Starting phenix.real_space_refine on Fri Feb 14 22:24:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ew7_31349/02_2025/7ew7_31349.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ew7_31349/02_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_31349/02_2025/7ew7_31349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ew7_31349/02_2025/7ew7_31349.map" model { file = "/net/cci-nas-00/data/ceres_data/7ew7_31349/02_2025/7ew7_31349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ew7_31349/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.88, per 1000 atoms: 0.65 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: 2.72 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.36 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: 2.60 Time building geometry restraints manager: 3.05 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: 3.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 23.760 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.720 ------------------------------------------------------------------------------- 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 9185 Z= 0.192 Angle : 0.595 9.368 12432 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 *********************** 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 : 0.988 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: 0.2697 time to fit residues: 62.1454 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 : 0.973 ------------------------------------------------------------------------------- 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 = 48)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.130637 restraints weight = 10418.153| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.17 r_work: 0.3565 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 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 9185 Z= 0.178 Angle : 0.514 7.655 12432 Z= 0.269 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 *********************** 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 : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 268 ASN cc_start: 0.7912 (t0) cc_final: 0.7588 (t0) REVERT: D 68 LEU cc_start: 0.8586 (mm) cc_final: 0.8201 (mm) REVERT: D 80 MET cc_start: 0.8240 (tpt) cc_final: 0.7836 (tpt) REVERT: D 81 TYR cc_start: 0.8350 (m-80) cc_final: 0.8092 (m-80) REVERT: D 141 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7384 (tm-30) REVERT: D 149 MET cc_start: 0.7788 (mtt) cc_final: 0.6708 (mmt) REVERT: D 151 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7294 (tt) REVERT: D 292 ARG cc_start: 0.8021 (mtp85) cc_final: 0.6633 (mpp-170) REVERT: D 323 ILE cc_start: 0.8756 (mm) cc_final: 0.8539 (mt) REVERT: E 39 GLN cc_start: 0.8358 (tm-30) cc_final: 0.7306 (tm-30) REVERT: E 183 GLN cc_start: 0.8370 (pm20) cc_final: 0.8043 (pm20) outliers start: 21 outliers final: 19 residues processed: 145 average time/residue: 0.2147 time to fit residues: 43.2931 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 : 0.953 ------------------------------------------------------------------------------- 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: 0.9980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 46 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 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 = 0.193015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.130905 restraints weight = 10533.914| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.19 r_work: 0.3585 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9185 Z= 0.153 Angle : 0.479 7.325 12432 Z= 0.250 Chirality : 0.040 0.158 1422 Planarity : 0.003 0.054 1553 Dihedral : 4.447 52.297 1261 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.23 % Allowed : 14.62 % Favored : 83.15 % 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 0.018 0.001 PHE E 108 TYR 0.018 0.001 TYR E 190 ARG 0.002 0.000 ARG B 219 *********************** 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 156 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8252 (pt0) cc_final: 0.7264 (pm20) REVERT: B 268 ASN cc_start: 0.7948 (t0) cc_final: 0.7598 (t0) REVERT: D 68 LEU cc_start: 0.8564 (mm) cc_final: 0.8129 (mm) REVERT: D 80 MET cc_start: 0.8223 (tpt) cc_final: 0.7813 (tpt) REVERT: D 81 TYR cc_start: 0.8426 (m-80) cc_final: 0.8223 (m-80) REVERT: D 141 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7356 (tm-30) REVERT: D 149 MET cc_start: 0.7906 (mtt) cc_final: 0.6891 (mmt) REVERT: D 151 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7237 (tt) REVERT: D 292 ARG cc_start: 0.8043 (mtp85) cc_final: 0.6655 (mpp-170) REVERT: D 323 ILE cc_start: 0.8716 (mm) cc_final: 0.8471 (mt) REVERT: E 39 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7334 (tm-30) REVERT: E 93 MET cc_start: 0.6605 (mmm) cc_final: 0.6363 (mmm) REVERT: E 183 GLN cc_start: 0.8362 (pm20) cc_final: 0.7999 (pm20) outliers start: 22 outliers final: 19 residues processed: 149 average time/residue: 0.1954 time to fit residues: 40.8901 Evaluate side-chains 140 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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: 5.9990 chunk 106 optimal weight: 0.0050 chunk 93 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 46 optimal weight: 8.9990 chunk 41 optimal weight: 0.0470 chunk 104 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.4894 ------------------------------------------------------------------------------- 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 = 0.4410 r_free = 0.4410 target = 0.194161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.132468 restraints weight = 10428.572| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.14 r_work: 0.3610 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9185 Z= 0.127 Angle : 0.459 6.831 12432 Z= 0.239 Chirality : 0.039 0.149 1422 Planarity : 0.003 0.052 1553 Dihedral : 4.239 50.701 1259 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.44 % Allowed : 16.45 % Favored : 81.12 % 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: 2.51 (0.28), residues: 367 sheet: -0.91 (0.33), residues: 251 loop : -1.92 (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 0.015 0.001 TYR E 190 ARG 0.004 0.000 ARG A 21 *********************** 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: 24 poor density : 133 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8243 (pt0) cc_final: 0.7253 (pm20) REVERT: B 268 ASN cc_start: 0.7966 (t0) cc_final: 0.7611 (t0) REVERT: D 68 LEU cc_start: 0.8539 (mm) cc_final: 0.8253 (mt) REVERT: D 80 MET cc_start: 0.8152 (tpt) cc_final: 0.7781 (tpt) REVERT: D 141 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7358 (tm-30) REVERT: D 149 MET cc_start: 0.7896 (mtt) cc_final: 0.6788 (mmt) REVERT: D 151 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7351 (tt) REVERT: D 152 HIS cc_start: 0.6080 (OUTLIER) cc_final: 0.5125 (p-80) REVERT: D 220 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6851 (mp) REVERT: D 292 ARG cc_start: 0.8047 (mtp85) cc_final: 0.6674 (mpp-170) REVERT: D 323 ILE cc_start: 0.8703 (mm) cc_final: 0.8451 (mt) REVERT: E 39 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7289 (tm-30) REVERT: E 183 GLN cc_start: 0.8166 (pm20) cc_final: 0.7816 (pm20) outliers start: 24 outliers final: 18 residues processed: 149 average time/residue: 0.1945 time to fit residues: 40.7902 Evaluate side-chains 139 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 58 optimal weight: 0.0570 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.190837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.128666 restraints weight = 10471.027| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.15 r_work: 0.3564 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9185 Z= 0.198 Angle : 0.490 6.798 12432 Z= 0.258 Chirality : 0.040 0.176 1422 Planarity : 0.003 0.053 1553 Dihedral : 4.345 50.718 1259 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.25 % Allowed : 16.75 % Favored : 80.00 % 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 (0.25), residues: 1126 helix: 2.56 (0.28), residues: 366 sheet: -0.98 (0.33), residues: 242 loop : -1.87 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.003 0.001 HIS E 167 PHE 0.016 0.001 PHE E 177 TYR 0.020 0.001 TYR E 190 ARG 0.003 0.000 ARG A 21 *********************** 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 152 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 268 ASN cc_start: 0.7982 (t0) cc_final: 0.7619 (t0) REVERT: D 68 LEU cc_start: 0.8569 (mm) cc_final: 0.8126 (mm) REVERT: D 80 MET cc_start: 0.8172 (tpt) cc_final: 0.7739 (tpt) REVERT: D 141 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7276 (tm-30) REVERT: D 149 MET cc_start: 0.7929 (mtt) cc_final: 0.6914 (mmt) REVERT: D 151 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7345 (tt) REVERT: D 152 HIS cc_start: 0.6058 (OUTLIER) cc_final: 0.5080 (p-80) REVERT: D 220 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6853 (mp) REVERT: D 292 ARG cc_start: 0.8084 (mtp85) cc_final: 0.6700 (mpp-170) REVERT: D 323 ILE cc_start: 0.8727 (mm) cc_final: 0.8488 (mt) REVERT: E 39 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7233 (tm-30) REVERT: E 183 GLN cc_start: 0.8169 (pm20) cc_final: 0.7816 (pm20) REVERT: E 230 MET cc_start: 0.7967 (ttt) cc_final: 0.7242 (ttt) outliers start: 32 outliers final: 25 residues processed: 141 average time/residue: 0.1919 time to fit residues: 38.7386 Evaluate side-chains 139 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 47 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 263 THR 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 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 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: 0.6980 chunk 51 optimal weight: 5.9990 chunk 54 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.192297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.130467 restraints weight = 10417.843| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.15 r_work: 0.3593 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9185 Z= 0.146 Angle : 0.461 6.182 12432 Z= 0.242 Chirality : 0.039 0.154 1422 Planarity : 0.003 0.052 1553 Dihedral : 4.259 50.883 1259 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.25 % Allowed : 17.36 % Favored : 79.39 % 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: -0.12 (0.25), residues: 1126 helix: 2.67 (0.28), residues: 366 sheet: -0.83 (0.32), residues: 253 loop : -1.84 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 111 HIS 0.002 0.000 HIS E 167 PHE 0.011 0.001 PHE E 177 TYR 0.015 0.001 TYR E 190 ARG 0.003 0.000 ARG A 21 *********************** 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: 32 poor density : 123 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 268 ASN cc_start: 0.7979 (t0) cc_final: 0.7742 (t0) REVERT: D 68 LEU cc_start: 0.8574 (mm) cc_final: 0.8172 (mm) REVERT: D 80 MET cc_start: 0.8102 (tpt) cc_final: 0.7690 (tpt) REVERT: D 141 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7318 (tm-30) REVERT: D 149 MET cc_start: 0.7810 (mtt) cc_final: 0.6849 (mmt) REVERT: D 151 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7411 (tt) REVERT: D 152 HIS cc_start: 0.5801 (OUTLIER) cc_final: 0.4962 (p-80) REVERT: D 220 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6849 (mp) REVERT: D 292 ARG cc_start: 0.8074 (mtp85) cc_final: 0.6698 (mpp-170) REVERT: D 323 ILE cc_start: 0.8701 (mm) cc_final: 0.8457 (mt) REVERT: E 39 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7245 (tm-30) REVERT: E 183 GLN cc_start: 0.8090 (pm20) cc_final: 0.7741 (pm20) REVERT: E 230 MET cc_start: 0.7829 (ttt) cc_final: 0.7137 (ttt) outliers start: 32 outliers final: 26 residues processed: 146 average time/residue: 0.1938 time to fit residues: 40.5270 Evaluate side-chains 145 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 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 316 SER 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 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: 4.9990 chunk 83 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 24 optimal weight: 50.0000 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.191206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.129065 restraints weight = 10570.770| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 3.17 r_work: 0.3571 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9185 Z= 0.166 Angle : 0.473 6.327 12432 Z= 0.249 Chirality : 0.040 0.157 1422 Planarity : 0.003 0.055 1553 Dihedral : 4.273 51.430 1259 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.65 % Allowed : 18.07 % Favored : 78.27 % 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: -0.08 (0.26), residues: 1126 helix: 2.72 (0.28), residues: 366 sheet: -0.82 (0.33), residues: 253 loop : -1.82 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 47 HIS 0.003 0.001 HIS E 167 PHE 0.012 0.001 PHE E 177 TYR 0.018 0.001 TYR E 190 ARG 0.005 0.000 ARG B 219 *********************** 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 160 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 268 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7787 (t0) REVERT: D 68 LEU cc_start: 0.8609 (mm) cc_final: 0.8249 (mm) REVERT: D 80 MET cc_start: 0.8132 (tpt) cc_final: 0.7704 (tpt) REVERT: D 141 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7248 (tm-30) REVERT: D 149 MET cc_start: 0.7853 (mtt) cc_final: 0.6939 (mmt) REVERT: D 151 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7422 (tt) REVERT: D 152 HIS cc_start: 0.5816 (OUTLIER) cc_final: 0.4904 (p-80) REVERT: D 185 ILE cc_start: 0.7109 (pt) cc_final: 0.6657 (mp) REVERT: D 220 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6863 (mp) REVERT: D 292 ARG cc_start: 0.8055 (mtp85) cc_final: 0.6663 (mpp-170) REVERT: D 323 ILE cc_start: 0.8710 (mm) cc_final: 0.8470 (mt) REVERT: E 39 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7149 (tm-30) REVERT: E 183 GLN cc_start: 0.8063 (pm20) cc_final: 0.7712 (pm20) REVERT: E 230 MET cc_start: 0.7942 (ttt) cc_final: 0.7419 (ttt) outliers start: 36 outliers final: 28 residues processed: 149 average time/residue: 0.1974 time to fit residues: 41.7146 Evaluate side-chains 152 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 47 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.0040 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- 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 B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.189285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.126880 restraints weight = 10668.645| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.18 r_work: 0.3545 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9185 Z= 0.212 Angle : 0.511 9.482 12432 Z= 0.267 Chirality : 0.041 0.174 1422 Planarity : 0.004 0.054 1553 Dihedral : 4.379 52.031 1259 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.45 % Allowed : 18.88 % Favored : 77.66 % 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: -0.16 (0.25), residues: 1126 helix: 2.70 (0.28), residues: 366 sheet: -1.07 (0.32), residues: 244 loop : -1.78 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS E 167 PHE 0.015 0.001 PHE E 177 TYR 0.021 0.001 TYR E 190 ARG 0.006 0.000 ARG B 219 *********************** 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 155 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8311 (pt0) cc_final: 0.7223 (pm20) REVERT: B 268 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7799 (t0) REVERT: D 68 LEU cc_start: 0.8659 (mm) cc_final: 0.8308 (mm) REVERT: D 80 MET cc_start: 0.8145 (tpt) cc_final: 0.7662 (tpt) REVERT: D 141 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7266 (tm-30) REVERT: D 149 MET cc_start: 0.7869 (mtt) cc_final: 0.6989 (mmt) REVERT: D 151 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7351 (tt) REVERT: D 152 HIS cc_start: 0.5887 (OUTLIER) cc_final: 0.5625 (m-70) REVERT: D 185 ILE cc_start: 0.7213 (pt) cc_final: 0.6762 (mp) REVERT: D 220 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6893 (mp) REVERT: D 292 ARG cc_start: 0.8072 (mtp85) cc_final: 0.6712 (mpp-170) REVERT: D 323 ILE cc_start: 0.8720 (mm) cc_final: 0.8485 (mt) REVERT: E 39 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7167 (tm-30) REVERT: E 142 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6623 (mm110) REVERT: E 183 GLN cc_start: 0.8071 (pm20) cc_final: 0.7712 (pm20) REVERT: E 230 MET cc_start: 0.8027 (ttt) cc_final: 0.7580 (ttt) outliers start: 34 outliers final: 27 residues processed: 144 average time/residue: 0.2001 time to fit residues: 40.5304 Evaluate side-chains 143 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 47 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 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 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: 0.8980 chunk 109 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.190554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.137556 restraints weight = 10429.548| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 3.35 r_work: 0.3548 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9185 Z= 0.164 Angle : 0.505 10.560 12432 Z= 0.261 Chirality : 0.040 0.156 1422 Planarity : 0.003 0.054 1553 Dihedral : 4.325 51.970 1259 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.45 % Allowed : 18.78 % Favored : 77.77 % 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: -0.10 (0.25), residues: 1126 helix: 2.74 (0.28), residues: 367 sheet: -1.01 (0.33), residues: 242 loop : -1.75 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.003 0.001 HIS E 167 PHE 0.013 0.001 PHE E 108 TYR 0.017 0.001 TYR E 190 ARG 0.006 0.000 ARG B 219 *********************** 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 153 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: B 268 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7714 (t0) REVERT: D 68 LEU cc_start: 0.8644 (mm) cc_final: 0.8295 (mm) REVERT: D 80 MET cc_start: 0.8121 (tpt) cc_final: 0.7718 (tpt) REVERT: D 141 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7272 (tm-30) REVERT: D 149 MET cc_start: 0.7829 (mtt) cc_final: 0.6960 (mmt) REVERT: D 151 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7380 (tt) REVERT: D 152 HIS cc_start: 0.5864 (OUTLIER) cc_final: 0.5618 (m-70) REVERT: D 185 ILE cc_start: 0.7216 (pt) cc_final: 0.6795 (mp) REVERT: D 220 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6882 (mp) REVERT: D 292 ARG cc_start: 0.7980 (mtp85) cc_final: 0.6591 (mpp-170) REVERT: D 323 ILE cc_start: 0.8723 (mm) cc_final: 0.8484 (mt) REVERT: E 39 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7162 (tm-30) REVERT: E 142 GLN cc_start: 0.7102 (mm-40) cc_final: 0.6661 (mm110) REVERT: E 183 GLN cc_start: 0.8076 (pm20) cc_final: 0.7719 (pm20) REVERT: E 230 MET cc_start: 0.7974 (ttt) cc_final: 0.7522 (ttt) outliers start: 34 outliers final: 29 residues processed: 142 average time/residue: 0.1943 time to fit residues: 39.5974 Evaluate side-chains 150 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 47 THR Chi-restraints excluded: chain B residue 65 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 20.0000 chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.188527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.126330 restraints weight = 10666.135| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.16 r_work: 0.3538 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9185 Z= 0.236 Angle : 0.536 10.346 12432 Z= 0.278 Chirality : 0.041 0.177 1422 Planarity : 0.004 0.055 1553 Dihedral : 4.417 52.331 1259 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.55 % Allowed : 18.78 % Favored : 77.66 % 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: -0.18 (0.25), residues: 1126 helix: 2.66 (0.28), residues: 367 sheet: -1.10 (0.32), residues: 244 loop : -1.77 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS E 167 PHE 0.016 0.002 PHE E 177 TYR 0.022 0.001 TYR E 190 ARG 0.006 0.000 ARG B 219 ********************** 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 153 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8330 (pt0) cc_final: 0.7230 (pm20) REVERT: B 268 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7768 (t0) REVERT: D 68 LEU cc_start: 0.8648 (mm) cc_final: 0.8301 (mm) REVERT: D 80 MET cc_start: 0.8162 (tpt) cc_final: 0.7659 (tpt) REVERT: D 141 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7315 (tm-30) REVERT: D 149 MET cc_start: 0.7851 (mtt) cc_final: 0.6977 (mmt) REVERT: D 151 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7457 (tt) REVERT: D 152 HIS cc_start: 0.5906 (OUTLIER) cc_final: 0.5667 (m-70) REVERT: D 185 ILE cc_start: 0.7157 (pt) cc_final: 0.6744 (mp) REVERT: D 220 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6928 (mp) REVERT: D 292 ARG cc_start: 0.8053 (mtp85) cc_final: 0.6685 (mpp-170) REVERT: D 323 ILE cc_start: 0.8736 (mm) cc_final: 0.8499 (mt) REVERT: E 39 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7165 (tm-30) REVERT: E 142 GLN cc_start: 0.7138 (mm-40) cc_final: 0.6686 (mm110) REVERT: E 183 GLN cc_start: 0.8075 (pm20) cc_final: 0.7714 (pm20) REVERT: E 230 MET cc_start: 0.8028 (ttt) cc_final: 0.7612 (ttt) outliers start: 35 outliers final: 30 residues processed: 141 average time/residue: 0.2047 time to fit residues: 42.2650 Evaluate side-chains 149 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 47 THR Chi-restraints excluded: chain B residue 65 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** E 231 GLN ** 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 = 0.4350 r_free = 0.4350 target = 0.186319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.128902 restraints weight = 10486.041| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.13 r_work: 0.3532 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9185 Z= 0.260 Angle : 0.551 10.200 12432 Z= 0.287 Chirality : 0.042 0.187 1422 Planarity : 0.004 0.054 1553 Dihedral : 4.505 52.621 1259 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.35 % Allowed : 19.19 % 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: -0.25 (0.25), residues: 1126 helix: 2.60 (0.28), residues: 367 sheet: -1.14 (0.32), residues: 244 loop : -1.80 (0.25), residues: 515 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 0.017 0.002 PHE E 177 TYR 0.023 0.001 TYR E 190 ARG 0.005 0.000 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4949.91 seconds wall clock time: 89 minutes 0.51 seconds (5340.51 seconds total)