Starting phenix.real_space_refine on Mon Jul 28 21:39:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ew7_31349/07_2025/7ew7_31349.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ew7_31349/07_2025/7ew7_31349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ew7_31349/07_2025/7ew7_31349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ew7_31349/07_2025/7ew7_31349.map" model { file = "/net/cci-nas-00/data/ceres_data/7ew7_31349/07_2025/7ew7_31349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ew7_31349/07_2025/7ew7_31349.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1983 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 65 5.16 5 C 5743 2.51 5 N 1520 2.21 5 O 1670 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9004 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1838 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "D" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2297 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 6, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" 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: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'JEX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.26, per 1000 atoms: 0.58 Number of scatterers: 9004 At special positions: 0 Unit cell: (96.05, 119.85, 133.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 F 6 9.00 O 1670 8.00 N 1520 7.00 C 5743 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS D 282 " - pdb=" SG CYS D 287 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 981.9 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 36.6% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 8 through 28 removed outlier: 3.600A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.506A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 removed outlier: 4.000A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.611A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.872A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.994A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.008A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.710A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.507A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.809A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 removed outlier: 4.328A pdb=" N GLN C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.975A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'D' and resid 23 through 33 removed outlier: 3.703A pdb=" N ARG D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 73 removed outlier: 3.854A pdb=" N VAL D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR D 73 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 105 removed outlier: 3.838A pdb=" N PHE D 83 " --> pdb=" O PRO D 79 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE D 84 " --> pdb=" O MET D 80 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY D 85 " --> pdb=" O TYR D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 111 removed outlier: 3.578A pdb=" N THR D 109 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR D 110 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 148 removed outlier: 4.101A pdb=" N MET D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 181 removed outlier: 4.205A pdb=" N LEU D 160 " --> pdb=" O ASN D 156 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU D 162 " --> pdb=" O PHE D 158 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.565A pdb=" N GLY D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 235 removed outlier: 3.951A pdb=" N ILE D 203 " --> pdb=" O HIS D 199 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR D 208 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 209 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 269 removed outlier: 3.514A pdb=" N ALA D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP D 269 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 282 Processing helix chain 'D' and resid 288 through 292 Processing helix chain 'D' and resid 297 through 313 removed outlier: 3.857A pdb=" N VAL D 301 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 315 through 325 removed outlier: 3.712A pdb=" N ARG D 319 " --> pdb=" O ASN D 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.561A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.526A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.732A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.856A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 114 removed outlier: 6.328A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.043A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.978A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.594A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.594A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.528A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.754A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.754A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 141 through 142 removed outlier: 3.620A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.342A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.342A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1083 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: 2.46 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1727 1.33 - 1.45: 2319 1.45 - 1.57: 5046 1.57 - 1.69: 0 1.69 - 1.82: 93 Bond restraints: 9185 Sorted by residual: bond pdb=" C07 JEX D 401 " pdb=" C08 JEX D 401 " ideal model delta sigma weight residual 1.474 1.383 0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C17 JEX D 401 " pdb=" C19 JEX D 401 " ideal model delta sigma weight residual 1.463 1.377 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C23 JEX D 401 " pdb=" C25 JEX D 401 " ideal model delta sigma weight residual 1.498 1.548 -0.050 2.00e-02 2.50e+03 6.25e+00 bond pdb=" CA MET D 149 " pdb=" C MET D 149 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.30e-02 5.92e+03 6.22e+00 bond pdb=" C05 JEX D 401 " pdb=" C14 JEX D 401 " ideal model delta sigma weight residual 1.439 1.390 0.049 2.00e-02 2.50e+03 5.98e+00 ... (remaining 9180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 12241 1.87 - 3.75: 147 3.75 - 5.62: 28 5.62 - 7.49: 10 7.49 - 9.37: 6 Bond angle restraints: 12432 Sorted by residual: angle pdb=" N LYS D 150 " pdb=" CA LYS D 150 " pdb=" C LYS D 150 " ideal model delta sigma weight residual 111.36 119.73 -8.37 1.09e+00 8.42e-01 5.89e+01 angle pdb=" N ASN D 153 " pdb=" CA ASN D 153 " pdb=" C ASN D 153 " ideal model delta sigma weight residual 111.28 119.24 -7.96 1.09e+00 8.42e-01 5.33e+01 angle pdb=" N LEU D 147 " pdb=" CA LEU D 147 " pdb=" C LEU D 147 " ideal model delta sigma weight residual 111.07 116.80 -5.73 1.07e+00 8.73e-01 2.87e+01 angle pdb=" N HIS D 152 " pdb=" CA HIS D 152 " pdb=" C HIS D 152 " ideal model delta sigma weight residual 108.75 117.66 -8.91 1.71e+00 3.42e-01 2.71e+01 angle pdb=" N SER D 49 " pdb=" CA SER D 49 " pdb=" C SER D 49 " ideal model delta sigma weight residual 111.11 116.18 -5.07 1.20e+00 6.94e-01 1.79e+01 ... (remaining 12427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4950 17.84 - 35.68: 420 35.68 - 53.52: 73 53.52 - 71.36: 13 71.36 - 89.20: 7 Dihedral angle restraints: 5463 sinusoidal: 2143 harmonic: 3320 Sorted by residual: dihedral pdb=" CB CYS D 184 " pdb=" SG CYS D 184 " pdb=" SG CYS D 191 " pdb=" CB CYS D 191 " ideal model delta sinusoidal sigma weight residual -86.00 -126.75 40.75 1 1.00e+01 1.00e-02 2.33e+01 dihedral pdb=" C HIS D 152 " pdb=" N HIS D 152 " pdb=" CA HIS D 152 " pdb=" CB HIS D 152 " ideal model delta harmonic sigma weight residual -122.60 -131.63 9.03 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" N HIS D 152 " pdb=" C HIS D 152 " pdb=" CA HIS D 152 " pdb=" CB HIS D 152 " ideal model delta harmonic sigma weight residual 122.80 131.74 -8.94 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 5460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1322 0.079 - 0.157: 92 0.157 - 0.236: 3 0.236 - 0.314: 2 0.314 - 0.393: 3 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA HIS D 152 " pdb=" N HIS D 152 " pdb=" C HIS D 152 " pdb=" CB HIS D 152 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA LYS D 150 " pdb=" N LYS D 150 " pdb=" C LYS D 150 " pdb=" CB LYS D 150 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA ASN D 153 " pdb=" N ASN D 153 " pdb=" C ASN D 153 " pdb=" CB ASN D 153 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 1419 not shown) Planarity restraints: 1553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 JEX D 401 " -0.010 2.00e-02 2.50e+03 1.79e-02 6.44e+00 pdb=" C03 JEX D 401 " -0.003 2.00e-02 2.50e+03 pdb=" C05 JEX D 401 " 0.033 2.00e-02 2.50e+03 pdb=" C06 JEX D 401 " 0.008 2.00e-02 2.50e+03 pdb=" C07 JEX D 401 " 0.004 2.00e-02 2.50e+03 pdb=" C08 JEX D 401 " -0.008 2.00e-02 2.50e+03 pdb=" C14 JEX D 401 " -0.034 2.00e-02 2.50e+03 pdb=" S04 JEX D 401 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 JEX D 401 " -0.025 2.00e-02 2.50e+03 1.81e-02 5.71e+00 pdb=" C14 JEX D 401 " 0.039 2.00e-02 2.50e+03 pdb=" C17 JEX D 401 " -0.003 2.00e-02 2.50e+03 pdb=" C19 JEX D 401 " -0.005 2.00e-02 2.50e+03 pdb=" N16 JEX D 401 " -0.005 2.00e-02 2.50e+03 pdb=" N18 JEX D 401 " 0.003 2.00e-02 2.50e+03 pdb=" O15 JEX D 401 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 150 " 0.010 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C LYS D 150 " -0.037 2.00e-02 2.50e+03 pdb=" O LYS D 150 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU D 151 " 0.013 2.00e-02 2.50e+03 ... (remaining 1550 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 69 2.59 - 3.17: 7219 3.17 - 3.75: 13132 3.75 - 4.32: 17249 4.32 - 4.90: 30228 Nonbonded interactions: 67897 Sorted by model distance: nonbonded pdb=" O SER D 232 " pdb=" OG1 THR D 236 " model vdw 2.016 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.218 3.040 nonbonded pdb=" OG SER E 17 " pdb=" O MET E 83 " model vdw 2.222 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.275 3.040 nonbonded pdb=" OG SER D 192 " pdb=" O LEU D 195 " model vdw 2.278 3.040 ... (remaining 67892 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.030 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 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 : 0.003 0.091 9188 Z= 0.167 Angle : 0.596 9.368 12438 Z= 0.343 Chirality : 0.044 0.393 1422 Planarity : 0.003 0.050 1553 Dihedral : 13.517 89.196 3312 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.71 % Allowed : 4.47 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.23), residues: 1126 helix: 0.10 (0.25), residues: 380 sheet: -1.53 (0.31), residues: 265 loop : -2.66 (0.22), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 176 HIS 0.002 0.000 HIS D 152 PHE 0.020 0.001 PHE E 108 TYR 0.015 0.001 TYR E 190 ARG 0.006 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.19626 ( 371) hydrogen bonds : angle 6.33888 ( 1083) SS BOND : bond 0.00468 ( 3) SS BOND : angle 1.94411 ( 6) covalent geometry : bond 0.00295 ( 9185) covalent geometry : angle 0.59461 (12432) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 169 time to evaluate : 0.924 Fit side-chains REVERT: A 25 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7446 (tm-30) REVERT: A 51 LYS cc_start: 0.8419 (ptmm) cc_final: 0.8024 (pttm) REVERT: B 268 ASN cc_start: 0.7754 (t0) cc_final: 0.7484 (t0) REVERT: D 68 LEU cc_start: 0.8510 (mm) cc_final: 0.8185 (mm) REVERT: D 80 MET cc_start: 0.7852 (tpt) cc_final: 0.7621 (tpt) REVERT: D 81 TYR cc_start: 0.7927 (m-80) cc_final: 0.7420 (m-80) REVERT: D 141 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6659 (tm-30) REVERT: D 149 MET cc_start: 0.7558 (mtt) cc_final: 0.6657 (mmt) REVERT: D 151 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7010 (tt) REVERT: D 292 ARG cc_start: 0.8159 (mtp85) cc_final: 0.6748 (ptp90) REVERT: D 323 ILE cc_start: 0.8832 (mm) cc_final: 0.8618 (mt) REVERT: E 39 GLN cc_start: 0.7738 (tm-30) cc_final: 0.6608 (tm-30) REVERT: E 183 GLN cc_start: 0.8395 (pm20) cc_final: 0.8030 (pm20) outliers start: 7 outliers final: 5 residues processed: 176 average time/residue: 0.2612 time to fit residues: 60.3583 Evaluate side-chains 135 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 158 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 294 ASN A 333 GLN B 75 GLN B 220 GLN B 239 ASN C 11 GLN D 116 GLN D 183 ASN D 303 ASN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.192827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.130624 restraints weight = 10418.153| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.17 r_work: 0.3565 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9188 Z= 0.120 Angle : 0.515 7.655 12438 Z= 0.270 Chirality : 0.041 0.162 1422 Planarity : 0.004 0.055 1553 Dihedral : 4.591 56.354 1265 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.13 % Allowed : 11.37 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1126 helix: 1.48 (0.27), residues: 384 sheet: -1.22 (0.33), residues: 240 loop : -2.31 (0.23), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.004 0.001 HIS E 167 PHE 0.019 0.001 PHE E 108 TYR 0.019 0.001 TYR E 190 ARG 0.002 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 371) hydrogen bonds : angle 4.09278 ( 1083) SS BOND : bond 0.00541 ( 3) SS BOND : angle 1.42637 ( 6) covalent geometry : bond 0.00272 ( 9185) covalent geometry : angle 0.51381 (12432) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 268 ASN cc_start: 0.7921 (t0) cc_final: 0.7597 (t0) REVERT: D 68 LEU cc_start: 0.8583 (mm) cc_final: 0.8199 (mm) REVERT: D 80 MET cc_start: 0.8242 (tpt) cc_final: 0.7836 (tpt) REVERT: D 81 TYR cc_start: 0.8350 (m-80) cc_final: 0.8089 (m-80) REVERT: D 141 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7381 (tm-30) REVERT: D 149 MET cc_start: 0.7786 (mtt) cc_final: 0.6708 (mmt) REVERT: D 151 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7297 (tt) REVERT: D 292 ARG cc_start: 0.8018 (mtp85) cc_final: 0.6626 (mpp-170) REVERT: D 323 ILE cc_start: 0.8752 (mm) cc_final: 0.8537 (mt) REVERT: E 39 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7307 (tm-30) REVERT: E 183 GLN cc_start: 0.8375 (pm20) cc_final: 0.8047 (pm20) outliers start: 21 outliers final: 19 residues processed: 145 average time/residue: 0.2502 time to fit residues: 51.4634 Evaluate side-chains 141 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 97 optimal weight: 0.3980 chunk 77 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 220 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.193012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.130907 restraints weight = 10533.628| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.19 r_work: 0.3586 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9188 Z= 0.104 Angle : 0.481 7.408 12438 Z= 0.251 Chirality : 0.040 0.157 1422 Planarity : 0.003 0.054 1553 Dihedral : 4.445 52.219 1261 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.34 % Allowed : 14.42 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1126 helix: 2.14 (0.28), residues: 373 sheet: -1.04 (0.33), residues: 251 loop : -2.12 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS E 167 PHE 0.019 0.001 PHE E 108 TYR 0.018 0.001 TYR E 190 ARG 0.004 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 371) hydrogen bonds : angle 3.73998 ( 1083) SS BOND : bond 0.00457 ( 3) SS BOND : angle 1.70175 ( 6) covalent geometry : bond 0.00234 ( 9185) covalent geometry : angle 0.47992 (12432) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8252 (pt0) cc_final: 0.7260 (pm20) REVERT: B 268 ASN cc_start: 0.7965 (t0) cc_final: 0.7619 (t0) REVERT: D 68 LEU cc_start: 0.8571 (mm) cc_final: 0.8133 (mm) REVERT: D 80 MET cc_start: 0.8223 (tpt) cc_final: 0.7812 (tpt) REVERT: D 81 TYR cc_start: 0.8427 (m-80) cc_final: 0.8224 (m-80) REVERT: D 141 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7360 (tm-30) REVERT: D 149 MET cc_start: 0.7901 (mtt) cc_final: 0.6886 (mmt) REVERT: D 151 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7459 (tt) REVERT: D 292 ARG cc_start: 0.8044 (mtp85) cc_final: 0.6659 (mpp-170) REVERT: D 323 ILE cc_start: 0.8717 (mm) cc_final: 0.8471 (mt) REVERT: E 39 GLN cc_start: 0.8350 (tm-30) cc_final: 0.7344 (tm-30) REVERT: E 183 GLN cc_start: 0.8363 (pm20) cc_final: 0.7999 (pm20) outliers start: 23 outliers final: 19 residues processed: 151 average time/residue: 0.1981 time to fit residues: 42.1402 Evaluate side-chains 141 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 7.9990 chunk 106 optimal weight: 0.0070 chunk 93 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 82 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.192898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.130831 restraints weight = 10463.702| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 3.16 r_work: 0.3589 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9188 Z= 0.101 Angle : 0.471 6.849 12438 Z= 0.246 Chirality : 0.040 0.165 1422 Planarity : 0.003 0.052 1553 Dihedral : 4.280 50.547 1259 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.64 % Allowed : 16.55 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1126 helix: 2.46 (0.28), residues: 367 sheet: -0.93 (0.33), residues: 251 loop : -1.95 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.002 0.001 HIS E 167 PHE 0.015 0.001 PHE E 108 TYR 0.017 0.001 TYR E 190 ARG 0.004 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 371) hydrogen bonds : angle 3.60326 ( 1083) SS BOND : bond 0.00352 ( 3) SS BOND : angle 1.59946 ( 6) covalent geometry : bond 0.00228 ( 9185) covalent geometry : angle 0.46994 (12432) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 118 ASP cc_start: 0.7339 (t0) cc_final: 0.7135 (t0) REVERT: B 175 GLN cc_start: 0.8269 (pt0) cc_final: 0.7281 (pm20) REVERT: B 268 ASN cc_start: 0.7948 (t0) cc_final: 0.7597 (t0) REVERT: D 68 LEU cc_start: 0.8552 (mm) cc_final: 0.8267 (mt) REVERT: D 80 MET cc_start: 0.8205 (tpt) cc_final: 0.7791 (tpt) REVERT: D 141 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7403 (tm-30) REVERT: D 149 MET cc_start: 0.7965 (mtt) cc_final: 0.6894 (mmt) REVERT: D 151 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7375 (tt) REVERT: D 152 HIS cc_start: 0.6108 (OUTLIER) cc_final: 0.5142 (p-80) REVERT: D 292 ARG cc_start: 0.8060 (mtp85) cc_final: 0.6687 (mpp-170) REVERT: D 323 ILE cc_start: 0.8706 (mm) cc_final: 0.8458 (mt) REVERT: E 39 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7294 (tm-30) REVERT: E 183 GLN cc_start: 0.8174 (pm20) cc_final: 0.7824 (pm20) outliers start: 26 outliers final: 21 residues processed: 148 average time/residue: 0.1959 time to fit residues: 41.7949 Evaluate side-chains 145 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.188318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.129663 restraints weight = 10516.748| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.45 r_work: 0.3521 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9188 Z= 0.158 Angle : 0.527 7.694 12438 Z= 0.278 Chirality : 0.042 0.202 1422 Planarity : 0.004 0.051 1553 Dihedral : 4.511 51.230 1259 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.45 % Allowed : 16.65 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1126 helix: 2.45 (0.28), residues: 366 sheet: -1.11 (0.33), residues: 242 loop : -1.94 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS E 167 PHE 0.018 0.002 PHE E 108 TYR 0.025 0.001 TYR E 190 ARG 0.003 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 371) hydrogen bonds : angle 3.82248 ( 1083) SS BOND : bond 0.00450 ( 3) SS BOND : angle 1.44027 ( 6) covalent geometry : bond 0.00382 ( 9185) covalent geometry : angle 0.52573 (12432) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8361 (pt0) cc_final: 0.7375 (pm20) REVERT: B 268 ASN cc_start: 0.7970 (t0) cc_final: 0.7616 (t0) REVERT: D 68 LEU cc_start: 0.8606 (mm) cc_final: 0.8205 (mm) REVERT: D 80 MET cc_start: 0.8206 (tpt) cc_final: 0.7677 (tpt) REVERT: D 141 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7277 (tm-30) REVERT: D 149 MET cc_start: 0.7951 (mtt) cc_final: 0.6932 (mmt) REVERT: D 151 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7379 (tt) REVERT: D 185 ILE cc_start: 0.7095 (pt) cc_final: 0.6625 (mp) REVERT: D 220 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.6914 (mp) REVERT: D 292 ARG cc_start: 0.8096 (mtp85) cc_final: 0.6686 (mpp-170) REVERT: D 323 ILE cc_start: 0.8708 (mm) cc_final: 0.8480 (mt) REVERT: E 39 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7243 (tm-30) REVERT: E 183 GLN cc_start: 0.8198 (pm20) cc_final: 0.7851 (pm20) REVERT: E 230 MET cc_start: 0.8015 (ttt) cc_final: 0.7256 (ttt) outliers start: 34 outliers final: 26 residues processed: 144 average time/residue: 0.1899 time to fit residues: 39.4406 Evaluate side-chains 142 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.0970 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.191928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.130014 restraints weight = 10420.063| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.15 r_work: 0.3583 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9188 Z= 0.095 Angle : 0.465 6.375 12438 Z= 0.244 Chirality : 0.039 0.165 1422 Planarity : 0.003 0.051 1553 Dihedral : 4.319 51.125 1259 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.94 % Allowed : 18.38 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1126 helix: 2.64 (0.28), residues: 366 sheet: -0.93 (0.32), residues: 253 loop : -1.87 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.002 0.000 HIS A 213 PHE 0.015 0.001 PHE E 108 TYR 0.014 0.001 TYR E 190 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 371) hydrogen bonds : angle 3.54627 ( 1083) SS BOND : bond 0.00434 ( 3) SS BOND : angle 1.32292 ( 6) covalent geometry : bond 0.00212 ( 9185) covalent geometry : angle 0.46420 (12432) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8317 (pt0) cc_final: 0.7347 (pm20) REVERT: B 268 ASN cc_start: 0.7949 (t0) cc_final: 0.7720 (t0) REVERT: D 68 LEU cc_start: 0.8612 (mm) cc_final: 0.8225 (mm) REVERT: D 80 MET cc_start: 0.8135 (tpt) cc_final: 0.7715 (tpt) REVERT: D 141 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7254 (tm-30) REVERT: D 149 MET cc_start: 0.7817 (mtt) cc_final: 0.6859 (mmt) REVERT: D 151 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7349 (tt) REVERT: D 152 HIS cc_start: 0.5881 (OUTLIER) cc_final: 0.4979 (p-80) REVERT: D 220 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6871 (mp) REVERT: D 292 ARG cc_start: 0.8084 (mtp85) cc_final: 0.6701 (mpp-170) REVERT: D 323 ILE cc_start: 0.8697 (mm) cc_final: 0.8447 (mt) REVERT: E 39 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7282 (tm-30) REVERT: E 183 GLN cc_start: 0.8096 (pm20) cc_final: 0.7747 (pm20) REVERT: E 230 MET cc_start: 0.7823 (ttt) cc_final: 0.7092 (ttt) outliers start: 29 outliers final: 23 residues processed: 145 average time/residue: 0.1813 time to fit residues: 37.7882 Evaluate side-chains 142 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.0970 chunk 66 optimal weight: 5.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.192354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.139385 restraints weight = 10543.276| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 3.29 r_work: 0.3552 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9188 Z= 0.094 Angle : 0.465 6.332 12438 Z= 0.244 Chirality : 0.039 0.158 1422 Planarity : 0.003 0.054 1553 Dihedral : 4.248 51.558 1259 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.25 % Allowed : 18.78 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1126 helix: 2.73 (0.28), residues: 366 sheet: -0.85 (0.33), residues: 253 loop : -1.80 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.002 0.000 HIS A 213 PHE 0.015 0.001 PHE E 108 TYR 0.015 0.001 TYR E 190 ARG 0.006 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 371) hydrogen bonds : angle 3.46848 ( 1083) SS BOND : bond 0.00394 ( 3) SS BOND : angle 1.21045 ( 6) covalent geometry : bond 0.00209 ( 9185) covalent geometry : angle 0.46415 (12432) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 268 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7674 (t0) REVERT: D 68 LEU cc_start: 0.8537 (mm) cc_final: 0.8175 (mm) REVERT: D 80 MET cc_start: 0.8119 (tpt) cc_final: 0.7695 (tpt) REVERT: D 141 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7273 (tm-30) REVERT: D 149 MET cc_start: 0.7830 (mtt) cc_final: 0.6907 (mmt) REVERT: D 151 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7439 (tt) REVERT: D 152 HIS cc_start: 0.5823 (OUTLIER) cc_final: 0.4902 (p-80) REVERT: D 220 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6823 (mp) REVERT: D 292 ARG cc_start: 0.8026 (mtp85) cc_final: 0.6634 (mpp-170) REVERT: D 323 ILE cc_start: 0.8689 (mm) cc_final: 0.8452 (mt) REVERT: E 39 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7258 (tm-30) REVERT: E 183 GLN cc_start: 0.8036 (pm20) cc_final: 0.7680 (pm20) REVERT: E 230 MET cc_start: 0.7885 (ttt) cc_final: 0.7382 (ttt) outliers start: 32 outliers final: 26 residues processed: 143 average time/residue: 0.2102 time to fit residues: 43.4160 Evaluate side-chains 143 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 0.0370 chunk 38 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 268 ASN ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.187465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.125133 restraints weight = 10700.431| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.15 r_work: 0.3505 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9188 Z= 0.169 Angle : 0.548 9.934 12438 Z= 0.288 Chirality : 0.042 0.233 1422 Planarity : 0.004 0.055 1553 Dihedral : 4.509 51.741 1259 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.76 % Allowed : 18.98 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1126 helix: 2.57 (0.28), residues: 367 sheet: -1.15 (0.32), residues: 244 loop : -1.82 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS E 167 PHE 0.036 0.002 PHE E 108 TYR 0.025 0.001 TYR E 190 ARG 0.005 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 371) hydrogen bonds : angle 3.70291 ( 1083) SS BOND : bond 0.00404 ( 3) SS BOND : angle 1.21898 ( 6) covalent geometry : bond 0.00410 ( 9185) covalent geometry : angle 0.54748 (12432) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: B 268 ASN cc_start: 0.8052 (OUTLIER) cc_final: 0.7804 (t0) REVERT: D 68 LEU cc_start: 0.8648 (mm) cc_final: 0.8298 (mm) REVERT: D 80 MET cc_start: 0.8204 (tpt) cc_final: 0.7673 (tpt) REVERT: D 141 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7280 (tm-30) REVERT: D 149 MET cc_start: 0.7940 (mtt) cc_final: 0.7012 (mmt) REVERT: D 151 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7376 (tt) REVERT: D 152 HIS cc_start: 0.5911 (OUTLIER) cc_final: 0.5656 (m-70) REVERT: D 185 ILE cc_start: 0.7194 (pt) cc_final: 0.6750 (mp) REVERT: D 220 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6900 (mp) REVERT: D 292 ARG cc_start: 0.8091 (mtp85) cc_final: 0.6725 (mpp-170) REVERT: D 323 ILE cc_start: 0.8709 (mm) cc_final: 0.8476 (mt) REVERT: E 39 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7172 (tm-30) REVERT: E 183 GLN cc_start: 0.8043 (pm20) cc_final: 0.7684 (pm20) outliers start: 37 outliers final: 26 residues processed: 143 average time/residue: 0.2074 time to fit residues: 42.3983 Evaluate side-chains 142 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.188417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.130880 restraints weight = 10480.456| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 3.28 r_work: 0.3530 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9188 Z= 0.136 Angle : 0.523 9.244 12438 Z= 0.275 Chirality : 0.041 0.230 1422 Planarity : 0.003 0.053 1553 Dihedral : 4.478 51.781 1259 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.25 % Allowed : 19.29 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1126 helix: 2.60 (0.28), residues: 367 sheet: -1.17 (0.32), residues: 254 loop : -1.75 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS E 167 PHE 0.035 0.002 PHE E 108 TYR 0.021 0.001 TYR E 190 ARG 0.005 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 371) hydrogen bonds : angle 3.66232 ( 1083) SS BOND : bond 0.00481 ( 3) SS BOND : angle 1.43616 ( 6) covalent geometry : bond 0.00323 ( 9185) covalent geometry : angle 0.52216 (12432) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8371 (pt0) cc_final: 0.7403 (pm20) REVERT: B 268 ASN cc_start: 0.7979 (OUTLIER) cc_final: 0.7731 (t0) REVERT: D 68 LEU cc_start: 0.8660 (mm) cc_final: 0.8312 (mm) REVERT: D 80 MET cc_start: 0.8186 (tpt) cc_final: 0.7695 (tpt) REVERT: D 141 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7289 (tm-30) REVERT: D 149 MET cc_start: 0.7884 (mtt) cc_final: 0.6994 (mmt) REVERT: D 151 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7380 (tt) REVERT: D 152 HIS cc_start: 0.5870 (OUTLIER) cc_final: 0.5616 (m-70) REVERT: D 185 ILE cc_start: 0.7210 (pt) cc_final: 0.6745 (mp) REVERT: D 220 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6895 (mp) REVERT: D 292 ARG cc_start: 0.8055 (mtp85) cc_final: 0.6682 (mpp-170) REVERT: D 323 ILE cc_start: 0.8719 (mm) cc_final: 0.8482 (mt) REVERT: E 39 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7254 (tm-30) REVERT: E 183 GLN cc_start: 0.8065 (pm20) cc_final: 0.7701 (pm20) REVERT: E 230 MET cc_start: 0.7895 (ttt) cc_final: 0.7047 (tpt) outliers start: 32 outliers final: 26 residues processed: 138 average time/residue: 0.2068 time to fit residues: 40.8921 Evaluate side-chains 141 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 105 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.188397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.130434 restraints weight = 10659.131| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 3.37 r_work: 0.3510 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9188 Z= 0.140 Angle : 0.539 10.720 12438 Z= 0.280 Chirality : 0.041 0.231 1422 Planarity : 0.004 0.055 1553 Dihedral : 4.486 51.876 1259 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.35 % Allowed : 19.29 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1126 helix: 2.60 (0.28), residues: 367 sheet: -1.17 (0.32), residues: 252 loop : -1.76 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS E 167 PHE 0.033 0.002 PHE E 108 TYR 0.021 0.001 TYR E 190 ARG 0.005 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 371) hydrogen bonds : angle 3.68392 ( 1083) SS BOND : bond 0.00485 ( 3) SS BOND : angle 1.38682 ( 6) covalent geometry : bond 0.00334 ( 9185) covalent geometry : angle 0.53800 (12432) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: D 68 LEU cc_start: 0.8616 (mm) cc_final: 0.8281 (mm) REVERT: D 80 MET cc_start: 0.8181 (tpt) cc_final: 0.7676 (tpt) REVERT: D 141 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7242 (tm-30) REVERT: D 149 MET cc_start: 0.7915 (mtt) cc_final: 0.6990 (mmt) REVERT: D 151 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7361 (tt) REVERT: D 152 HIS cc_start: 0.5959 (OUTLIER) cc_final: 0.5713 (m-70) REVERT: D 185 ILE cc_start: 0.7143 (pt) cc_final: 0.6696 (mp) REVERT: D 220 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6860 (mp) REVERT: D 292 ARG cc_start: 0.8056 (mtp85) cc_final: 0.6663 (mpp-170) REVERT: D 323 ILE cc_start: 0.8700 (mm) cc_final: 0.8473 (mt) REVERT: E 39 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7214 (tm-30) REVERT: E 183 GLN cc_start: 0.8025 (pm20) cc_final: 0.7664 (pm20) REVERT: E 230 MET cc_start: 0.7943 (ttt) cc_final: 0.7120 (tpt) outliers start: 33 outliers final: 27 residues processed: 133 average time/residue: 0.2638 time to fit residues: 52.5840 Evaluate side-chains 143 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 152 HIS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.186340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.128485 restraints weight = 10484.615| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 3.13 r_work: 0.3532 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9188 Z= 0.153 Angle : 0.558 10.047 12438 Z= 0.292 Chirality : 0.042 0.250 1422 Planarity : 0.004 0.054 1553 Dihedral : 4.572 52.233 1259 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.35 % Allowed : 19.70 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1126 helix: 2.57 (0.28), residues: 367 sheet: -1.29 (0.31), residues: 258 loop : -1.70 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS E 167 PHE 0.033 0.002 PHE E 108 TYR 0.023 0.001 TYR E 190 ARG 0.004 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 371) hydrogen bonds : angle 3.75900 ( 1083) SS BOND : bond 0.00494 ( 3) SS BOND : angle 1.38464 ( 6) covalent geometry : bond 0.00369 ( 9185) covalent geometry : angle 0.55781 (12432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5549.80 seconds wall clock time: 100 minutes 12.32 seconds (6012.32 seconds total)