 2) link_TRANS : angle 2.42496 / 0.82 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3932.32 seconds wall clock time: 67 minutes 42.70 seconds (4062.70 seconds total)