Starting phenix.real_space_refine on Sat May 2 20:46:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8feg_29026/05_2026/8feg_29026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8feg_29026/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8feg_29026/05_2026/8feg_29026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8feg_29026/05_2026/8feg_29026.map" model { file = "/net/cci-nas-00/data/ceres_data/8feg_29026/05_2026/8feg_29026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8feg_29026/05_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 2} 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} Modifications used: {'PEPT-D': 1} Link IDs: {None: 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: 2.64, per 1000 atoms: 0.31 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: 0.98 Conformation dependent library (CDL) restraints added in 307.7 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: 0.31 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: 1.21 Time building geometry restraints manager: 1.24 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: 205 5.39 - 8.08: 38 8.08 - 10.78: 4 10.78 - 13.47: 5 Bond angle restraints: 11831 Sorted by residual: angle pdb=" CA DPN A 9 " pdb=" CB DPN A 9 " pdb=" CG DPN A 9 " ideal model delta sigma weight residual 113.80 105.17 8.63 1.00e+00 1.00e+00 7.45e+01 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 ... (remaining 11826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 4634 17.40 - 34.80: 426 34.80 - 52.20: 97 52.20 - 69.60: 20 69.60 - 87.00: 5 Dihedral angle restraints: 5182 sinusoidal: 1969 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 5179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1276 0.099 - 0.197: 99 0.197 - 0.296: 5 0.296 - 0.394: 1 0.394 - 0.492: 2 Chirality restraints: 1383 Sorted by residual: chirality pdb=" C32 XT9 A 101 " pdb=" C29 XT9 A 101 " pdb=" C33 XT9 A 101 " pdb=" O51 XT9 A 101 " both_signs ideal model delta sigma weight residual False -2.51 -2.02 -0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CB ILE B 290 " pdb=" CA ILE B 290 " pdb=" CG1 ILE B 290 " pdb=" CG2 ILE B 290 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C33 XT9 A 101 " pdb=" C32 XT9 A 101 " pdb=" C34 XT9 A 101 " pdb=" C44 XT9 A 101 " both_signs ideal model delta sigma weight residual False 2.94 2.63 0.31 2.00e-01 2.50e+01 2.44e+00 ... (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: 2.120 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: 0.020 Set scattering table: 0.030 Process input model: 9.590 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 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= 0.528 Angle : 0.912 13.471 11841 Z= 0.505 Chirality : 0.056 0.492 1383 Planarity : 0.006 0.065 1478 Dihedral : 14.315 87.003 3094 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 covalent geometry : bond 0.00868 ( 8711) covalent geometry : angle 0.90798 (11831) SS BOND : bond 0.00479 ( 2) SS BOND : angle 1.72072 ( 4) hydrogen bonds : bond 0.13742 ( 444) hydrogen bonds : angle 6.48069 ( 1260) Misc. bond : bond 0.07813 ( 2) link_TRANS : bond 0.16520 ( 2) link_TRANS : angle 3.83266 ( 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 : 0.361 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: 0.4867 time to fit residues: 96.1708 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 : 0.306 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4195 r_free = 0.4195 target = 0.169385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.140307 restraints weight = 11937.724| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.92 r_work: 0.3703 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8717 Z= 0.115 Angle : 0.584 8.442 11841 Z= 0.299 Chirality : 0.042 0.155 1383 Planarity : 0.004 0.055 1478 Dihedral : 8.161 58.124 1265 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.07 % Allowed : 11.97 % Favored : 85.96 % 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: -0.14 (0.25), residues: 1079 helix: 1.41 (0.27), residues: 362 sheet: -0.19 (0.30), residues: 263 loop : -1.26 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 219 TYR 0.015 0.001 TYR B 140 PHE 0.021 0.001 PHE B 293 TRP 0.025 0.002 TRP D 332 HIS 0.003 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8711) covalent geometry : angle 0.58398 (11831) SS BOND : bond 0.00398 ( 2) SS BOND : angle 1.00253 ( 4) hydrogen bonds : bond 0.04140 ( 444) hydrogen bonds : angle 4.86433 ( 1260) Misc. bond : bond 0.00087 ( 2) link_TRANS : bond 0.00244 ( 2) link_TRANS : angle 0.37879 ( 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 187 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.351 Fit side-chains REVERT: D 219 ARG cc_start: 0.8093 (ttm-80) cc_final: 0.7727 (ttm-80) REVERT: D 325 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7688 (mmm) REVERT: B 208 ILE cc_start: 0.7432 (mm) cc_final: 0.7226 (mp) REVERT: B 305 SER cc_start: 0.8172 (m) cc_final: 0.7294 (p) REVERT: A 2 TYR cc_start: 0.2000 (OUTLIER) cc_final: 0.0750 (t80) outliers start: 19 outliers final: 12 residues processed: 178 average time/residue: 0.4403 time to fit residues: 84.8591 Evaluate side-chains 179 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4155 r_free = 0.4155 target = 0.165752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.135918 restraints weight = 11762.444| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.94 r_work: 0.3641 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8717 Z= 0.206 Angle : 0.630 9.170 11841 Z= 0.322 Chirality : 0.044 0.173 1383 Planarity : 0.004 0.051 1478 Dihedral : 8.029 59.316 1261 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.37 % Allowed : 14.58 % Favored : 82.05 % 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: 0.09 (0.25), residues: 1079 helix: 1.79 (0.28), residues: 362 sheet: -0.17 (0.30), residues: 267 loop : -1.24 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 314 TYR 0.018 0.002 TYR F 178 PHE 0.013 0.001 PHE B 231 TRP 0.014 0.002 TRP D 169 HIS 0.009 0.001 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 8711) covalent geometry : angle 0.62908 (11831) SS BOND : bond 0.00603 ( 2) SS BOND : angle 1.70977 ( 4) hydrogen bonds : bond 0.04736 ( 444) hydrogen bonds : angle 4.77863 ( 1260) Misc. bond : bond 0.00127 ( 2) link_TRANS : bond 0.00094 ( 2) link_TRANS : angle 0.48276 ( 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 197 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.306 Fit side-chains REVERT: D 211 TRP cc_start: 0.8716 (m100) cc_final: 0.8347 (m100) REVERT: D 258 ASP cc_start: 0.7618 (t0) cc_final: 0.7023 (t0) REVERT: D 325 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7876 (mmt) REVERT: F 38 ARG cc_start: 0.8388 (ttp-170) cc_final: 0.8149 (ttm170) REVERT: B 305 SER cc_start: 0.8272 (m) cc_final: 0.7562 (p) REVERT: A 2 TYR cc_start: 0.2303 (OUTLIER) cc_final: 0.1178 (t80) outliers start: 31 outliers final: 18 residues processed: 178 average time/residue: 0.4734 time to fit residues: 90.7908 Evaluate side-chains 184 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 135 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 58 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 121 MET 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: 2.9990 chunk 43 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 F 130 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.164420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.134505 restraints weight = 11935.572| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.93 r_work: 0.3625 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8717 Z= 0.237 Angle : 0.664 9.890 11841 Z= 0.338 Chirality : 0.046 0.238 1383 Planarity : 0.004 0.053 1478 Dihedral : 7.736 58.348 1258 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.92 % Allowed : 16.10 % Favored : 79.98 % 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: 0.07 (0.25), residues: 1079 helix: 1.84 (0.28), residues: 358 sheet: -0.19 (0.30), residues: 267 loop : -1.28 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 314 TYR 0.019 0.002 TYR F 178 PHE 0.016 0.002 PHE B 231 TRP 0.024 0.002 TRP D 332 HIS 0.005 0.001 HIS D 91 Details of bonding type rmsd covalent geometry : bond 0.00551 ( 8711) covalent geometry : angle 0.66308 (11831) SS BOND : bond 0.00632 ( 2) SS BOND : angle 1.84076 ( 4) hydrogen bonds : bond 0.04912 ( 444) hydrogen bonds : angle 4.78015 ( 1260) Misc. bond : bond 0.00117 ( 2) link_TRANS : bond 0.00050 ( 2) link_TRANS : angle 0.47466 ( 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 194 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: D 211 TRP cc_start: 0.8772 (m100) cc_final: 0.8310 (m100) REVERT: D 258 ASP cc_start: 0.7642 (t0) cc_final: 0.7047 (t0) REVERT: D 325 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8006 (mmt) REVERT: B 305 SER cc_start: 0.8360 (m) cc_final: 0.7537 (p) REVERT: A 2 TYR cc_start: 0.2524 (OUTLIER) cc_final: 0.1342 (t80) outliers start: 36 outliers final: 21 residues processed: 174 average time/residue: 0.5196 time to fit residues: 96.7393 Evaluate side-chains 181 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 130 GLU 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 325 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 121 MET 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 259 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 6 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 88 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 ASN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 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 = 0.4143 r_free = 0.4143 target = 0.164779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.135003 restraints weight = 11891.732| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.93 r_work: 0.3627 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8717 Z= 0.187 Angle : 0.625 10.635 11841 Z= 0.317 Chirality : 0.044 0.208 1383 Planarity : 0.004 0.053 1478 Dihedral : 7.054 57.971 1249 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.24 % Allowed : 17.30 % Favored : 78.45 % 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: 0.07 (0.25), residues: 1079 helix: 1.78 (0.28), residues: 369 sheet: -0.21 (0.30), residues: 267 loop : -1.28 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 271 TYR 0.019 0.002 TYR F 178 PHE 0.013 0.001 PHE B 293 TRP 0.026 0.002 TRP D 332 HIS 0.005 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8711) covalent geometry : angle 0.62416 (11831) SS BOND : bond 0.00540 ( 2) SS BOND : angle 1.62842 ( 4) hydrogen bonds : bond 0.04509 ( 444) hydrogen bonds : angle 4.66957 ( 1260) Misc. bond : bond 0.00111 ( 2) link_TRANS : bond 0.00009 ( 2) link_TRANS : angle 0.41613 ( 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 200 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.339 Fit side-chains REVERT: D 211 TRP cc_start: 0.8751 (m100) cc_final: 0.8382 (m100) REVERT: D 217 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6779 (pmt) REVERT: D 258 ASP cc_start: 0.7627 (t0) cc_final: 0.7055 (t0) REVERT: D 325 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7991 (mmt) REVERT: F 38 ARG cc_start: 0.8377 (ttp-170) cc_final: 0.8143 (ttm170) REVERT: B 305 SER cc_start: 0.8372 (m) cc_final: 0.7916 (m) REVERT: A 2 TYR cc_start: 0.2785 (OUTLIER) cc_final: 0.1589 (t80) outliers start: 39 outliers final: 26 residues processed: 175 average time/residue: 0.4881 time to fit residues: 91.8983 Evaluate side-chains 188 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 198 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 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 293 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 12 VAL 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 121 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.0000 chunk 29 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 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 = 0.4145 r_free = 0.4145 target = 0.164966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.135395 restraints weight = 11833.743| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.91 r_work: 0.3635 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1980 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= 0.163 Angle : 0.610 11.541 11841 Z= 0.309 Chirality : 0.043 0.180 1383 Planarity : 0.004 0.053 1478 Dihedral : 6.974 58.115 1249 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.11 % Allowed : 17.41 % Favored : 77.48 % 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: 0.09 (0.25), residues: 1079 helix: 1.83 (0.28), residues: 369 sheet: -0.23 (0.30), residues: 267 loop : -1.28 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 314 TYR 0.019 0.002 TYR F 178 PHE 0.014 0.001 PHE B 293 TRP 0.031 0.002 TRP D 332 HIS 0.004 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8711) covalent geometry : angle 0.60907 (11831) SS BOND : bond 0.00497 ( 2) SS BOND : angle 1.54414 ( 4) hydrogen bonds : bond 0.04268 ( 444) hydrogen bonds : angle 4.58149 ( 1260) Misc. bond : bond 0.00096 ( 2) link_TRANS : bond 0.00039 ( 2) link_TRANS : angle 0.37683 ( 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 207 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.322 Fit side-chains REVERT: C 243 MET cc_start: 0.6340 (mmm) cc_final: 0.6036 (mmm) REVERT: D 211 TRP cc_start: 0.8730 (m100) cc_final: 0.8095 (m100) REVERT: D 217 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6862 (pmt) REVERT: D 258 ASP cc_start: 0.7610 (t0) cc_final: 0.7034 (t0) REVERT: D 325 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8021 (mmt) REVERT: B 305 SER cc_start: 0.8393 (m) cc_final: 0.7935 (m) REVERT: B 321 THR cc_start: 0.8379 (p) cc_final: 0.8066 (t) REVERT: A 2 TYR cc_start: 0.2957 (OUTLIER) cc_final: 0.1709 (t80) outliers start: 47 outliers final: 31 residues processed: 178 average time/residue: 0.4829 time to fit residues: 92.2970 Evaluate side-chains 193 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 52 ARG 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 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 D residue 293 ASN Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 325 MET 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 12 VAL 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 121 MET 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 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: 0.6980 chunk 88 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 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 = 0.4127 r_free = 0.4127 target = 0.163412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.133778 restraints weight = 11931.485| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.91 r_work: 0.3612 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8717 Z= 0.246 Angle : 0.681 12.581 11841 Z= 0.347 Chirality : 0.047 0.233 1383 Planarity : 0.004 0.053 1478 Dihedral : 7.204 59.660 1249 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.46 % Allowed : 19.04 % Favored : 76.50 % 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: 0.03 (0.25), residues: 1079 helix: 1.70 (0.28), residues: 369 sheet: -0.22 (0.30), residues: 267 loop : -1.27 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 46 TYR 0.021 0.002 TYR F 178 PHE 0.016 0.002 PHE B 293 TRP 0.040 0.002 TRP D 332 HIS 0.005 0.001 HIS D 91 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 8711) covalent geometry : angle 0.67977 (11831) SS BOND : bond 0.00606 ( 2) SS BOND : angle 2.00498 ( 4) hydrogen bonds : bond 0.04899 ( 444) hydrogen bonds : angle 4.75819 ( 1260) Misc. bond : bond 0.00104 ( 2) link_TRANS : bond 0.00029 ( 2) link_TRANS : angle 0.64936 ( 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 201 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: C 243 MET cc_start: 0.6349 (mmm) cc_final: 0.6068 (mmm) REVERT: D 45 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.6864 (mtt) REVERT: D 217 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6926 (pmt) REVERT: D 258 ASP cc_start: 0.7664 (t0) cc_final: 0.7079 (t0) REVERT: D 325 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7989 (mmt) REVERT: E 37 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7722 (mp) REVERT: B 305 SER cc_start: 0.8409 (m) cc_final: 0.7962 (m) REVERT: B 321 THR cc_start: 0.8380 (p) cc_final: 0.8064 (t) REVERT: A 2 TYR cc_start: 0.3373 (OUTLIER) cc_final: 0.2132 (t80) outliers start: 41 outliers final: 28 residues processed: 178 average time/residue: 0.4800 time to fit residues: 91.9531 Evaluate side-chains 193 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain D residue 45 MET 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 188 MET Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 325 MET 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 12 VAL 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 121 MET Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 196 LEU 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: 0.0170 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 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 = 0.4140 r_free = 0.4140 target = 0.164663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.135089 restraints weight = 11797.845| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.91 r_work: 0.3632 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2143 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= 0.169 Angle : 0.631 10.956 11841 Z= 0.321 Chirality : 0.044 0.209 1383 Planarity : 0.004 0.054 1478 Dihedral : 7.023 59.206 1249 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.79 % Allowed : 18.72 % Favored : 76.50 % 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: 0.11 (0.25), residues: 1079 helix: 1.81 (0.27), residues: 369 sheet: -0.18 (0.30), residues: 267 loop : -1.25 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 46 TYR 0.019 0.002 TYR F 178 PHE 0.018 0.001 PHE B 293 TRP 0.044 0.002 TRP D 332 HIS 0.005 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8711) covalent geometry : angle 0.63086 (11831) SS BOND : bond 0.00507 ( 2) SS BOND : angle 1.57829 ( 4) hydrogen bonds : bond 0.04346 ( 444) hydrogen bonds : angle 4.66081 ( 1260) Misc. bond : bond 0.00064 ( 2) link_TRANS : bond 0.00019 ( 2) link_TRANS : angle 0.44904 ( 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 203 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: C 243 MET cc_start: 0.6351 (mmm) cc_final: 0.6077 (mmm) REVERT: D 49 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.6897 (mmt90) REVERT: D 258 ASP cc_start: 0.7639 (t0) cc_final: 0.7058 (t0) REVERT: D 325 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8012 (mmt) REVERT: E 37 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7724 (mp) REVERT: B 81 MET cc_start: 0.4559 (mpp) cc_final: 0.4358 (mpp) REVERT: B 224 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7037 (tm) REVERT: B 305 SER cc_start: 0.8406 (m) cc_final: 0.7966 (m) REVERT: B 321 THR cc_start: 0.8387 (p) cc_final: 0.8085 (t) REVERT: A 2 TYR cc_start: 0.3274 (OUTLIER) cc_final: 0.2052 (t80) outliers start: 44 outliers final: 26 residues processed: 177 average time/residue: 0.4853 time to fit residues: 92.2541 Evaluate side-chains 189 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain D residue 49 ARG 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 188 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 325 MET 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 12 VAL 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 121 MET Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain A residue 2 TYR 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: 0.5980 chunk 85 optimal weight: 0.3980 chunk 90 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 67 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 63 optimal weight: 0.0870 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 GLN F 77 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 = 0.4170 r_free = 0.4170 target = 0.167272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.137905 restraints weight = 11877.679| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.91 r_work: 0.3670 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2197 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= 0.109 Angle : 0.581 9.913 11841 Z= 0.292 Chirality : 0.042 0.169 1383 Planarity : 0.004 0.054 1478 Dihedral : 6.687 59.910 1249 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.70 % Allowed : 19.91 % Favored : 76.39 % 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: 0.29 (0.26), residues: 1079 helix: 2.04 (0.27), residues: 366 sheet: -0.07 (0.29), residues: 285 loop : -1.26 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 46 TYR 0.020 0.001 TYR B 140 PHE 0.020 0.001 PHE B 293 TRP 0.047 0.002 TRP D 332 HIS 0.004 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8711) covalent geometry : angle 0.58052 (11831) SS BOND : bond 0.00341 ( 2) SS BOND : angle 1.06341 ( 4) hydrogen bonds : bond 0.03587 ( 444) hydrogen bonds : angle 4.41798 ( 1260) Misc. bond : bond 0.00020 ( 2) link_TRANS : bond 0.00058 ( 2) link_TRANS : angle 0.24903 ( 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 200 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.345 Fit side-chains REVERT: C 243 MET cc_start: 0.6353 (mmm) cc_final: 0.6033 (mmm) REVERT: D 101 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8246 (mtp) REVERT: D 325 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.8064 (mmt) REVERT: F 38 ARG cc_start: 0.8235 (ttp-170) cc_final: 0.7983 (ttm170) REVERT: B 117 THR cc_start: 0.5938 (OUTLIER) cc_final: 0.5713 (t) REVERT: B 305 SER cc_start: 0.8373 (m) cc_final: 0.7902 (m) REVERT: B 321 THR cc_start: 0.8374 (p) cc_final: 0.8080 (t) REVERT: A 2 TYR cc_start: 0.3066 (OUTLIER) cc_final: 0.1740 (t80) outliers start: 34 outliers final: 15 residues processed: 180 average time/residue: 0.4658 time to fit residues: 90.2083 Evaluate side-chains 180 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 63 THR 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 121 MET Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 295 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: 0.9980 chunk 63 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 86 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.165600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136067 restraints weight = 11845.032| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.91 r_work: 0.3644 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8717 Z= 0.152 Angle : 0.626 12.454 11841 Z= 0.315 Chirality : 0.043 0.195 1383 Planarity : 0.004 0.053 1478 Dihedral : 6.795 59.631 1249 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 3.05 % Allowed : 20.13 % Favored : 76.82 % 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: 0.29 (0.25), residues: 1079 helix: 2.05 (0.27), residues: 367 sheet: -0.12 (0.29), residues: 276 loop : -1.23 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 46 TYR 0.017 0.001 TYR F 178 PHE 0.038 0.001 PHE B 293 TRP 0.055 0.002 TRP D 332 HIS 0.004 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8711) covalent geometry : angle 0.62592 (11831) SS BOND : bond 0.00472 ( 2) SS BOND : angle 1.48520 ( 4) hydrogen bonds : bond 0.04058 ( 444) hydrogen bonds : angle 4.51131 ( 1260) Misc. bond : bond 0.00030 ( 2) link_TRANS : bond 0.00024 ( 2) link_TRANS : angle 0.38218 ( 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 183 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.308 Fit side-chains REVERT: C 243 MET cc_start: 0.6343 (mmm) cc_final: 0.5950 (mmm) REVERT: D 217 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6923 (pmt) REVERT: D 325 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.8012 (mmt) REVERT: F 38 ARG cc_start: 0.8323 (ttp-170) cc_final: 0.8073 (ttm170) REVERT: B 117 THR cc_start: 0.5960 (OUTLIER) cc_final: 0.5735 (t) REVERT: B 305 SER cc_start: 0.8374 (m) cc_final: 0.7901 (m) REVERT: B 321 THR cc_start: 0.8341 (p) cc_final: 0.8044 (t) REVERT: A 2 TYR cc_start: 0.3181 (OUTLIER) cc_final: 0.1760 (t80) outliers start: 28 outliers final: 17 residues processed: 169 average time/residue: 0.4911 time to fit residues: 89.1753 Evaluate side-chains 173 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 116 THR 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 121 MET Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 295 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: 2.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 86 optimal weight: 0.0270 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.164828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.135254 restraints weight = 11791.731| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.90 r_work: 0.3633 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8717 Z= 0.174 Angle : 0.644 11.738 11841 Z= 0.327 Chirality : 0.044 0.205 1383 Planarity : 0.004 0.052 1478 Dihedral : 6.894 58.851 1249 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 3.16 % Allowed : 20.13 % Favored : 76.71 % 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: 0.23 (0.25), residues: 1079 helix: 1.98 (0.27), residues: 368 sheet: -0.15 (0.29), residues: 276 loop : -1.25 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 46 TYR 0.018 0.002 TYR F 178 PHE 0.014 0.001 PHE B 293 TRP 0.063 0.002 TRP D 332 HIS 0.004 0.001 HIS D 91 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8711) covalent geometry : angle 0.64311 (11831) SS BOND : bond 0.00511 ( 2) SS BOND : angle 1.60935 ( 4) hydrogen bonds : bond 0.04295 ( 444) hydrogen bonds : angle 4.58801 ( 1260) Misc. bond : bond 0.00036 ( 2) link_TRANS : bond 0.00015 ( 2) link_TRANS : angle 0.47388 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4214.10 seconds wall clock time: 72 minutes 29.90 seconds (4349.90 seconds total)