Starting phenix.real_space_refine on Tue May 7 21:10:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoj_38531/05_2024/8xoj_38531.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoj_38531/05_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_38531/05_2024/8xoj_38531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoj_38531/05_2024/8xoj_38531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoj_38531/05_2024/8xoj_38531.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoj_38531/05_2024/8xoj_38531.pdb" } 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 Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "R GLU 115": "OE1" <-> "OE2" Residue "R GLU 218": "OE1" <-> "OE2" Residue "R GLU 275": "OE1" <-> "OE2" Residue "R TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 4.54, per 1000 atoms: 0.52 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 - 3.50 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 Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.6 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: 0.97 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: 2.45 Time building geometry restraints manager: 3.51 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: 100.31 - 107.06: 204 107.06 - 113.81: 5004 113.81 - 120.55: 3527 120.55 - 127.30: 3308 127.30 - 134.05: 93 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 2.440 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 2.440 nonbonded pdb=" OD2 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.335 2.440 nonbonded pdb=" O THR B 34 " pdb=" NZ LYS B 301 " model vdw 2.352 2.520 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.240 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.370 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.610 ------------------------------------------------------------------------------- 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 : 1.054 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: 0.2517 time to fit residues: 57.3911 Evaluate side-chains 152 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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: 5.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 B 340 ASN R 197 HIS R 282 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8964 Z= 0.259 Angle : 0.564 6.250 12136 Z= 0.302 Chirality : 0.043 0.172 1377 Planarity : 0.004 0.048 1542 Dihedral : 5.104 56.265 1217 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.00 % Allowed : 13.26 % Favored : 84.74 % 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: 1.38 (0.25), residues: 1093 helix: 1.99 (0.25), residues: 406 sheet: 0.71 (0.31), residues: 263 loop : 0.07 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.003 0.001 HIS R 282 PHE 0.016 0.002 PHE R 326 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 181 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8466 (mmtp) cc_final: 0.7863 (mttt) REVERT: E 82 GLN cc_start: 0.8056 (tp40) cc_final: 0.7620 (tp-100) REVERT: E 164 SER cc_start: 0.8535 (t) cc_final: 0.8245 (p) REVERT: E 183 GLN cc_start: 0.7294 (mp10) cc_final: 0.6920 (mp10) REVERT: E 202 ARG cc_start: 0.7925 (mtm110) cc_final: 0.7554 (mtm110) REVERT: G 21 MET cc_start: 0.8598 (mmm) cc_final: 0.7944 (mmm) REVERT: R 59 LEU cc_start: 0.8855 (tp) cc_final: 0.8422 (mp) outliers start: 19 outliers final: 8 residues processed: 172 average time/residue: 0.2498 time to fit residues: 57.2944 Evaluate side-chains 155 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain R residue 163 MET 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: 3.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 371 ASN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8964 Z= 0.294 Angle : 0.553 6.014 12136 Z= 0.294 Chirality : 0.043 0.180 1377 Planarity : 0.004 0.046 1542 Dihedral : 4.621 54.381 1214 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.74 % Allowed : 13.89 % Favored : 83.37 % 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: 1.37 (0.25), residues: 1093 helix: 2.03 (0.25), residues: 405 sheet: 0.66 (0.32), residues: 261 loop : 0.07 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.015 0.002 PHE R 326 TYR 0.012 0.001 TYR E 190 ARG 0.007 0.000 ARG G 62 *********************** 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 177 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8365 (mmtp) cc_final: 0.7741 (mttt) REVERT: B 68 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.9042 (ttt180) REVERT: B 234 PHE cc_start: 0.9353 (OUTLIER) cc_final: 0.9060 (m-80) REVERT: E 43 LYS cc_start: 0.8345 (ptpt) cc_final: 0.7757 (ptpp) REVERT: E 164 SER cc_start: 0.8602 (t) cc_final: 0.8279 (p) REVERT: E 183 GLN cc_start: 0.7347 (mp10) cc_final: 0.6967 (mp10) REVERT: E 202 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7450 (mtm110) REVERT: G 62 ARG cc_start: 0.6646 (mmm160) cc_final: 0.5566 (mtm-85) REVERT: R 59 LEU cc_start: 0.8716 (tp) cc_final: 0.8320 (mp) REVERT: R 119 LEU cc_start: 0.7972 (mp) cc_final: 0.7321 (tt) REVERT: R 327 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8001 (mp) outliers start: 26 outliers final: 19 residues processed: 165 average time/residue: 0.2587 time to fit residues: 56.3363 Evaluate side-chains 169 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 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 68 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 163 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8964 Z= 0.208 Angle : 0.503 5.607 12136 Z= 0.268 Chirality : 0.041 0.168 1377 Planarity : 0.003 0.044 1542 Dihedral : 4.431 53.614 1214 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.58 % Allowed : 14.42 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.25), residues: 1093 helix: 2.13 (0.25), residues: 405 sheet: 0.66 (0.32), residues: 256 loop : -0.01 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS G 44 PHE 0.012 0.001 PHE R 193 TYR 0.012 0.001 TYR E 103 ARG 0.006 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 196 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 162 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8355 (mmtp) cc_final: 0.7776 (mttt) REVERT: B 68 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.9045 (ttt180) REVERT: B 153 ASP cc_start: 0.8067 (t70) cc_final: 0.7858 (t70) REVERT: B 214 ARG cc_start: 0.7827 (mtt-85) cc_final: 0.7590 (mtt-85) REVERT: B 226 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7194 (mm-30) REVERT: B 234 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.9071 (m-80) REVERT: E 43 LYS cc_start: 0.8362 (ptpt) cc_final: 0.7748 (ptpp) REVERT: E 164 SER cc_start: 0.8522 (t) cc_final: 0.8205 (p) REVERT: G 38 MET cc_start: 0.7648 (mtm) cc_final: 0.7246 (mtp) REVERT: R 59 LEU cc_start: 0.8727 (tp) cc_final: 0.8308 (mp) REVERT: R 119 LEU cc_start: 0.8058 (mp) cc_final: 0.7440 (tt) REVERT: R 125 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: R 327 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7938 (mp) outliers start: 34 outliers final: 20 residues processed: 185 average time/residue: 0.2422 time to fit residues: 59.9678 Evaluate side-chains 173 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 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 173 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU 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 125 ASP Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 327 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 0.0970 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 chunk 89 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.2982 ------------------------------------------------------------------------------- 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 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8964 Z= 0.336 Angle : 0.558 6.490 12136 Z= 0.296 Chirality : 0.044 0.279 1377 Planarity : 0.004 0.042 1542 Dihedral : 4.535 52.680 1214 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.68 % Allowed : 15.37 % 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: 1.23 (0.25), residues: 1093 helix: 2.00 (0.25), residues: 406 sheet: 0.52 (0.31), residues: 264 loop : -0.08 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.004 0.001 HIS G 44 PHE 0.016 0.002 PHE R 326 TYR 0.013 0.001 TYR E 103 ARG 0.008 0.000 ARG A 280 *********************** 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 187 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 152 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8344 (mmtp) cc_final: 0.7763 (mttt) REVERT: B 68 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.9050 (ttt180) REVERT: B 234 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.9032 (m-80) REVERT: E 43 LYS cc_start: 0.8395 (ptpt) cc_final: 0.7832 (ptpp) REVERT: E 164 SER cc_start: 0.8554 (t) cc_final: 0.8236 (p) REVERT: G 62 ARG cc_start: 0.6609 (mmm160) cc_final: 0.5608 (mtm-85) REVERT: R 59 LEU cc_start: 0.8675 (tp) cc_final: 0.8312 (mp) REVERT: R 119 LEU cc_start: 0.8047 (mp) cc_final: 0.7432 (tt) REVERT: R 246 ARG cc_start: 0.7645 (ttm-80) cc_final: 0.7368 (ttm170) REVERT: R 327 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7981 (mp) outliers start: 35 outliers final: 22 residues processed: 175 average time/residue: 0.2466 time to fit residues: 57.3036 Evaluate side-chains 170 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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 81 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 235 SER 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: 0.8980 chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.0050 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 0.0570 chunk 48 optimal weight: 0.0050 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.3526 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8964 Z= 0.127 Angle : 0.470 5.703 12136 Z= 0.251 Chirality : 0.040 0.195 1377 Planarity : 0.003 0.037 1542 Dihedral : 4.198 52.472 1214 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.53 % Allowed : 16.42 % Favored : 81.05 % 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: 2.31 (0.25), residues: 404 sheet: 0.60 (0.31), residues: 258 loop : -0.13 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.002 0.001 HIS A 220 PHE 0.012 0.001 PHE R 193 TYR 0.010 0.001 TYR E 190 ARG 0.005 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 179 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8299 (mmtp) cc_final: 0.7743 (mttt) REVERT: A 333 ARG cc_start: 0.8485 (ptp-110) cc_final: 0.8276 (mtm110) REVERT: A 368 ASP cc_start: 0.6897 (m-30) cc_final: 0.6613 (m-30) REVERT: B 226 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7154 (mm-30) REVERT: B 234 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.9037 (m-80) REVERT: B 251 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8203 (mpt180) REVERT: E 164 SER cc_start: 0.8477 (t) cc_final: 0.8136 (p) REVERT: G 38 MET cc_start: 0.7525 (mtm) cc_final: 0.7165 (mtp) REVERT: R 119 LEU cc_start: 0.8075 (mp) cc_final: 0.7486 (tt) outliers start: 24 outliers final: 13 residues processed: 175 average time/residue: 0.2402 time to fit residues: 56.7975 Evaluate side-chains 161 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS 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 71 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 235 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8964 Z= 0.195 Angle : 0.508 7.968 12136 Z= 0.266 Chirality : 0.041 0.199 1377 Planarity : 0.003 0.036 1542 Dihedral : 4.194 52.498 1214 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.74 % Allowed : 17.05 % Favored : 80.21 % 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: 2.37 (0.25), residues: 404 sheet: 0.55 (0.31), residues: 263 loop : -0.17 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE R 193 TYR 0.011 0.001 TYR E 103 ARG 0.008 0.000 ARG G 62 *********************** 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 169 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8291 (mmtp) cc_final: 0.7751 (mttt) REVERT: A 333 ARG cc_start: 0.8480 (ptp-110) cc_final: 0.8277 (mtm110) REVERT: B 68 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.9018 (ttt180) REVERT: B 234 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8969 (m-80) REVERT: B 251 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8158 (mpt180) REVERT: E 164 SER cc_start: 0.8470 (t) cc_final: 0.8124 (p) REVERT: G 38 MET cc_start: 0.7502 (mtm) cc_final: 0.7151 (mtp) REVERT: R 119 LEU cc_start: 0.8083 (mp) cc_final: 0.7478 (tt) outliers start: 26 outliers final: 17 residues processed: 163 average time/residue: 0.2521 time to fit residues: 54.3962 Evaluate side-chains 157 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 211 LYS 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 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 266 HIS 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 152 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 282 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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** R 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2280 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= 0.182 Angle : 0.500 6.113 12136 Z= 0.265 Chirality : 0.042 0.265 1377 Planarity : 0.003 0.036 1542 Dihedral : 4.171 52.437 1214 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.74 % Allowed : 17.37 % Favored : 79.89 % 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: 1.38 (0.25), residues: 1093 helix: 2.37 (0.25), residues: 404 sheet: 0.49 (0.31), residues: 263 loop : -0.18 (0.30), residues: 426 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 0.014 0.001 PHE R 193 TYR 0.011 0.001 TYR E 103 ARG 0.009 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 167 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8300 (mmtp) cc_final: 0.7766 (mttt) REVERT: B 68 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.9029 (ttt180) REVERT: B 234 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.8967 (m-80) REVERT: B 251 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8150 (mpt180) REVERT: E 154 SER cc_start: 0.8089 (p) cc_final: 0.7797 (m) REVERT: E 164 SER cc_start: 0.8458 (t) cc_final: 0.8105 (p) REVERT: G 38 MET cc_start: 0.7486 (mtm) cc_final: 0.7140 (mtp) REVERT: G 62 ARG cc_start: 0.6396 (mmm160) cc_final: 0.5509 (mtm-85) REVERT: R 119 LEU cc_start: 0.8092 (mp) cc_final: 0.7501 (tt) outliers start: 26 outliers final: 21 residues processed: 163 average time/residue: 0.2304 time to fit residues: 50.5817 Evaluate side-chains 162 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 211 LYS 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 32 GLN 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 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 ASN 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 152 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 282 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2307 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= 0.179 Angle : 0.501 6.140 12136 Z= 0.265 Chirality : 0.041 0.233 1377 Planarity : 0.003 0.038 1542 Dihedral : 4.149 52.396 1214 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.84 % Allowed : 17.47 % Favored : 79.68 % 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: 1.46 (0.25), residues: 1093 helix: 2.50 (0.25), residues: 398 sheet: 0.44 (0.31), residues: 263 loop : -0.09 (0.30), residues: 432 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 0.014 0.001 PHE R 193 TYR 0.011 0.001 TYR E 103 ARG 0.008 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 167 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8282 (mmtp) cc_final: 0.7751 (mttt) REVERT: B 68 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.9022 (ttt180) REVERT: B 234 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.8966 (m-80) REVERT: B 251 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8196 (mpt180) REVERT: E 154 SER cc_start: 0.8084 (p) cc_final: 0.7806 (m) REVERT: E 164 SER cc_start: 0.8445 (t) cc_final: 0.8098 (p) REVERT: G 38 MET cc_start: 0.7467 (mtm) cc_final: 0.7141 (mtp) REVERT: G 62 ARG cc_start: 0.6307 (mmm160) cc_final: 0.5484 (mtm-85) REVERT: R 119 LEU cc_start: 0.7955 (mp) cc_final: 0.7340 (tt) outliers start: 27 outliers final: 23 residues processed: 162 average time/residue: 0.2373 time to fit residues: 52.0682 Evaluate side-chains 163 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 211 LYS 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 32 GLN 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 100 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 270 VAL 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: 0.7980 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8964 Z= 0.171 Angle : 0.497 5.776 12136 Z= 0.266 Chirality : 0.041 0.216 1377 Planarity : 0.003 0.036 1542 Dihedral : 4.106 52.251 1214 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.95 % Allowed : 17.47 % Favored : 79.58 % 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: 1.45 (0.25), residues: 1093 helix: 2.50 (0.25), residues: 398 sheet: 0.38 (0.31), residues: 265 loop : -0.08 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS A 357 PHE 0.014 0.001 PHE R 193 TYR 0.010 0.001 TYR E 103 ARG 0.007 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 174 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8292 (mmtp) cc_final: 0.7764 (mttt) REVERT: A 333 ARG cc_start: 0.8440 (ptp-110) cc_final: 0.8227 (mtm110) REVERT: B 68 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.9031 (ttt180) REVERT: B 197 ARG cc_start: 0.7793 (mtp-110) cc_final: 0.7432 (mmm160) REVERT: B 214 ARG cc_start: 0.7878 (mtt-85) cc_final: 0.7357 (mtt-85) REVERT: B 234 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.8963 (m-80) REVERT: B 251 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8184 (mpt180) REVERT: E 18 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7178 (ttt90) REVERT: E 19 LYS cc_start: 0.8931 (tptt) cc_final: 0.8701 (tptt) REVERT: E 154 SER cc_start: 0.8077 (p) cc_final: 0.7817 (m) REVERT: E 164 SER cc_start: 0.8426 (t) cc_final: 0.8074 (p) REVERT: E 202 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7548 (mtm110) REVERT: G 38 MET cc_start: 0.7478 (mtm) cc_final: 0.7148 (mtp) REVERT: G 62 ARG cc_start: 0.6378 (mmm160) cc_final: 0.5540 (mtm-85) REVERT: R 119 LEU cc_start: 0.7943 (mp) cc_final: 0.7429 (tt) outliers start: 28 outliers final: 24 residues processed: 167 average time/residue: 0.2362 time to fit residues: 53.5367 Evaluate side-chains 167 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 139 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER 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 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 71 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 ASN 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 18 ARG Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 270 VAL 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: 1.9990 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.0370 chunk 75 optimal weight: 8.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.161210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111659 restraints weight = 10676.622| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.49 r_work: 0.3097 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8964 Z= 0.171 Angle : 0.500 5.826 12136 Z= 0.267 Chirality : 0.041 0.203 1377 Planarity : 0.003 0.037 1542 Dihedral : 4.097 52.186 1214 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.05 % Allowed : 17.68 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1093 helix: 2.54 (0.25), residues: 398 sheet: 0.34 (0.30), residues: 264 loop : -0.10 (0.30), residues: 431 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 0.014 0.001 PHE R 193 TYR 0.010 0.001 TYR E 103 ARG 0.008 0.000 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2242.45 seconds wall clock time: 41 minutes 38.30 seconds (2498.30 seconds total)