Starting phenix.real_space_refine on Thu Feb 15 03:45:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evy_31341/02_2024/7evy_31341_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evy_31341/02_2024/7evy_31341.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evy_31341/02_2024/7evy_31341_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evy_31341/02_2024/7evy_31341_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evy_31341/02_2024/7evy_31341_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evy_31341/02_2024/7evy_31341.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evy_31341/02_2024/7evy_31341.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evy_31341/02_2024/7evy_31341_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evy_31341/02_2024/7evy_31341_updated.pdb" } resolution = 2.98 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= 0.000 sd= 0.087 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 64 5.16 5 C 5758 2.51 5 N 1521 2.21 5 O 1678 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 289": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D ARG 234": "NH1" <-> "NH2" Residue "D GLU 317": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9024 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: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2296 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'J8C': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.98, per 1000 atoms: 0.55 Number of scatterers: 9024 At special positions: 0 Unit cell: (91.485, 122.265, 134.235, 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 64 16.00 F 3 9.00 O 1678 8.00 N 1521 7.00 C 5758 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=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied NAG-ASN " NAG D 402 " - " ASN D 30 " Time building additional restraints: 4.08 Conformation dependent library (CDL) restraints added in 3.1 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... running ksdssp... Secondary structure from input PDB file: 23 helices and 14 sheets defined 31.9% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.810A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.511A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 328 through 350 Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 8 through 22 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'D' and resid 23 through 32 Processing helix chain 'D' and resid 51 through 72 Processing helix chain 'D' and resid 79 through 104 removed outlier: 3.534A pdb=" N PHE D 83 " --> pdb=" O MET D 80 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE D 84 " --> pdb=" O TYR D 81 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 104 " --> pdb=" O ASN D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 147 removed outlier: 3.778A pdb=" N ALA D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU D 128 " --> pdb=" O MET D 124 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER D 129 " --> pdb=" O PHE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 180 removed outlier: 3.846A pdb=" N SER D 171 " --> pdb=" O CYS D 167 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 200 through 233 Processing helix chain 'D' and resid 249 through 281 removed outlier: 3.972A pdb=" N VAL D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP D 269 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Proline residue: D 271 - end of helix Processing helix chain 'D' and resid 294 through 313 removed outlier: 3.604A pdb=" N SER D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 316 through 324 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.860A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 221 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.871A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE B 93 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.520A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.994A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.082A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.747A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.923A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.731A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.462A pdb=" N THR E 118 " --> pdb=" O VAL E 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 115 through 117 removed outlier: 3.506A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.816A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 155 through 160 Processing sheet with id= N, first strand: chain 'E' and resid 226 through 231 removed outlier: 3.727A pdb=" N TRP E 176 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1026 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: 3.65 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1507 1.32 - 1.44: 2479 1.44 - 1.57: 5127 1.57 - 1.69: 1 1.69 - 1.81: 91 Bond restraints: 9205 Sorted by residual: bond pdb=" C16 J8C D 401 " pdb=" C19 J8C D 401 " ideal model delta sigma weight residual 0.000 1.526 -1.526 2.00e-02 2.50e+03 5.82e+03 bond pdb=" C12 J8C D 401 " pdb=" C13 J8C D 401 " ideal model delta sigma weight residual 1.958 1.528 0.430 2.00e-02 2.50e+03 4.63e+02 bond pdb=" C16 J8C D 401 " pdb=" C17 J8C D 401 " ideal model delta sigma weight residual 1.524 1.370 0.154 2.00e-02 2.50e+03 5.90e+01 bond pdb=" C25 J8C D 401 " pdb=" F28 J8C D 401 " ideal model delta sigma weight residual 1.506 1.354 0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C13 J8C D 401 " pdb=" C18 J8C D 401 " ideal model delta sigma weight residual 1.506 1.375 0.131 2.00e-02 2.50e+03 4.27e+01 ... (remaining 9200 not shown) Histogram of bond angle deviations from ideal: 88.84 - 97.87: 4 97.87 - 106.90: 188 106.90 - 115.92: 5849 115.92 - 124.95: 6286 124.95 - 133.98: 131 Bond angle restraints: 12458 Sorted by residual: angle pdb=" N ARG D 233 " pdb=" CA ARG D 233 " pdb=" C ARG D 233 " ideal model delta sigma weight residual 111.36 117.76 -6.40 1.09e+00 8.42e-01 3.45e+01 angle pdb=" N MET E 192 " pdb=" CA MET E 192 " pdb=" C MET E 192 " ideal model delta sigma weight residual 113.12 118.89 -5.77 1.25e+00 6.40e-01 2.13e+01 angle pdb=" C12 J8C D 401 " pdb=" C13 J8C D 401 " pdb=" C14 J8C D 401 " ideal model delta sigma weight residual 105.15 118.97 -13.82 3.00e+00 1.11e-01 2.12e+01 angle pdb=" N PHE D 237 " pdb=" CA PHE D 237 " pdb=" C PHE D 237 " ideal model delta sigma weight residual 110.97 115.78 -4.81 1.09e+00 8.42e-01 1.95e+01 angle pdb=" N ARG D 238 " pdb=" CA ARG D 238 " pdb=" C ARG D 238 " ideal model delta sigma weight residual 109.07 116.14 -7.07 1.61e+00 3.86e-01 1.93e+01 ... (remaining 12453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.22: 5240 24.22 - 48.45: 215 48.45 - 72.67: 20 72.67 - 96.89: 4 96.89 - 121.12: 2 Dihedral angle restraints: 5481 sinusoidal: 2161 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 -138.12 52.12 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" N MET E 192 " pdb=" C MET E 192 " pdb=" CA MET E 192 " pdb=" CB MET E 192 " ideal model delta harmonic sigma weight residual 122.80 132.89 -10.09 0 2.50e+00 1.60e-01 1.63e+01 dihedral pdb=" C20 J8C D 401 " pdb=" C21 J8C D 401 " pdb=" C22 J8C D 401 " pdb=" C23 J8C D 401 " ideal model delta sinusoidal sigma weight residual 53.28 -67.84 121.12 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 5478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.125: 1427 1.125 - 2.250: 0 2.250 - 3.375: 0 3.375 - 4.500: 0 4.500 - 5.626: 1 Chirality restraints: 1428 Sorted by residual: chirality pdb=" C33 J8C D 401 " pdb=" C32 J8C D 401 " pdb=" C34 J8C D 401 " pdb=" C35 J8C D 401 " both_signs ideal model delta sigma weight residual False -2.82 2.81 -5.63 2.00e-01 2.50e+01 7.91e+02 chirality pdb=" CA MET E 192 " pdb=" N MET E 192 " pdb=" C MET E 192 " pdb=" CB MET E 192 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CA VAL D 258 " pdb=" N VAL D 258 " pdb=" C VAL D 258 " pdb=" CB VAL D 258 " both_signs ideal model delta sigma weight residual False 2.44 2.18 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1425 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 402 " 0.088 2.00e-02 2.50e+03 7.19e-02 6.46e+01 pdb=" C7 NAG D 402 " -0.026 2.00e-02 2.50e+03 pdb=" C8 NAG D 402 " 0.067 2.00e-02 2.50e+03 pdb=" N2 NAG D 402 " -0.113 2.00e-02 2.50e+03 pdb=" O7 NAG D 402 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 231 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C ARG D 231 " 0.047 2.00e-02 2.50e+03 pdb=" O ARG D 231 " -0.017 2.00e-02 2.50e+03 pdb=" N SER D 232 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO E 236 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " -0.031 5.00e-02 4.00e+02 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 94 2.63 - 3.20: 7738 3.20 - 3.76: 13151 3.76 - 4.33: 17891 4.33 - 4.90: 30963 Nonbonded interactions: 69837 Sorted by model distance: nonbonded pdb=" O3 NAG D 402 " pdb=" O7 NAG D 402 " model vdw 2.061 2.440 nonbonded pdb=" CD2 LEU D 276 " pdb=" F26 J8C D 401 " model vdw 2.164 3.410 nonbonded pdb=" OG SER A 293 " pdb=" OE2 GLU A 298 " model vdw 2.180 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.218 2.440 nonbonded pdb=" O LEU E 174 " pdb=" O ARG E 191 " model vdw 2.226 3.040 ... (remaining 69832 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 3.940 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.930 Find NCS groups from input model: 0.200 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:15.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 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 : 0.017 1.526 9205 Z= 1.212 Angle : 0.620 13.820 12458 Z= 0.352 Chirality : 0.156 5.626 1428 Planarity : 0.004 0.072 1555 Dihedral : 12.533 121.118 3330 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.91 % Allowed : 3.65 % Favored : 95.43 % 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: -1.68 (0.22), residues: 1126 helix: 0.16 (0.24), residues: 381 sheet: -0.82 (0.30), residues: 274 loop : -2.37 (0.23), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 47 HIS 0.002 0.000 HIS B 142 PHE 0.009 0.001 PHE B 199 TYR 0.012 0.001 TYR E 190 ARG 0.003 0.000 ARG E 191 *********************** 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 210 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 201 time to evaluate : 0.736 Fit side-chains REVERT: A 25 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 240 MET cc_start: 0.8188 (tmm) cc_final: 0.7545 (pp-130) REVERT: A 242 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7092 (mtm-85) REVERT: A 276 GLU cc_start: 0.7420 (tp30) cc_final: 0.7120 (tp30) REVERT: A 289 GLU cc_start: 0.7787 (pm20) cc_final: 0.7407 (pp20) REVERT: A 302 TYR cc_start: 0.8241 (t80) cc_final: 0.8040 (t80) REVERT: B 226 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8048 (mm-30) REVERT: B 268 ASN cc_start: 0.8253 (t0) cc_final: 0.8049 (t0) REVERT: B 303 ASP cc_start: 0.6919 (m-30) cc_final: 0.6404 (p0) REVERT: D 24 ILE cc_start: 0.7287 (mm) cc_final: 0.7072 (mt) REVERT: D 295 TYR cc_start: 0.6966 (m-80) cc_final: 0.6748 (m-80) REVERT: E 11 LEU cc_start: 0.8701 (tp) cc_final: 0.8418 (tm) REVERT: E 76 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8150 (pttt) REVERT: E 89 GLU cc_start: 0.8530 (pt0) cc_final: 0.8148 (tm-30) REVERT: E 204 SER cc_start: 0.8513 (t) cc_final: 0.7956 (p) REVERT: E 220 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6470 (mm-30) REVERT: E 234 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6562 (mt-10) outliers start: 9 outliers final: 7 residues processed: 209 average time/residue: 1.1458 time to fit residues: 254.8729 Evaluate side-chains 140 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain E residue 191 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 10.0000 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 75 GLN B 110 ASN B 220 GLN B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 9205 Z= 0.178 Angle : 0.582 12.651 12458 Z= 0.287 Chirality : 0.041 0.207 1428 Planarity : 0.004 0.053 1555 Dihedral : 6.446 76.888 1293 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.05 % Allowed : 13.60 % Favored : 83.35 % 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: -0.97 (0.24), residues: 1126 helix: 1.01 (0.26), residues: 378 sheet: -0.60 (0.30), residues: 276 loop : -2.07 (0.24), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 47 HIS 0.002 0.000 HIS E 35 PHE 0.017 0.001 PHE D 237 TYR 0.016 0.001 TYR D 31 ARG 0.007 0.000 ARG A 32 *********************** 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 172 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 1.043 Fit side-chains REVERT: A 25 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7452 (tm-30) REVERT: A 51 LYS cc_start: 0.8802 (tmmm) cc_final: 0.8550 (tmmt) REVERT: A 242 ARG cc_start: 0.7569 (mtt180) cc_final: 0.7304 (mtm-85) REVERT: A 276 GLU cc_start: 0.7451 (tp30) cc_final: 0.7089 (tp30) REVERT: B 118 ASP cc_start: 0.7435 (t0) cc_final: 0.7225 (t0) REVERT: B 197 ARG cc_start: 0.7856 (ttm-80) cc_final: 0.7258 (ttt-90) REVERT: B 214 ARG cc_start: 0.8273 (mmt90) cc_final: 0.8012 (mmt90) REVERT: B 226 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8027 (mm-30) REVERT: B 268 ASN cc_start: 0.8260 (t0) cc_final: 0.8021 (t0) REVERT: B 303 ASP cc_start: 0.6920 (m-30) cc_final: 0.6382 (p0) REVERT: D 80 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7674 (tpt) REVERT: D 183 ASN cc_start: 0.7899 (t0) cc_final: 0.7519 (t0) REVERT: E 11 LEU cc_start: 0.8695 (tp) cc_final: 0.8417 (tm) REVERT: E 89 GLU cc_start: 0.8546 (pt0) cc_final: 0.8140 (tm-30) REVERT: E 93 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6711 (tpt) REVERT: E 183 GLN cc_start: 0.8668 (pt0) cc_final: 0.8450 (pt0) REVERT: E 204 SER cc_start: 0.8349 (t) cc_final: 0.8030 (p) REVERT: E 234 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6640 (mt-10) outliers start: 30 outliers final: 15 residues processed: 155 average time/residue: 1.2755 time to fit residues: 210.0033 Evaluate side-chains 145 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain E residue 93 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 340 ASN C 59 ASN D 303 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 9205 Z= 0.251 Angle : 0.590 12.691 12458 Z= 0.294 Chirality : 0.041 0.135 1428 Planarity : 0.004 0.058 1555 Dihedral : 5.778 76.109 1284 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.96 % Allowed : 14.92 % 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: -0.76 (0.24), residues: 1126 helix: 1.19 (0.26), residues: 376 sheet: -0.47 (0.31), residues: 274 loop : -1.94 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.017 0.001 PHE D 237 TYR 0.014 0.002 TYR D 31 ARG 0.006 0.000 ARG A 32 *********************** 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 174 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7526 (tm-30) REVERT: A 51 LYS cc_start: 0.8843 (tmmm) cc_final: 0.8608 (tmmt) REVERT: A 209 LYS cc_start: 0.8626 (tttt) cc_final: 0.8396 (tttm) REVERT: A 242 ARG cc_start: 0.7576 (mtt180) cc_final: 0.7324 (mtm-85) REVERT: A 276 GLU cc_start: 0.7471 (tp30) cc_final: 0.7064 (tp30) REVERT: A 289 GLU cc_start: 0.8116 (pp20) cc_final: 0.7675 (pp20) REVERT: A 318 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6706 (mt-10) REVERT: B 96 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7616 (mtt90) REVERT: B 197 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7356 (ttt-90) REVERT: B 214 ARG cc_start: 0.8248 (mmt90) cc_final: 0.7886 (mmt90) REVERT: B 226 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8053 (mm-30) REVERT: B 268 ASN cc_start: 0.8247 (t0) cc_final: 0.8012 (t0) REVERT: D 183 ASN cc_start: 0.7967 (t0) cc_final: 0.7541 (t0) REVERT: E 11 LEU cc_start: 0.8686 (tp) cc_final: 0.8410 (tm) REVERT: E 65 LYS cc_start: 0.7551 (tptt) cc_final: 0.7234 (tptp) REVERT: E 89 GLU cc_start: 0.8551 (pt0) cc_final: 0.8166 (tm-30) REVERT: E 93 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6915 (tpt) REVERT: E 140 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8058 (mmm) REVERT: E 183 GLN cc_start: 0.8664 (pt0) cc_final: 0.8455 (pt0) REVERT: E 204 SER cc_start: 0.8352 (t) cc_final: 0.8016 (p) REVERT: E 234 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6967 (mt-10) outliers start: 39 outliers final: 20 residues processed: 159 average time/residue: 1.1991 time to fit residues: 203.0801 Evaluate side-chains 153 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 206 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 269 ASN D 101 ASN D 240 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9205 Z= 0.279 Angle : 0.613 11.300 12458 Z= 0.306 Chirality : 0.042 0.177 1428 Planarity : 0.004 0.059 1555 Dihedral : 5.764 73.595 1284 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.87 % Allowed : 16.75 % Favored : 78.38 % 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: -0.74 (0.24), residues: 1126 helix: 1.15 (0.26), residues: 385 sheet: -0.45 (0.30), residues: 277 loop : -1.95 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.016 0.002 PHE B 199 TYR 0.016 0.002 TYR D 31 ARG 0.015 0.001 ARG A 32 *********************** 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 172 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 124 time to evaluate : 1.106 Fit side-chains REVERT: A 25 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7580 (tm-30) REVERT: A 209 LYS cc_start: 0.8661 (tttt) cc_final: 0.8431 (tttm) REVERT: A 240 MET cc_start: 0.7555 (ppp) cc_final: 0.6563 (ppp) REVERT: A 242 ARG cc_start: 0.7569 (mtt180) cc_final: 0.7199 (mtm-85) REVERT: A 276 GLU cc_start: 0.7555 (tp30) cc_final: 0.7179 (tp30) REVERT: A 289 GLU cc_start: 0.8141 (pp20) cc_final: 0.7749 (pp20) REVERT: A 318 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6615 (tt0) REVERT: B 96 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7665 (mtt90) REVERT: B 118 ASP cc_start: 0.7503 (t0) cc_final: 0.7262 (t0) REVERT: B 197 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7350 (ttt-90) REVERT: B 214 ARG cc_start: 0.8249 (mmt90) cc_final: 0.7992 (mmt90) REVERT: B 226 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8078 (mm-30) REVERT: B 268 ASN cc_start: 0.8252 (t0) cc_final: 0.8013 (t0) REVERT: D 68 LEU cc_start: 0.7542 (pp) cc_final: 0.7055 (mp) REVERT: D 80 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7361 (tpp) REVERT: D 183 ASN cc_start: 0.7945 (t0) cc_final: 0.7554 (t0) REVERT: E 11 LEU cc_start: 0.8660 (tp) cc_final: 0.8378 (tm) REVERT: E 65 LYS cc_start: 0.7630 (tptt) cc_final: 0.7281 (tptp) REVERT: E 89 GLU cc_start: 0.8569 (pt0) cc_final: 0.8172 (tm-30) REVERT: E 93 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6979 (tpt) REVERT: E 140 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.7991 (mmm) REVERT: E 204 SER cc_start: 0.8369 (t) cc_final: 0.8030 (p) REVERT: E 233 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8136 (tt) REVERT: E 234 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7091 (mt-10) outliers start: 48 outliers final: 30 residues processed: 158 average time/residue: 1.2516 time to fit residues: 210.5428 Evaluate side-chains 156 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 121 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 9205 Z= 0.352 Angle : 0.651 10.603 12458 Z= 0.328 Chirality : 0.044 0.178 1428 Planarity : 0.005 0.062 1555 Dihedral : 5.922 72.275 1284 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.28 % Allowed : 17.87 % Favored : 76.85 % 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: -0.85 (0.24), residues: 1126 helix: 1.08 (0.26), residues: 381 sheet: -0.66 (0.30), residues: 286 loop : -1.92 (0.25), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.017 0.002 PHE B 199 TYR 0.013 0.002 TYR D 31 ARG 0.010 0.001 ARG A 32 *********************** 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 180 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 128 time to evaluate : 1.020 Fit side-chains REVERT: A 25 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7527 (tm-30) REVERT: A 36 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6960 (pp) REVERT: A 242 ARG cc_start: 0.7747 (mtt180) cc_final: 0.7542 (mtm-85) REVERT: A 276 GLU cc_start: 0.7667 (tp30) cc_final: 0.7328 (tp30) REVERT: A 289 GLU cc_start: 0.8150 (pp20) cc_final: 0.7798 (pp20) REVERT: A 318 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6619 (tt0) REVERT: A 350 ASP cc_start: 0.7881 (t0) cc_final: 0.6904 (t0) REVERT: B 96 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7776 (mtt90) REVERT: B 118 ASP cc_start: 0.7528 (t0) cc_final: 0.7294 (t0) REVERT: B 186 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7751 (m-30) REVERT: B 197 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7389 (ttt-90) REVERT: B 214 ARG cc_start: 0.8208 (mmt90) cc_final: 0.7948 (mmt90) REVERT: B 226 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8084 (mm-30) REVERT: B 268 ASN cc_start: 0.8226 (t0) cc_final: 0.7984 (t0) REVERT: D 68 LEU cc_start: 0.7595 (pp) cc_final: 0.7069 (mt) REVERT: D 80 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7407 (tpp) REVERT: D 150 LYS cc_start: 0.7971 (ptpt) cc_final: 0.7692 (ptmm) REVERT: D 183 ASN cc_start: 0.8011 (t0) cc_final: 0.7571 (t0) REVERT: E 11 LEU cc_start: 0.8609 (tp) cc_final: 0.8324 (tm) REVERT: E 65 LYS cc_start: 0.7726 (tptt) cc_final: 0.7347 (tptp) REVERT: E 89 GLU cc_start: 0.8584 (pt0) cc_final: 0.8168 (tm-30) REVERT: E 93 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7044 (tpt) REVERT: E 158 SER cc_start: 0.8912 (t) cc_final: 0.8526 (m) REVERT: E 204 SER cc_start: 0.8365 (t) cc_final: 0.8006 (p) REVERT: E 233 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8034 (tt) REVERT: E 234 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7051 (mt-10) outliers start: 52 outliers final: 30 residues processed: 164 average time/residue: 1.3891 time to fit residues: 241.5875 Evaluate side-chains 157 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 121 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 110 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9205 Z= 0.235 Angle : 0.591 10.341 12458 Z= 0.297 Chirality : 0.041 0.193 1428 Planarity : 0.004 0.056 1555 Dihedral : 5.505 69.890 1280 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.16 % Allowed : 20.00 % Favored : 75.84 % 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: -0.71 (0.24), residues: 1126 helix: 1.24 (0.27), residues: 381 sheet: -0.50 (0.31), residues: 281 loop : -1.93 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.005 0.001 HIS B 142 PHE 0.014 0.001 PHE D 237 TYR 0.014 0.001 TYR D 31 ARG 0.006 0.000 ARG D 78 *********************** 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 164 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 123 time to evaluate : 1.034 Fit side-chains REVERT: A 25 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7631 (tm-30) REVERT: A 36 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6921 (pp) REVERT: A 245 GLU cc_start: 0.7503 (tt0) cc_final: 0.6988 (tm-30) REVERT: A 276 GLU cc_start: 0.7683 (tp30) cc_final: 0.7421 (tp30) REVERT: A 289 GLU cc_start: 0.8176 (pp20) cc_final: 0.7772 (pp20) REVERT: A 318 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6645 (tt0) REVERT: A 350 ASP cc_start: 0.7715 (t0) cc_final: 0.6884 (m-30) REVERT: B 96 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7779 (mtt90) REVERT: B 118 ASP cc_start: 0.7481 (t0) cc_final: 0.7252 (t0) REVERT: B 197 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7441 (mtt-85) REVERT: B 226 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8078 (mm-30) REVERT: B 268 ASN cc_start: 0.8270 (t0) cc_final: 0.8008 (t0) REVERT: D 68 LEU cc_start: 0.7588 (pp) cc_final: 0.7086 (mt) REVERT: D 80 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7355 (tpp) REVERT: D 150 LYS cc_start: 0.7960 (ptpt) cc_final: 0.7595 (ptmm) REVERT: D 153 ASN cc_start: 0.7072 (m-40) cc_final: 0.6689 (m-40) REVERT: D 183 ASN cc_start: 0.7911 (t0) cc_final: 0.7505 (t0) REVERT: D 238 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6924 (ppt-90) REVERT: E 11 LEU cc_start: 0.8602 (tp) cc_final: 0.8316 (tm) REVERT: E 65 LYS cc_start: 0.7709 (tptt) cc_final: 0.7322 (tptp) REVERT: E 89 GLU cc_start: 0.8574 (pt0) cc_final: 0.8119 (tm-30) REVERT: E 93 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.7025 (tpt) REVERT: E 158 SER cc_start: 0.8891 (t) cc_final: 0.8521 (m) REVERT: E 204 SER cc_start: 0.8382 (t) cc_final: 0.7987 (p) REVERT: E 233 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7929 (tt) REVERT: E 234 GLU cc_start: 0.7541 (mt-10) cc_final: 0.6966 (mt-10) outliers start: 41 outliers final: 25 residues processed: 152 average time/residue: 1.2968 time to fit residues: 209.5409 Evaluate side-chains 150 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 110 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 9205 Z= 0.200 Angle : 0.575 9.668 12458 Z= 0.289 Chirality : 0.041 0.204 1428 Planarity : 0.004 0.057 1555 Dihedral : 5.356 67.612 1280 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.67 % Allowed : 20.00 % Favored : 75.33 % 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: -0.57 (0.25), residues: 1126 helix: 1.36 (0.27), residues: 385 sheet: -0.41 (0.31), residues: 279 loop : -1.88 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE A 189 TYR 0.014 0.001 TYR D 31 ARG 0.009 0.001 ARG D 78 *********************** 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 174 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 128 time to evaluate : 1.087 Fit side-chains REVERT: A 25 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7633 (tm-30) REVERT: A 245 GLU cc_start: 0.7549 (tt0) cc_final: 0.7078 (tm-30) REVERT: A 276 GLU cc_start: 0.7703 (tp30) cc_final: 0.7435 (tp30) REVERT: A 289 GLU cc_start: 0.8200 (pp20) cc_final: 0.7811 (pp20) REVERT: A 318 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6658 (tt0) REVERT: A 350 ASP cc_start: 0.7730 (t0) cc_final: 0.6892 (m-30) REVERT: B 96 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7736 (mtt90) REVERT: B 118 ASP cc_start: 0.7438 (t0) cc_final: 0.7202 (t0) REVERT: B 186 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7641 (m-30) REVERT: B 197 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7551 (mtt-85) REVERT: B 214 ARG cc_start: 0.8247 (mmt90) cc_final: 0.8036 (mmt90) REVERT: B 226 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8101 (mm-30) REVERT: B 268 ASN cc_start: 0.8272 (t0) cc_final: 0.8004 (t0) REVERT: D 68 LEU cc_start: 0.7580 (pp) cc_final: 0.7130 (mt) REVERT: D 80 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7323 (tpp) REVERT: D 150 LYS cc_start: 0.8009 (ptpt) cc_final: 0.7684 (ptmm) REVERT: D 153 ASN cc_start: 0.6891 (m-40) cc_final: 0.6485 (m-40) REVERT: D 183 ASN cc_start: 0.7912 (t0) cc_final: 0.7480 (t0) REVERT: D 238 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6756 (ppt-90) REVERT: E 11 LEU cc_start: 0.8593 (tp) cc_final: 0.8308 (tm) REVERT: E 65 LYS cc_start: 0.7681 (tptt) cc_final: 0.7302 (tptp) REVERT: E 89 GLU cc_start: 0.8559 (pt0) cc_final: 0.8101 (tm-30) REVERT: E 93 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6997 (tpt) REVERT: E 140 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8137 (mtm) REVERT: E 158 SER cc_start: 0.8882 (t) cc_final: 0.8530 (m) REVERT: E 204 SER cc_start: 0.8379 (t) cc_final: 0.7982 (p) REVERT: E 233 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7966 (tt) outliers start: 46 outliers final: 25 residues processed: 161 average time/residue: 1.2628 time to fit residues: 216.3501 Evaluate side-chains 156 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 73 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 110 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 9205 Z= 0.178 Angle : 0.573 10.843 12458 Z= 0.286 Chirality : 0.041 0.279 1428 Planarity : 0.004 0.055 1555 Dihedral : 5.293 66.042 1280 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.96 % Allowed : 21.62 % Favored : 74.42 % 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: -0.49 (0.25), residues: 1126 helix: 1.45 (0.27), residues: 386 sheet: -0.47 (0.31), residues: 285 loop : -1.80 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.002 0.001 HIS E 35 PHE 0.011 0.001 PHE A 189 TYR 0.011 0.001 TYR D 31 ARG 0.010 0.001 ARG D 78 *********************** 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 166 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 1.041 Fit side-chains REVERT: A 25 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 36 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6970 (pp) REVERT: A 245 GLU cc_start: 0.7537 (tt0) cc_final: 0.7073 (tm-30) REVERT: A 276 GLU cc_start: 0.7710 (tp30) cc_final: 0.7419 (tp30) REVERT: A 289 GLU cc_start: 0.8190 (pp20) cc_final: 0.7695 (pp20) REVERT: A 318 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6660 (tt0) REVERT: A 350 ASP cc_start: 0.7743 (t0) cc_final: 0.6881 (m-30) REVERT: B 96 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7745 (mtt90) REVERT: B 118 ASP cc_start: 0.7363 (t0) cc_final: 0.7141 (t0) REVERT: B 186 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: B 197 ARG cc_start: 0.7937 (ttm-80) cc_final: 0.7575 (mtt-85) REVERT: B 214 ARG cc_start: 0.8238 (mmt90) cc_final: 0.8013 (mmt90) REVERT: B 226 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8095 (mm-30) REVERT: B 268 ASN cc_start: 0.8275 (t0) cc_final: 0.8004 (t0) REVERT: D 68 LEU cc_start: 0.7599 (pp) cc_final: 0.7184 (mt) REVERT: D 80 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7299 (tpp) REVERT: D 150 LYS cc_start: 0.8020 (ptpt) cc_final: 0.7661 (ptmm) REVERT: D 153 ASN cc_start: 0.6962 (m-40) cc_final: 0.6519 (m-40) REVERT: D 183 ASN cc_start: 0.7896 (t0) cc_final: 0.7495 (t0) REVERT: D 238 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6760 (ppt-90) REVERT: E 11 LEU cc_start: 0.8590 (tp) cc_final: 0.8305 (tm) REVERT: E 65 LYS cc_start: 0.7784 (tptt) cc_final: 0.7409 (tptp) REVERT: E 89 GLU cc_start: 0.8560 (pt0) cc_final: 0.8092 (tm-30) REVERT: E 93 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.7003 (tpt) REVERT: E 140 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8130 (mtm) REVERT: E 158 SER cc_start: 0.8858 (t) cc_final: 0.8509 (m) REVERT: E 204 SER cc_start: 0.8383 (t) cc_final: 0.7988 (p) REVERT: E 233 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7955 (tt) REVERT: E 234 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6822 (mt-10) outliers start: 39 outliers final: 21 residues processed: 154 average time/residue: 1.3047 time to fit residues: 213.4210 Evaluate side-chains 152 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 123 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 103 optimal weight: 0.0970 chunk 60 optimal weight: 0.0970 chunk 43 optimal weight: 0.0980 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.0570 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.1894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 110 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 9205 Z= 0.154 Angle : 0.554 10.106 12458 Z= 0.277 Chirality : 0.040 0.193 1428 Planarity : 0.004 0.053 1555 Dihedral : 5.072 63.294 1280 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.94 % Allowed : 22.54 % Favored : 74.52 % 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: 1.63 (0.27), residues: 386 sheet: -0.36 (0.31), residues: 284 loop : -1.69 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.001 0.000 HIS E 35 PHE 0.014 0.001 PHE D 65 TYR 0.010 0.001 TYR E 60 ARG 0.010 0.001 ARG D 78 *********************** 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 161 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7536 (tm-30) REVERT: A 276 GLU cc_start: 0.7743 (tp30) cc_final: 0.7432 (tp30) REVERT: A 289 GLU cc_start: 0.8196 (pp20) cc_final: 0.7701 (pp20) REVERT: A 318 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6678 (tt0) REVERT: A 350 ASP cc_start: 0.7720 (t0) cc_final: 0.6836 (m-30) REVERT: B 96 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7715 (mtt90) REVERT: B 118 ASP cc_start: 0.7248 (t0) cc_final: 0.7006 (t0) REVERT: B 197 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7622 (mtp180) REVERT: B 226 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8096 (mm-30) REVERT: B 259 GLN cc_start: 0.8229 (tt0) cc_final: 0.8006 (tt0) REVERT: B 268 ASN cc_start: 0.8271 (t0) cc_final: 0.8001 (t0) REVERT: D 68 LEU cc_start: 0.7560 (pp) cc_final: 0.7170 (mt) REVERT: D 80 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7270 (tpp) REVERT: D 150 LYS cc_start: 0.8008 (ptpt) cc_final: 0.7667 (ptmm) REVERT: D 153 ASN cc_start: 0.7054 (m-40) cc_final: 0.6629 (m-40) REVERT: D 183 ASN cc_start: 0.7818 (t0) cc_final: 0.7380 (t0) REVERT: D 238 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6784 (ppt-90) REVERT: E 11 LEU cc_start: 0.8583 (tp) cc_final: 0.8305 (tm) REVERT: E 89 GLU cc_start: 0.8556 (pt0) cc_final: 0.8135 (tm-30) REVERT: E 93 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6788 (tpt) REVERT: E 158 SER cc_start: 0.8837 (t) cc_final: 0.8494 (m) REVERT: E 204 SER cc_start: 0.8385 (t) cc_final: 0.7991 (p) REVERT: E 233 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7976 (tt) REVERT: E 234 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6655 (mt-10) outliers start: 29 outliers final: 18 residues processed: 154 average time/residue: 1.2883 time to fit residues: 211.2672 Evaluate side-chains 150 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 40.0000 chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.0370 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 110 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9205 Z= 0.237 Angle : 0.597 10.837 12458 Z= 0.297 Chirality : 0.041 0.221 1428 Planarity : 0.004 0.060 1555 Dihedral : 5.136 63.510 1280 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.84 % Allowed : 22.54 % Favored : 74.62 % 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: -0.36 (0.25), residues: 1126 helix: 1.52 (0.27), residues: 386 sheet: -0.36 (0.31), residues: 285 loop : -1.72 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE B 199 TYR 0.010 0.001 TYR E 60 ARG 0.010 0.001 ARG D 78 ********************** 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 152 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 245 GLU cc_start: 0.7576 (tt0) cc_final: 0.7203 (tm-30) REVERT: A 276 GLU cc_start: 0.7770 (tp30) cc_final: 0.7458 (tp30) REVERT: A 289 GLU cc_start: 0.8259 (pp20) cc_final: 0.7783 (pp20) REVERT: A 318 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6695 (tt0) REVERT: A 350 ASP cc_start: 0.7741 (t0) cc_final: 0.6859 (m-30) REVERT: B 96 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7774 (mtt90) REVERT: B 118 ASP cc_start: 0.7348 (t0) cc_final: 0.7131 (t0) REVERT: B 186 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7598 (m-30) REVERT: B 197 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7620 (mtp180) REVERT: B 226 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8098 (mm-30) REVERT: B 268 ASN cc_start: 0.8256 (t0) cc_final: 0.8002 (t0) REVERT: B 303 ASP cc_start: 0.7056 (m-30) cc_final: 0.6546 (m-30) REVERT: D 68 LEU cc_start: 0.7684 (pp) cc_final: 0.7194 (mt) REVERT: D 80 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7244 (tpp) REVERT: D 150 LYS cc_start: 0.8082 (ptpt) cc_final: 0.7720 (ptmm) REVERT: D 153 ASN cc_start: 0.7023 (m-40) cc_final: 0.6602 (m-40) REVERT: D 183 ASN cc_start: 0.7877 (t0) cc_final: 0.7420 (t0) REVERT: D 238 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6867 (ppt-90) REVERT: D 240 ASN cc_start: 0.5416 (OUTLIER) cc_final: 0.5122 (t0) REVERT: E 11 LEU cc_start: 0.8562 (tp) cc_final: 0.8270 (tm) REVERT: E 65 LYS cc_start: 0.7635 (tptt) cc_final: 0.7269 (tptp) REVERT: E 89 GLU cc_start: 0.8581 (pt0) cc_final: 0.8118 (tm-30) REVERT: E 93 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.7018 (tpt) REVERT: E 158 SER cc_start: 0.8850 (t) cc_final: 0.8505 (m) REVERT: E 204 SER cc_start: 0.8358 (t) cc_final: 0.7972 (p) REVERT: E 233 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8009 (tt) REVERT: E 234 GLU cc_start: 0.7556 (mt-10) cc_final: 0.6881 (mt-10) outliers start: 28 outliers final: 19 residues processed: 147 average time/residue: 1.4055 time to fit residues: 219.1290 Evaluate side-chains 148 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.0170 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 110 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.163727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.110918 restraints weight = 13399.816| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.92 r_work: 0.3183 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 9205 Z= 0.205 Angle : 0.583 9.619 12458 Z= 0.291 Chirality : 0.041 0.224 1428 Planarity : 0.004 0.054 1555 Dihedral : 5.073 62.764 1280 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.94 % Allowed : 22.74 % Favored : 74.31 % 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: -0.30 (0.25), residues: 1126 helix: 1.57 (0.27), residues: 386 sheet: -0.36 (0.31), residues: 293 loop : -1.69 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 234 TYR 0.010 0.001 TYR E 60 ARG 0.010 0.001 ARG D 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4113.31 seconds wall clock time: 74 minutes 29.95 seconds (4469.95 seconds total)