Starting phenix.real_space_refine on Tue Sep 24 18:47:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoj_38531/09_2024/8xoj_38531.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoj_38531/09_2024/8xoj_38531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoj_38531/09_2024/8xoj_38531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoj_38531/09_2024/8xoj_38531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoj_38531/09_2024/8xoj_38531.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoj_38531/09_2024/8xoj_38531.cif" } resolution = 3.1 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= -0.007 sd= 0.109 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5585 2.51 5 N 1531 2.21 5 O 1615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8785 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1864 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2573 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1736 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2177 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 7, 'TRANS': 258} Chain breaks: 3 Time building chain proxies: 5.39, per 1000 atoms: 0.61 Number of scatterers: 8785 At special positions: 0 Unit cell: (91.035, 121.023, 128.52, 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 54 16.00 O 1615 8.00 N 1531 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 41.4% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.789A pdb=" N ALA A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.517A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.950A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.464A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.564A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.075A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'G' and resid 7 through 25 removed outlier: 4.169A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.508A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 51 through 87 removed outlier: 4.273A pdb=" N PHE R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 88 through 91 Processing helix chain 'R' and resid 92 through 116 removed outlier: 3.617A pdb=" N TYR R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 123 removed outlier: 5.806A pdb=" N HIS R 120 " --> pdb=" O PHE R 117 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU R 121 " --> pdb=" O ASN R 118 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR R 123 " --> pdb=" O HIS R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 161 Processing helix chain 'R' and resid 170 through 200 Proline residue: R 192 - end of helix Processing helix chain 'R' and resid 211 through 223 Processing helix chain 'R' and resid 223 through 248 removed outlier: 3.744A pdb=" N HIS R 247 " --> pdb=" O ARG R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 285 removed outlier: 3.541A pdb=" N VAL R 265 " --> pdb=" O ILE R 261 " (cutoff:3.500A) Proline residue: R 274 - end of helix Processing helix chain 'R' and resid 302 through 325 removed outlier: 3.608A pdb=" N HIS R 307 " --> pdb=" O PRO R 303 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN R 316 " --> pdb=" O ALA R 312 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER R 317 " --> pdb=" O ALA R 313 " (cutoff:3.500A) Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 328 through 342 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.422A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.711A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.629A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.778A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.681A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.563A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.634A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.691A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.539A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.547A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1320 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: 2.47 Time building geometry restraints manager: 2.68 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: 2865 1.34 - 1.46: 1546 1.46 - 1.57: 4474 1.57 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 8964 Sorted by residual: bond pdb=" CA ASN A 292 " pdb=" CB ASN A 292 " ideal model delta sigma weight residual 1.528 1.563 -0.035 1.61e-02 3.86e+03 4.82e+00 bond pdb=" N THR G 6 " pdb=" CA THR G 6 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.51e+00 bond pdb=" N GLU B 3 " pdb=" CA GLU B 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N VAL E 2 " pdb=" CA VAL E 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" N GLU A 15 " pdb=" CA GLU A 15 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 ... (remaining 8959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 11618 1.24 - 2.47: 438 2.47 - 3.71: 56 3.71 - 4.94: 18 4.94 - 6.18: 6 Bond angle restraints: 12136 Sorted by residual: angle pdb=" N MET E 192 " pdb=" CA MET E 192 " pdb=" CB MET E 192 " ideal model delta sigma weight residual 114.17 109.08 5.09 1.14e+00 7.69e-01 1.99e+01 angle pdb=" N TYR B 105 " pdb=" CA TYR B 105 " pdb=" C TYR B 105 " ideal model delta sigma weight residual 108.34 102.16 6.18 1.64e+00 3.72e-01 1.42e+01 angle pdb=" C SER R 325 " pdb=" N PHE R 326 " pdb=" CA PHE R 326 " ideal model delta sigma weight residual 122.65 117.24 5.41 1.60e+00 3.91e-01 1.15e+01 angle pdb=" N ASN A 292 " pdb=" CA ASN A 292 " pdb=" C ASN A 292 " ideal model delta sigma weight residual 110.53 114.89 -4.36 1.29e+00 6.01e-01 1.14e+01 angle pdb=" N ASP B 290 " pdb=" CA ASP B 290 " pdb=" CB ASP B 290 " ideal model delta sigma weight residual 110.39 116.09 -5.70 1.75e+00 3.27e-01 1.06e+01 ... (remaining 12131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4748 17.95 - 35.90: 442 35.90 - 53.84: 97 53.84 - 71.79: 19 71.79 - 89.74: 11 Dihedral angle restraints: 5317 sinusoidal: 2076 harmonic: 3241 Sorted by residual: dihedral pdb=" CA HIS R 302 " pdb=" C HIS R 302 " pdb=" N PRO R 303 " pdb=" CA PRO R 303 " ideal model delta harmonic sigma weight residual -180.00 -160.99 -19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 161.45 18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1025 0.039 - 0.077: 249 0.077 - 0.116: 81 0.116 - 0.155: 21 0.155 - 0.193: 1 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CA TYR B 105 " pdb=" N TYR B 105 " pdb=" C TYR B 105 " pdb=" CB TYR B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA ASN B 340 " pdb=" N ASN B 340 " pdb=" C ASN B 340 " pdb=" CB ASN B 340 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA LEU A 291 " pdb=" N LEU A 291 " pdb=" C LEU A 291 " pdb=" CB LEU A 291 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 1374 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 13 " -0.211 9.50e-02 1.11e+02 9.45e-02 5.61e+00 pdb=" NE ARG G 13 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG G 13 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG G 13 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG G 13 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 147 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO E 148 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 148 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 148 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 62 " 0.119 9.50e-02 1.11e+02 5.35e-02 1.97e+00 pdb=" NE ARG G 62 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG G 62 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG G 62 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 62 " 0.002 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2812 2.83 - 3.35: 8448 3.35 - 3.86: 14235 3.86 - 4.38: 16883 4.38 - 4.90: 29921 Nonbonded interactions: 72299 Sorted by model distance: nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.311 3.040 nonbonded pdb=" O ASN A 239 " pdb=" OD1 ASP A 240 " model vdw 2.326 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.329 3.040 nonbonded pdb=" OD2 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.335 3.040 nonbonded pdb=" O THR B 34 " pdb=" NZ LYS B 301 " model vdw 2.352 3.120 ... (remaining 72294 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.560 Find NCS groups from input model: 0.110 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8964 Z= 0.198 Angle : 0.564 6.178 12136 Z= 0.332 Chirality : 0.040 0.193 1377 Planarity : 0.004 0.094 1542 Dihedral : 15.110 89.740 3217 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.32 % Allowed : 11.58 % Favored : 88.11 % 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: 1.17 (0.26), residues: 1093 helix: 1.74 (0.25), residues: 403 sheet: 0.28 (0.31), residues: 278 loop : 0.33 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 216 HIS 0.003 0.001 HIS R 197 PHE 0.010 0.001 PHE R 193 TYR 0.010 0.001 TYR E 103 ARG 0.013 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8435 (mmtp) cc_final: 0.7784 (mttt) REVERT: A 25 MET cc_start: 0.8322 (mmm) cc_final: 0.8120 (mtp) REVERT: B 33 ILE cc_start: 0.8517 (mm) cc_final: 0.8304 (mt) REVERT: B 209 LYS cc_start: 0.9223 (mttm) cc_final: 0.8879 (mttm) REVERT: E 82 GLN cc_start: 0.7929 (tp40) cc_final: 0.7545 (tp40) REVERT: E 93 MET cc_start: 0.8391 (ttp) cc_final: 0.8154 (ttm) REVERT: E 202 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7866 (mtm110) REVERT: G 29 LYS cc_start: 0.8693 (mmtm) cc_final: 0.8259 (ttpp) REVERT: G 38 MET cc_start: 0.7677 (mtm) cc_final: 0.7399 (mtp) REVERT: R 59 LEU cc_start: 0.8973 (tp) cc_final: 0.8507 (mp) REVERT: R 302 HIS cc_start: 0.5649 (m90) cc_final: 0.5359 (m-70) outliers start: 3 outliers final: 2 residues processed: 173 average time/residue: 0.2426 time to fit residues: 55.2575 Evaluate side-chains 152 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain G residue 17 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 0.0980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 259 GLN R 282 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8964 Z= 0.183 Angle : 0.543 5.776 12136 Z= 0.292 Chirality : 0.042 0.165 1377 Planarity : 0.004 0.049 1542 Dihedral : 5.051 58.336 1217 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.47 % Allowed : 12.42 % Favored : 86.11 % 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: 1.50 (0.25), residues: 1093 helix: 2.06 (0.25), residues: 407 sheet: 0.70 (0.32), residues: 264 loop : 0.24 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.003 0.001 HIS R 197 PHE 0.016 0.001 PHE R 136 TYR 0.013 0.001 TYR E 190 ARG 0.005 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8465 (mmtp) cc_final: 0.7884 (mttt) REVERT: B 164 THR cc_start: 0.9110 (p) cc_final: 0.8898 (p) REVERT: E 82 GLN cc_start: 0.8043 (tp40) cc_final: 0.7620 (tp-100) REVERT: E 164 SER cc_start: 0.8557 (t) cc_final: 0.8193 (p) REVERT: E 183 GLN cc_start: 0.7308 (mp10) cc_final: 0.6887 (mp10) REVERT: E 202 ARG cc_start: 0.8034 (mtm110) cc_final: 0.7797 (mtm110) REVERT: G 21 MET cc_start: 0.8569 (mmm) cc_final: 0.7761 (mmm) REVERT: R 59 LEU cc_start: 0.8851 (tp) cc_final: 0.8416 (mp) outliers start: 14 outliers final: 7 residues processed: 170 average time/residue: 0.2374 time to fit residues: 53.8153 Evaluate side-chains 158 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 270 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN A 371 ASN B 268 ASN R 197 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8964 Z= 0.292 Angle : 0.559 6.514 12136 Z= 0.298 Chirality : 0.044 0.183 1377 Planarity : 0.004 0.047 1542 Dihedral : 4.614 56.337 1214 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.32 % Allowed : 14.00 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1093 helix: 1.98 (0.25), residues: 407 sheet: 0.51 (0.31), residues: 270 loop : 0.18 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.002 PHE R 326 TYR 0.013 0.001 TYR E 190 ARG 0.005 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 158 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8361 (mmtp) cc_final: 0.7759 (mttt) REVERT: A 25 MET cc_start: 0.8247 (mtp) cc_final: 0.7985 (mtp) REVERT: A 216 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8451 (mtmm) REVERT: B 153 ASP cc_start: 0.8073 (t70) cc_final: 0.7845 (t70) REVERT: B 234 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.9069 (m-80) REVERT: E 43 LYS cc_start: 0.8347 (ptpt) cc_final: 0.7761 (ptpp) REVERT: E 164 SER cc_start: 0.8523 (t) cc_final: 0.8186 (p) REVERT: E 202 ARG cc_start: 0.8096 (mtm110) cc_final: 0.7810 (mtm110) REVERT: R 59 LEU cc_start: 0.8714 (tp) cc_final: 0.8317 (mp) REVERT: R 119 LEU cc_start: 0.7985 (mp) cc_final: 0.7315 (tt) outliers start: 22 outliers final: 16 residues processed: 171 average time/residue: 0.2346 time to fit residues: 53.5532 Evaluate side-chains 170 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 270 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8964 Z= 0.174 Angle : 0.501 5.402 12136 Z= 0.268 Chirality : 0.041 0.165 1377 Planarity : 0.003 0.043 1542 Dihedral : 4.424 56.059 1214 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.00 % Allowed : 15.79 % Favored : 82.21 % 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: 1.41 (0.25), residues: 1093 helix: 2.17 (0.25), residues: 405 sheet: 0.54 (0.31), residues: 264 loop : 0.08 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE R 193 TYR 0.012 0.001 TYR E 190 ARG 0.005 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8359 (mmtp) cc_final: 0.7811 (mttt) REVERT: A 25 MET cc_start: 0.8178 (mtp) cc_final: 0.7893 (mtp) REVERT: A 333 ARG cc_start: 0.8545 (ptp-170) cc_final: 0.8315 (mtm110) REVERT: B 68 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.9045 (ttt180) REVERT: B 153 ASP cc_start: 0.8007 (t70) cc_final: 0.7804 (t70) REVERT: B 234 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.9037 (m-80) REVERT: B 258 ASP cc_start: 0.8759 (t0) cc_final: 0.8522 (t0) REVERT: E 43 LYS cc_start: 0.8342 (ptpt) cc_final: 0.7756 (ptpp) REVERT: E 164 SER cc_start: 0.8478 (t) cc_final: 0.8139 (p) REVERT: E 202 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7670 (mtm110) REVERT: G 38 MET cc_start: 0.7600 (mtm) cc_final: 0.7202 (mtp) REVERT: R 119 LEU cc_start: 0.8003 (mp) cc_final: 0.7362 (tt) outliers start: 19 outliers final: 12 residues processed: 169 average time/residue: 0.2297 time to fit residues: 51.8576 Evaluate side-chains 165 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 270 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.0270 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN E 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8964 Z= 0.302 Angle : 0.555 6.874 12136 Z= 0.295 Chirality : 0.044 0.267 1377 Planarity : 0.004 0.042 1542 Dihedral : 4.511 55.912 1214 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.47 % Allowed : 15.37 % Favored : 81.16 % 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: 1.26 (0.25), residues: 1093 helix: 2.07 (0.25), residues: 405 sheet: 0.33 (0.31), residues: 270 loop : 0.06 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.002 PHE R 193 TYR 0.013 0.001 TYR E 103 ARG 0.004 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 150 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8345 (mmtp) cc_final: 0.7771 (mttt) REVERT: A 368 ASP cc_start: 0.6707 (m-30) cc_final: 0.6479 (m-30) REVERT: B 68 ARG cc_start: 0.9308 (OUTLIER) cc_final: 0.9061 (ttt180) REVERT: B 234 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.9007 (m-80) REVERT: B 251 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7761 (mpt180) REVERT: B 258 ASP cc_start: 0.8823 (t0) cc_final: 0.8533 (t0) REVERT: E 43 LYS cc_start: 0.8413 (ptpt) cc_final: 0.7834 (ptpp) REVERT: E 164 SER cc_start: 0.8505 (t) cc_final: 0.8182 (p) REVERT: E 171 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8377 (m110) REVERT: E 202 ARG cc_start: 0.8083 (mtm110) cc_final: 0.7686 (mtm110) REVERT: G 38 MET cc_start: 0.7568 (mtm) cc_final: 0.7200 (mtp) REVERT: R 119 LEU cc_start: 0.8044 (mp) cc_final: 0.7421 (tt) REVERT: R 327 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7989 (mp) outliers start: 33 outliers final: 18 residues processed: 173 average time/residue: 0.2544 time to fit residues: 58.0398 Evaluate side-chains 169 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 171 ASN Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 327 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8964 Z= 0.145 Angle : 0.497 5.774 12136 Z= 0.263 Chirality : 0.041 0.194 1377 Planarity : 0.003 0.039 1542 Dihedral : 4.317 56.025 1214 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.95 % Allowed : 15.47 % Favored : 81.58 % 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: 1.39 (0.25), residues: 1093 helix: 2.30 (0.25), residues: 404 sheet: 0.39 (0.30), residues: 270 loop : 0.00 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS A 357 PHE 0.012 0.001 PHE R 193 TYR 0.012 0.001 TYR E 190 ARG 0.008 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8336 (mmtp) cc_final: 0.7820 (mttt) REVERT: A 368 ASP cc_start: 0.6841 (m-30) cc_final: 0.6591 (m-30) REVERT: A 385 GLN cc_start: 0.8078 (tp40) cc_final: 0.7757 (tp40) REVERT: B 38 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7879 (m-30) REVERT: B 68 ARG cc_start: 0.9287 (OUTLIER) cc_final: 0.9021 (ttt180) REVERT: B 226 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7125 (mm-30) REVERT: B 234 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.9024 (m-80) REVERT: B 251 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8042 (mpt180) REVERT: E 43 LYS cc_start: 0.8375 (ptpt) cc_final: 0.7770 (ptpp) REVERT: E 164 SER cc_start: 0.8430 (t) cc_final: 0.8069 (p) REVERT: E 202 ARG cc_start: 0.8018 (mtm110) cc_final: 0.7629 (mtm110) REVERT: G 38 MET cc_start: 0.7490 (mtm) cc_final: 0.7129 (mtp) REVERT: R 119 LEU cc_start: 0.8051 (mp) cc_final: 0.7445 (tt) REVERT: R 246 ARG cc_start: 0.7597 (ttm-80) cc_final: 0.7370 (ttm170) outliers start: 28 outliers final: 13 residues processed: 175 average time/residue: 0.2499 time to fit residues: 58.5018 Evaluate side-chains 159 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 167 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 65 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN R 197 HIS ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8964 Z= 0.175 Angle : 0.498 5.372 12136 Z= 0.267 Chirality : 0.041 0.169 1377 Planarity : 0.003 0.036 1542 Dihedral : 4.245 55.927 1214 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.63 % Allowed : 16.42 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.25), residues: 1093 helix: 2.36 (0.25), residues: 404 sheet: 0.29 (0.30), residues: 273 loop : -0.00 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE R 193 TYR 0.011 0.001 TYR E 190 ARG 0.006 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8321 (mmtp) cc_final: 0.7815 (mttt) REVERT: A 333 ARG cc_start: 0.8407 (ptp-110) cc_final: 0.8195 (mtm110) REVERT: B 38 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: B 68 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.9048 (ttt180) REVERT: B 226 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: B 234 PHE cc_start: 0.9323 (OUTLIER) cc_final: 0.9023 (m-80) REVERT: B 251 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8156 (mpt180) REVERT: E 43 LYS cc_start: 0.8341 (ptpt) cc_final: 0.8016 (ptpp) REVERT: E 164 SER cc_start: 0.8415 (t) cc_final: 0.8050 (p) REVERT: E 202 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7601 (mtm110) REVERT: R 119 LEU cc_start: 0.7927 (mp) cc_final: 0.7307 (tt) REVERT: R 246 ARG cc_start: 0.7533 (ttm-80) cc_final: 0.7292 (ttm170) outliers start: 25 outliers final: 13 residues processed: 164 average time/residue: 0.2497 time to fit residues: 53.8214 Evaluate side-chains 160 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 217 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8964 Z= 0.165 Angle : 0.501 5.817 12136 Z= 0.268 Chirality : 0.041 0.167 1377 Planarity : 0.003 0.036 1542 Dihedral : 4.215 55.985 1214 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.84 % Allowed : 16.42 % Favored : 80.74 % 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: 1.41 (0.25), residues: 1093 helix: 2.39 (0.25), residues: 404 sheet: 0.30 (0.30), residues: 273 loop : 0.01 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.024 0.001 PHE R 168 TYR 0.011 0.001 TYR E 190 ARG 0.005 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8312 (mmtp) cc_final: 0.7812 (mttt) REVERT: A 333 ARG cc_start: 0.8460 (ptp-110) cc_final: 0.8233 (mtm110) REVERT: B 38 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7885 (m-30) REVERT: B 68 ARG cc_start: 0.9308 (OUTLIER) cc_final: 0.9058 (ttt180) REVERT: B 226 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: B 234 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.9012 (m-80) REVERT: B 251 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8144 (mpt180) REVERT: E 43 LYS cc_start: 0.8349 (ptpt) cc_final: 0.8026 (ptpp) REVERT: E 164 SER cc_start: 0.8396 (t) cc_final: 0.8035 (p) REVERT: E 202 ARG cc_start: 0.8051 (mtm110) cc_final: 0.7525 (mtm110) REVERT: G 38 MET cc_start: 0.7488 (mtm) cc_final: 0.7155 (mtp) REVERT: R 119 LEU cc_start: 0.7849 (mp) cc_final: 0.7341 (tt) outliers start: 27 outliers final: 18 residues processed: 164 average time/residue: 0.2421 time to fit residues: 52.8043 Evaluate side-chains 166 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 167 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8964 Z= 0.197 Angle : 0.512 6.444 12136 Z= 0.275 Chirality : 0.042 0.265 1377 Planarity : 0.003 0.036 1542 Dihedral : 4.216 56.059 1214 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.84 % Allowed : 16.63 % Favored : 80.53 % 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: 1.36 (0.25), residues: 1093 helix: 2.37 (0.25), residues: 404 sheet: 0.22 (0.30), residues: 274 loop : -0.00 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE R 168 TYR 0.011 0.001 TYR E 190 ARG 0.005 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8316 (mmtp) cc_final: 0.7823 (mttt) REVERT: A 333 ARG cc_start: 0.8456 (ptp-110) cc_final: 0.8234 (mtm110) REVERT: B 38 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7908 (m-30) REVERT: B 68 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.9060 (ttt180) REVERT: B 234 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.9030 (m-80) REVERT: B 251 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8076 (mpt180) REVERT: E 19 LYS cc_start: 0.8911 (tttp) cc_final: 0.8581 (tptt) REVERT: E 43 LYS cc_start: 0.8343 (ptpt) cc_final: 0.8016 (ptpp) REVERT: E 164 SER cc_start: 0.8397 (t) cc_final: 0.8040 (p) REVERT: E 202 ARG cc_start: 0.8069 (mtm110) cc_final: 0.7540 (mtm110) REVERT: G 38 MET cc_start: 0.7484 (mtm) cc_final: 0.7151 (mtp) REVERT: R 119 LEU cc_start: 0.7872 (mp) cc_final: 0.7338 (tt) outliers start: 27 outliers final: 21 residues processed: 164 average time/residue: 0.2738 time to fit residues: 59.8071 Evaluate side-chains 167 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 282 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 48 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 99 optimal weight: 0.0770 chunk 85 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 8964 Z= 0.135 Angle : 0.493 6.104 12136 Z= 0.264 Chirality : 0.041 0.226 1377 Planarity : 0.003 0.036 1542 Dihedral : 4.122 56.341 1214 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.63 % Allowed : 16.74 % Favored : 80.63 % 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: 1.53 (0.25), residues: 1093 helix: 2.58 (0.25), residues: 398 sheet: 0.30 (0.30), residues: 272 loop : 0.06 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.002 0.000 HIS A 357 PHE 0.017 0.001 PHE R 168 TYR 0.010 0.001 TYR E 190 ARG 0.004 0.000 ARG G 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8279 (mmtp) cc_final: 0.7799 (mttt) REVERT: B 38 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: B 68 ARG cc_start: 0.9282 (OUTLIER) cc_final: 0.9050 (ttt180) REVERT: B 226 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7132 (mm-30) REVERT: B 234 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8966 (m-80) REVERT: E 202 ARG cc_start: 0.8030 (mtm110) cc_final: 0.7502 (mtm110) REVERT: G 38 MET cc_start: 0.7401 (mtm) cc_final: 0.6617 (mtm) outliers start: 25 outliers final: 18 residues processed: 163 average time/residue: 0.2236 time to fit residues: 49.2144 Evaluate side-chains 164 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 282 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.161856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.119590 restraints weight = 10705.161| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.57 r_work: 0.3115 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8964 Z= 0.171 Angle : 0.504 6.220 12136 Z= 0.271 Chirality : 0.042 0.221 1377 Planarity : 0.003 0.038 1542 Dihedral : 4.138 56.314 1214 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.74 % Allowed : 16.95 % Favored : 80.32 % 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: 1.54 (0.25), residues: 1093 helix: 2.56 (0.25), residues: 398 sheet: 0.32 (0.30), residues: 272 loop : 0.09 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.002 0.001 HIS A 357 PHE 0.015 0.001 PHE R 168 TYR 0.010 0.001 TYR E 190 ARG 0.007 0.000 ARG A 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2191.33 seconds wall clock time: 39 minutes 48.11 seconds (2388.11 seconds total)