Starting phenix.real_space_refine on Fri Nov 15 09:42:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbg_36145/11_2024/8jbg_36145.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbg_36145/11_2024/8jbg_36145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbg_36145/11_2024/8jbg_36145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbg_36145/11_2024/8jbg_36145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbg_36145/11_2024/8jbg_36145.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbg_36145/11_2024/8jbg_36145.cif" } resolution = 2.8 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= -0.002 sd= 0.150 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 43 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: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5585 2.51 5 N 1486 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8750 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2077 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 2 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 145 Chain: "D" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2549 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 418 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 62 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1867 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.39, per 1000 atoms: 0.62 Number of scatterers: 8750 At special positions: 0 Unit cell: (86.67, 120.91, 123.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1620 8.00 N 1486 7.00 C 5585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.8% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'B' and resid 81 through 113 removed outlier: 3.543A pdb=" N VAL B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 121 through 137 Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 154 through 161 Processing helix chain 'B' and resid 163 through 189 Processing helix chain 'B' and resid 196 through 221 removed outlier: 3.572A pdb=" N LYS B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Proline residue: B 217 - end of helix Processing helix chain 'B' and resid 239 through 275 removed outlier: 3.864A pdb=" N GLN B 243 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS B 248 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N PHE B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.613A pdb=" N TYR B 267 " --> pdb=" O MET B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 325 removed outlier: 3.881A pdb=" N VAL B 298 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP B 312 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) Proline residue: B 314 - end of helix removed outlier: 3.624A pdb=" N PHE B 319 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.652A pdb=" N ARG B 330 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP B 331 " --> pdb=" O LEU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 347 removed outlier: 3.564A pdb=" N VAL B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 360 removed outlier: 3.753A pdb=" N TYR B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) Proline residue: B 353 - end of helix removed outlier: 3.658A pdb=" N ASN B 360 " --> pdb=" O TYR B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 368 Processing helix chain 'D' and resid 4 through 26 Processing helix chain 'D' and resid 29 through 35 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.579A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.762A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.574A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'C' and resid 8 through 33 removed outlier: 4.076A pdb=" N VAL C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 52 Processing helix chain 'C' and resid 210 through 216 Processing helix chain 'C' and resid 232 through 245 Processing helix chain 'C' and resid 260 through 270 removed outlier: 3.642A pdb=" N GLU C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 278 removed outlier: 3.654A pdb=" N ASP C 277 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 319 removed outlier: 3.579A pdb=" N PHE C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 358 Processing sheet with id=AA1, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 51 removed outlier: 6.349A pdb=" N THR D 47 " --> pdb=" O ASN D 340 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN D 340 " --> pdb=" O THR D 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.500A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU D 79 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA D 92 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.729A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 151 removed outlier: 3.636A pdb=" N CYS D 148 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.645A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.526A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.630A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.642A pdb=" N ARG E 18 " --> pdb=" O MET E 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.585A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.585A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.532A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.665A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 184 through 190 removed outlier: 4.533A pdb=" N VAL C 201 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLY C 40 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA C 220 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE C 221 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE C 257 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE C 223 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN C 259 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL C 225 " --> pdb=" O ASN C 259 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1230 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: 2.38 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2823 1.34 - 1.46: 1965 1.46 - 1.58: 4062 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8938 Sorted by residual: bond pdb=" N ASP C 217 " pdb=" CA ASP C 217 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.44e+00 bond pdb=" CB GLN E 82 " pdb=" CG GLN E 82 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 bond pdb=" CB ASN D 268 " pdb=" CG ASN D 268 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.00e-01 bond pdb=" CG PRO B 217 " pdb=" CD PRO B 217 " ideal model delta sigma weight residual 1.503 1.534 -0.031 3.40e-02 8.65e+02 8.45e-01 bond pdb=" CB ASP C 217 " pdb=" CG ASP C 217 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 6.04e-01 ... (remaining 8933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 11984 1.86 - 3.72: 133 3.72 - 5.58: 18 5.58 - 7.44: 7 7.44 - 9.30: 2 Bond angle restraints: 12144 Sorted by residual: angle pdb=" CA LEU B 328 " pdb=" CB LEU B 328 " pdb=" CG LEU B 328 " ideal model delta sigma weight residual 116.30 125.60 -9.30 3.50e+00 8.16e-02 7.06e+00 angle pdb=" CB MET B 346 " pdb=" CG MET B 346 " pdb=" SD MET B 346 " ideal model delta sigma weight residual 112.70 120.44 -7.74 3.00e+00 1.11e-01 6.66e+00 angle pdb=" C LEU A 9 " pdb=" N MET A 10 " pdb=" CA MET A 10 " ideal model delta sigma weight residual 121.70 125.98 -4.28 1.80e+00 3.09e-01 5.64e+00 angle pdb=" CB GLN E 82 " pdb=" CG GLN E 82 " pdb=" CD GLN E 82 " ideal model delta sigma weight residual 112.60 116.62 -4.02 1.70e+00 3.46e-01 5.58e+00 angle pdb=" CA LEU B 101 " pdb=" CB LEU B 101 " pdb=" CG LEU B 101 " ideal model delta sigma weight residual 116.30 123.66 -7.36 3.50e+00 8.16e-02 4.42e+00 ... (remaining 12139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4495 17.72 - 35.45: 552 35.45 - 53.17: 188 53.17 - 70.89: 25 70.89 - 88.62: 8 Dihedral angle restraints: 5268 sinusoidal: 1954 harmonic: 3314 Sorted by residual: dihedral pdb=" CA ASN B 138 " pdb=" C ASN B 138 " pdb=" N THR B 139 " pdb=" CA THR B 139 " ideal model delta harmonic sigma weight residual -180.00 -161.08 -18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA HIS B 148 " pdb=" C HIS B 148 " pdb=" N SER B 149 " pdb=" CA SER B 149 " ideal model delta harmonic sigma weight residual -180.00 -162.44 -17.56 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP C 298 " pdb=" CB ASP C 298 " pdb=" CG ASP C 298 " pdb=" OD1 ASP C 298 " ideal model delta sinusoidal sigma weight residual -30.00 -89.51 59.51 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 5265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 821 0.028 - 0.056: 341 0.056 - 0.084: 125 0.084 - 0.112: 90 0.112 - 0.139: 14 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA ASP C 217 " pdb=" N ASP C 217 " pdb=" C ASP C 217 " pdb=" CB ASP C 217 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA VAL D 327 " pdb=" N VAL D 327 " pdb=" C VAL D 327 " pdb=" CB VAL D 327 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA ILE D 58 " pdb=" N ILE D 58 " pdb=" C ILE D 58 " pdb=" CB ILE D 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 1388 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 216 " 0.054 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO B 217 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 298 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO C 299 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 299 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 299 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 253 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C ILE B 253 " 0.033 2.00e-02 2.50e+03 pdb=" O ILE B 253 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 254 " -0.011 2.00e-02 2.50e+03 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 171 2.66 - 3.22: 7958 3.22 - 3.78: 14028 3.78 - 4.34: 19510 4.34 - 4.90: 31920 Nonbonded interactions: 73587 Sorted by model distance: nonbonded pdb=" OG SER D 245 " pdb=" OD1 ASP D 247 " model vdw 2.106 3.040 nonbonded pdb=" N GLU C 276 " pdb=" OE1 GLU C 276 " model vdw 2.223 3.120 nonbonded pdb=" O ILE C 315 " pdb=" OG SER C 319 " model vdw 2.225 3.040 nonbonded pdb=" O ASN B 138 " pdb=" ND2 ASN B 142 " model vdw 2.228 3.120 nonbonded pdb=" OD1 ASP D 228 " pdb=" NH2 ARG C 209 " model vdw 2.247 3.120 ... (remaining 73582 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 22.720 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:10.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.002 0.031 8938 Z= 0.143 Angle : 0.542 9.299 12144 Z= 0.291 Chirality : 0.041 0.139 1391 Planarity : 0.004 0.081 1538 Dihedral : 17.536 88.617 3128 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.36 % Allowed : 30.61 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.26), residues: 1119 helix: 0.54 (0.27), residues: 391 sheet: 0.29 (0.34), residues: 270 loop : -0.73 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 275 HIS 0.005 0.001 HIS C 324 PHE 0.029 0.001 PHE A 6 TYR 0.009 0.001 TYR D 264 ARG 0.005 0.000 ARG C 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 1.124 Fit side-chains REVERT: E 79 LEU cc_start: 0.7114 (tp) cc_final: 0.6447 (tt) outliers start: 40 outliers final: 36 residues processed: 190 average time/residue: 1.1579 time to fit residues: 235.7184 Evaluate side-chains 183 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 142 ASN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8938 Z= 0.339 Angle : 0.651 8.665 12144 Z= 0.344 Chirality : 0.047 0.164 1391 Planarity : 0.005 0.054 1538 Dihedral : 7.245 62.237 1273 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 6.64 % Allowed : 26.25 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.17 (0.26), residues: 1119 helix: 1.00 (0.27), residues: 382 sheet: 0.43 (0.34), residues: 260 loop : -0.74 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 63 HIS 0.011 0.002 HIS C 324 PHE 0.015 0.002 PHE D 151 TYR 0.014 0.002 TYR B 315 ARG 0.006 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 149 time to evaluate : 0.959 Fit side-chains REVERT: B 210 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7523 (tm) REVERT: B 359 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7648 (mm) REVERT: D 57 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.8993 (ptpp) REVERT: D 75 GLN cc_start: 0.8714 (mt0) cc_final: 0.8353 (mt0) REVERT: D 181 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8114 (m) REVERT: D 220 GLN cc_start: 0.8743 (tt0) cc_final: 0.8513 (mt0) REVERT: C 53 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.6561 (mpp) outliers start: 61 outliers final: 31 residues processed: 189 average time/residue: 1.0854 time to fit residues: 218.8537 Evaluate side-chains 172 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 286 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 80 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN B 161 GLN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN D 340 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN C 231 ASN C 352 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8938 Z= 0.164 Angle : 0.551 9.770 12144 Z= 0.287 Chirality : 0.042 0.153 1391 Planarity : 0.004 0.050 1538 Dihedral : 6.429 63.642 1250 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.77 % Allowed : 26.91 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.42 (0.26), residues: 1119 helix: 1.39 (0.27), residues: 384 sheet: 0.46 (0.33), residues: 256 loop : -0.70 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 169 HIS 0.005 0.001 HIS C 324 PHE 0.019 0.001 PHE A 6 TYR 0.012 0.001 TYR E 190 ARG 0.005 0.000 ARG C 250 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 146 time to evaluate : 1.037 Fit side-chains REVERT: B 210 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7337 (tm) REVERT: B 302 ILE cc_start: 0.8176 (tt) cc_final: 0.7711 (mm) REVERT: B 359 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7754 (mm) REVERT: D 59 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.8561 (m-80) REVERT: E 46 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: C 53 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.6563 (mpp) REVERT: C 250 ARG cc_start: 0.7847 (mtt-85) cc_final: 0.7646 (mtm110) outliers start: 53 outliers final: 21 residues processed: 181 average time/residue: 1.3144 time to fit residues: 252.8672 Evaluate side-chains 160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8938 Z= 0.267 Angle : 0.607 10.016 12144 Z= 0.314 Chirality : 0.044 0.165 1391 Planarity : 0.005 0.047 1538 Dihedral : 6.161 62.910 1240 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 6.10 % Allowed : 27.45 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.37 (0.26), residues: 1119 helix: 1.37 (0.27), residues: 384 sheet: 0.37 (0.33), residues: 264 loop : -0.72 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 211 HIS 0.007 0.001 HIS C 324 PHE 0.016 0.002 PHE A 6 TYR 0.013 0.002 TYR B 315 ARG 0.004 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 143 time to evaluate : 1.004 Fit side-chains REVERT: B 210 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7387 (tm) REVERT: B 299 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8013 (mtmm) REVERT: B 302 ILE cc_start: 0.8197 (tt) cc_final: 0.7701 (mm) REVERT: B 359 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7759 (mm) REVERT: D 46 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7571 (ttm110) REVERT: E 46 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: C 53 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6445 (mpp) outliers start: 56 outliers final: 35 residues processed: 175 average time/residue: 1.2618 time to fit residues: 235.0457 Evaluate side-chains 177 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN B 162 ASN G 59 ASN C 231 ASN C 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8938 Z= 0.197 Angle : 0.573 10.237 12144 Z= 0.296 Chirality : 0.043 0.153 1391 Planarity : 0.004 0.043 1538 Dihedral : 6.065 61.438 1240 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.45 % Allowed : 28.65 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.49 (0.26), residues: 1119 helix: 1.53 (0.27), residues: 384 sheet: 0.42 (0.33), residues: 262 loop : -0.71 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.005 0.001 HIS C 324 PHE 0.022 0.001 PHE A 6 TYR 0.011 0.001 TYR E 190 ARG 0.003 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 1.064 Fit side-chains REVERT: B 210 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7373 (tm) REVERT: B 299 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7954 (mtmm) REVERT: B 302 ILE cc_start: 0.8170 (tt) cc_final: 0.7684 (mm) REVERT: B 359 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7794 (mm) REVERT: D 46 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7578 (ttm110) REVERT: D 57 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8975 (ptpp) REVERT: E 46 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: C 53 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6453 (mpp) outliers start: 50 outliers final: 31 residues processed: 176 average time/residue: 1.2826 time to fit residues: 239.9549 Evaluate side-chains 171 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN C 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8938 Z= 0.175 Angle : 0.568 10.562 12144 Z= 0.291 Chirality : 0.043 0.157 1391 Planarity : 0.004 0.047 1538 Dihedral : 5.906 57.738 1240 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.01 % Allowed : 29.30 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.60 (0.26), residues: 1119 helix: 1.65 (0.27), residues: 385 sheet: 0.39 (0.33), residues: 264 loop : -0.60 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.005 0.001 HIS C 324 PHE 0.025 0.001 PHE A 6 TYR 0.011 0.001 TYR E 190 ARG 0.003 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 1.034 Fit side-chains REVERT: B 210 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7312 (tm) REVERT: B 299 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7948 (mtmm) REVERT: B 302 ILE cc_start: 0.8130 (tt) cc_final: 0.7675 (mm) REVERT: D 23 LYS cc_start: 0.8068 (tmtm) cc_final: 0.6963 (ptmm) REVERT: C 53 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6469 (mpp) outliers start: 46 outliers final: 31 residues processed: 176 average time/residue: 1.3372 time to fit residues: 249.9138 Evaluate side-chains 165 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.1980 chunk 60 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 GLN ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8938 Z= 0.169 Angle : 0.568 10.686 12144 Z= 0.289 Chirality : 0.042 0.159 1391 Planarity : 0.004 0.040 1538 Dihedral : 5.195 56.353 1237 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.79 % Allowed : 29.85 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.65 (0.26), residues: 1119 helix: 1.68 (0.27), residues: 385 sheet: 0.37 (0.33), residues: 264 loop : -0.53 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 211 HIS 0.004 0.001 HIS C 324 PHE 0.021 0.001 PHE A 6 TYR 0.011 0.001 TYR E 190 ARG 0.003 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 1.099 Fit side-chains REVERT: B 210 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7325 (tm) REVERT: B 299 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7906 (mtmm) REVERT: B 302 ILE cc_start: 0.8123 (tt) cc_final: 0.7683 (mm) REVERT: D 23 LYS cc_start: 0.8064 (tmtm) cc_final: 0.6962 (ptmm) REVERT: D 75 GLN cc_start: 0.8592 (mt0) cc_final: 0.8318 (mt0) REVERT: D 217 MET cc_start: 0.8093 (pp-130) cc_final: 0.7877 (ppp) REVERT: E 46 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7323 (tt0) REVERT: C 53 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6503 (mpp) outliers start: 44 outliers final: 30 residues processed: 168 average time/residue: 1.2378 time to fit residues: 221.7099 Evaluate side-chains 165 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 6.9990 chunk 31 optimal weight: 0.0000 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 0.0040 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 340 ASN C 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8938 Z= 0.148 Angle : 0.555 9.723 12144 Z= 0.283 Chirality : 0.042 0.163 1391 Planarity : 0.004 0.036 1538 Dihedral : 4.597 52.823 1234 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.49 % Allowed : 31.05 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.69 (0.26), residues: 1119 helix: 1.72 (0.27), residues: 385 sheet: 0.38 (0.33), residues: 262 loop : -0.50 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 211 HIS 0.003 0.001 HIS C 324 PHE 0.017 0.001 PHE A 6 TYR 0.011 0.001 TYR E 190 ARG 0.003 0.000 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 1.056 Fit side-chains REVERT: B 210 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7324 (tm) REVERT: B 299 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7900 (mtmm) REVERT: B 302 ILE cc_start: 0.8113 (tt) cc_final: 0.7681 (mm) REVERT: D 23 LYS cc_start: 0.8010 (tmtm) cc_final: 0.6860 (ptmm) REVERT: E 46 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: C 53 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6511 (mpp) outliers start: 32 outliers final: 24 residues processed: 162 average time/residue: 1.2643 time to fit residues: 218.1907 Evaluate side-chains 160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8938 Z= 0.304 Angle : 0.639 10.556 12144 Z= 0.327 Chirality : 0.045 0.164 1391 Planarity : 0.005 0.045 1538 Dihedral : 5.214 55.284 1234 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.49 % Allowed : 31.37 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.49 (0.26), residues: 1119 helix: 1.45 (0.26), residues: 385 sheet: 0.35 (0.33), residues: 266 loop : -0.59 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 211 HIS 0.007 0.001 HIS C 324 PHE 0.024 0.002 PHE A 6 TYR 0.015 0.002 TYR B 315 ARG 0.005 0.001 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.966 Fit side-chains REVERT: B 210 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7540 (tm) REVERT: B 299 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7951 (mtmm) REVERT: B 302 ILE cc_start: 0.8182 (tt) cc_final: 0.7702 (mm) REVERT: D 23 LYS cc_start: 0.8025 (tmtm) cc_final: 0.6907 (ptmm) REVERT: D 75 GLN cc_start: 0.8639 (mt0) cc_final: 0.8323 (mt0) REVERT: E 46 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: C 53 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6500 (mpp) outliers start: 32 outliers final: 22 residues processed: 157 average time/residue: 1.3545 time to fit residues: 225.6639 Evaluate side-chains 160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 53 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN C 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8938 Z= 0.155 Angle : 0.569 10.789 12144 Z= 0.290 Chirality : 0.042 0.168 1391 Planarity : 0.004 0.039 1538 Dihedral : 4.616 54.045 1233 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.72 % Allowed : 32.24 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.66 (0.26), residues: 1119 helix: 1.67 (0.27), residues: 385 sheet: 0.43 (0.33), residues: 264 loop : -0.55 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 211 HIS 0.003 0.001 HIS C 324 PHE 0.016 0.001 PHE A 6 TYR 0.009 0.001 TYR E 190 ARG 0.004 0.000 ARG D 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.003 Fit side-chains REVERT: B 210 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7313 (tm) REVERT: B 299 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7890 (mtmm) REVERT: B 302 ILE cc_start: 0.8102 (tt) cc_final: 0.7671 (mm) REVERT: D 23 LYS cc_start: 0.8016 (tmtm) cc_final: 0.6871 (ptmm) REVERT: D 111 TYR cc_start: 0.8883 (m-80) cc_final: 0.8615 (m-80) REVERT: E 46 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7292 (tt0) REVERT: C 53 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6521 (mpp) outliers start: 25 outliers final: 20 residues processed: 154 average time/residue: 1.2749 time to fit residues: 209.2027 Evaluate side-chains 147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 286 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.0170 chunk 76 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 183 GLN C 231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.173514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131858 restraints weight = 9957.627| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.48 r_work: 0.3262 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8938 Z= 0.157 Angle : 0.573 10.806 12144 Z= 0.290 Chirality : 0.042 0.170 1391 Planarity : 0.004 0.035 1538 Dihedral : 4.510 52.561 1233 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.83 % Allowed : 32.57 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.81 (0.26), residues: 1119 helix: 1.78 (0.27), residues: 384 sheet: 0.48 (0.33), residues: 262 loop : -0.42 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 211 HIS 0.004 0.001 HIS C 324 PHE 0.016 0.001 PHE B 170 TYR 0.011 0.001 TYR E 190 ARG 0.003 0.000 ARG C 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3995.81 seconds wall clock time: 77 minutes 28.51 seconds (4648.51 seconds total)