Starting phenix.real_space_refine on Mon Mar 11 16:56:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiq_36324/03_2024/8jiq_36324.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiq_36324/03_2024/8jiq_36324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiq_36324/03_2024/8jiq_36324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiq_36324/03_2024/8jiq_36324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiq_36324/03_2024/8jiq_36324.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiq_36324/03_2024/8jiq_36324.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 55 5.16 5 C 5527 2.51 5 N 1524 2.21 5 O 1601 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 327": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "R GLU 406": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8707 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1817 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2510 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 326} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 363 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "E" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 234 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2810 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 15, 'TRANS': 363} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 190 Time building chain proxies: 5.15, per 1000 atoms: 0.59 Number of scatterers: 8707 At special positions: 0 Unit cell: (92.13, 98.77, 161.02, 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 55 16.00 O 1601 8.00 N 1524 7.00 C 5527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.03 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.03 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: 3.19 Conformation dependent library (CDL) restraints added in 1.9 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 42.0% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 5.010A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 removed outlier: 4.417A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.770A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 4.038A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.513A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.796A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.563A pdb=" N ALA C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 2 through 29 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.660A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 28 through 50 removed outlier: 4.306A pdb=" N GLN R 42 " --> pdb=" O LEU R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 89 removed outlier: 3.514A pdb=" N HIS R 89 " --> pdb=" O PRO R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 131 removed outlier: 4.278A pdb=" N GLU R 129 " --> pdb=" O GLU R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 164 removed outlier: 4.256A pdb=" N MET R 137 " --> pdb=" O GLU R 133 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL R 147 " --> pdb=" O VAL R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 203 removed outlier: 3.619A pdb=" N TYR R 202 " --> pdb=" O LEU R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 255 removed outlier: 3.719A pdb=" N VAL R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA R 222 " --> pdb=" O ASP R 218 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY R 223 " --> pdb=" O GLY R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 277 removed outlier: 3.991A pdb=" N ALA R 274 " --> pdb=" O ILE R 270 " (cutoff:3.500A) Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 278 through 290 Processing helix chain 'R' and resid 301 through 335 removed outlier: 3.975A pdb=" N ILE R 306 " --> pdb=" O GLY R 302 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU R 307 " --> pdb=" O PHE R 303 " (cutoff:3.500A) Proline residue: R 310 - end of helix removed outlier: 3.674A pdb=" N ALA R 331 " --> pdb=" O GLN R 327 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA R 335 " --> pdb=" O ALA R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 353 Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 361 through 368 removed outlier: 3.588A pdb=" N PHE R 365 " --> pdb=" O HIS R 361 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 402 removed outlier: 4.601A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE R 402 " --> pdb=" O VAL R 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 418 removed outlier: 4.098A pdb=" N GLU R 410 " --> pdb=" O GLU R 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.764A pdb=" N PHE A 222 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.666A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.105A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.222A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.794A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.758A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.680A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.950A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.721A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.832A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 57 through 58 removed outlier: 3.675A pdb=" N THR R 71 " --> pdb=" O CYS R 58 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 77 through 80 449 hydrogen bonds defined for protein. 1260 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: 2.46 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1509 1.32 - 1.44: 2410 1.44 - 1.57: 4897 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8892 Sorted by residual: bond pdb=" C ARG R 199 " pdb=" O ARG R 199 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.17e-02 7.31e+03 9.53e+00 bond pdb=" C GLY R 101 " pdb=" N PRO R 102 " ideal model delta sigma weight residual 1.335 1.374 -0.039 1.28e-02 6.10e+03 9.33e+00 bond pdb=" CA ARG R 116 " pdb=" C ARG R 116 " ideal model delta sigma weight residual 1.528 1.511 0.017 8.80e-03 1.29e+04 3.59e+00 bond pdb=" CA ASP R 208 " pdb=" C ASP R 208 " ideal model delta sigma weight residual 1.522 1.497 0.026 1.40e-02 5.10e+03 3.32e+00 bond pdb=" C THR R 71 " pdb=" O THR R 71 " ideal model delta sigma weight residual 1.238 1.215 0.023 1.28e-02 6.10e+03 3.30e+00 ... (remaining 8887 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.95: 207 106.95 - 114.40: 5160 114.40 - 121.85: 4789 121.85 - 129.30: 1829 129.30 - 136.75: 75 Bond angle restraints: 12060 Sorted by residual: angle pdb=" N ARG R 201 " pdb=" CA ARG R 201 " pdb=" C ARG R 201 " ideal model delta sigma weight residual 113.97 100.83 13.14 1.28e+00 6.10e-01 1.05e+02 angle pdb=" N ASP R 208 " pdb=" CA ASP R 208 " pdb=" C ASP R 208 " ideal model delta sigma weight residual 113.17 102.84 10.33 1.26e+00 6.30e-01 6.73e+01 angle pdb=" C THR R 71 " pdb=" N PRO R 72 " pdb=" CA PRO R 72 " ideal model delta sigma weight residual 119.85 113.94 5.91 1.01e+00 9.80e-01 3.43e+01 angle pdb=" C GLY R 101 " pdb=" N PRO R 102 " pdb=" CA PRO R 102 " ideal model delta sigma weight residual 119.28 113.44 5.84 1.10e+00 8.26e-01 2.82e+01 angle pdb=" CA GLN R 113 " pdb=" C GLN R 113 " pdb=" N PRO R 114 " ideal model delta sigma weight residual 120.79 116.76 4.03 9.70e-01 1.06e+00 1.72e+01 ... (remaining 12055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 4625 17.44 - 34.87: 496 34.87 - 52.31: 94 52.31 - 69.75: 27 69.75 - 87.18: 10 Dihedral angle restraints: 5252 sinusoidal: 1969 harmonic: 3283 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -37.12 -48.88 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS R 224 " pdb=" SG CYS R 224 " pdb=" SG CYS R 294 " pdb=" CB CYS R 294 " ideal model delta sinusoidal sigma weight residual 93.00 137.50 -44.50 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CB CYS R 81 " pdb=" SG CYS R 81 " pdb=" SG CYS R 121 " pdb=" CB CYS R 121 " ideal model delta sinusoidal sigma weight residual 93.00 53.66 39.34 1 1.00e+01 1.00e-02 2.18e+01 ... (remaining 5249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 993 0.044 - 0.088: 271 0.088 - 0.132: 78 0.132 - 0.175: 7 0.175 - 0.219: 4 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CA ASN R 74 " pdb=" N ASN R 74 " pdb=" C ASN R 74 " pdb=" CB ASN R 74 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASP R 209 " pdb=" N ASP R 209 " pdb=" C ASP R 209 " pdb=" CB ASP R 209 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ARG R 201 " pdb=" N ARG R 201 " pdb=" C ARG R 201 " pdb=" CB ARG R 201 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.19 2.00e-01 2.50e+01 9.49e-01 ... (remaining 1350 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 241 " -0.021 2.00e-02 2.50e+03 1.96e-02 9.61e+00 pdb=" CG TRP R 241 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP R 241 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP R 241 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 241 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP R 241 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 241 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 241 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 241 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP R 241 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 194 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C ILE R 194 " -0.033 2.00e-02 2.50e+03 pdb=" O ILE R 194 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP R 195 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 199 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C ARG R 199 " 0.033 2.00e-02 2.50e+03 pdb=" O ARG R 199 " -0.012 2.00e-02 2.50e+03 pdb=" N THR R 200 " -0.011 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 836 2.74 - 3.28: 8826 3.28 - 3.82: 14736 3.82 - 4.36: 16765 4.36 - 4.90: 29215 Nonbonded interactions: 70378 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.202 2.440 nonbonded pdb=" OD2 ASP A 240 " pdb=" NZ LYS B 57 " model vdw 2.247 2.520 nonbonded pdb=" OG1 THR R 172 " pdb=" OH TYR R 248 " model vdw 2.252 2.440 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.292 2.440 ... (remaining 70373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 3.880 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.140 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 0.042 8892 Z= 0.214 Angle : 0.637 13.140 12060 Z= 0.388 Chirality : 0.044 0.219 1353 Planarity : 0.003 0.035 1546 Dihedral : 15.174 87.182 3113 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.14 % Favored : 95.50 % Rotamer: Outliers : 2.47 % Allowed : 1.35 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1112 helix: 1.46 (0.27), residues: 402 sheet: -0.75 (0.35), residues: 224 loop : -0.87 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP R 241 HIS 0.005 0.001 HIS R 45 PHE 0.009 0.001 PHE A 212 TYR 0.016 0.001 TYR R 145 ARG 0.004 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 0.981 Fit side-chains REVERT: R 376 THR cc_start: 0.4124 (OUTLIER) cc_final: 0.3439 (p) REVERT: R 378 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.4137 (ptt90) outliers start: 22 outliers final: 0 residues processed: 171 average time/residue: 0.2194 time to fit residues: 50.9820 Evaluate side-chains 125 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain R residue 378 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9980 chunk 82 optimal weight: 20.0000 chunk 45 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 8892 Z= 0.156 Angle : 0.508 6.546 12060 Z= 0.265 Chirality : 0.041 0.157 1353 Planarity : 0.003 0.034 1546 Dihedral : 4.127 50.702 1226 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.33 % Favored : 96.49 % Rotamer: Outliers : 1.23 % Allowed : 11.90 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1112 helix: 1.68 (0.26), residues: 406 sheet: -0.61 (0.35), residues: 220 loop : -0.73 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 241 HIS 0.002 0.000 HIS B 183 PHE 0.026 0.001 PHE E 22 TYR 0.018 0.001 TYR R 145 ARG 0.002 0.000 ARG R 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: B 130 GLU cc_start: 0.7279 (mp0) cc_final: 0.7036 (mp0) REVERT: E 11 SER cc_start: 0.8698 (t) cc_final: 0.8434 (p) REVERT: R 355 ILE cc_start: 0.9095 (mt) cc_final: 0.8792 (mt) outliers start: 11 outliers final: 7 residues processed: 132 average time/residue: 0.2142 time to fit residues: 39.0534 Evaluate side-chains 124 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 378 ARG Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8892 Z= 0.271 Angle : 0.541 6.070 12060 Z= 0.283 Chirality : 0.042 0.154 1353 Planarity : 0.003 0.034 1546 Dihedral : 4.293 59.400 1225 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.46 % Allowed : 13.80 % 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: 0.23 (0.26), residues: 1112 helix: 1.73 (0.26), residues: 406 sheet: -0.81 (0.34), residues: 226 loop : -0.68 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 241 HIS 0.003 0.001 HIS B 183 PHE 0.018 0.001 PHE N 108 TYR 0.018 0.001 TYR B 111 ARG 0.003 0.000 ARG R 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.042 Fit side-chains REVERT: E 11 SER cc_start: 0.8742 (t) cc_final: 0.8441 (p) REVERT: R 338 MET cc_start: 0.5875 (mpp) cc_final: 0.5643 (mpp) REVERT: R 355 ILE cc_start: 0.9123 (mt) cc_final: 0.8761 (mt) REVERT: R 378 ARG cc_start: 0.6233 (OUTLIER) cc_final: 0.4394 (ppt170) outliers start: 13 outliers final: 7 residues processed: 139 average time/residue: 0.2043 time to fit residues: 39.6263 Evaluate side-chains 130 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain R residue 378 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 94 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8892 Z= 0.145 Angle : 0.483 6.505 12060 Z= 0.252 Chirality : 0.040 0.152 1353 Planarity : 0.003 0.034 1546 Dihedral : 3.956 52.130 1225 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.91 % Allowed : 15.26 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1112 helix: 1.91 (0.26), residues: 406 sheet: -0.73 (0.34), residues: 220 loop : -0.59 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 241 HIS 0.002 0.000 HIS R 44 PHE 0.011 0.001 PHE A 212 TYR 0.018 0.001 TYR A 360 ARG 0.001 0.000 ARG R 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.094 Fit side-chains REVERT: E 11 SER cc_start: 0.8690 (t) cc_final: 0.8410 (p) REVERT: R 355 ILE cc_start: 0.9050 (mt) cc_final: 0.8667 (mt) REVERT: R 378 ARG cc_start: 0.6121 (OUTLIER) cc_final: 0.4270 (ppt170) outliers start: 17 outliers final: 9 residues processed: 148 average time/residue: 0.2082 time to fit residues: 42.9600 Evaluate side-chains 130 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain R residue 378 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 0.0170 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 8892 Z= 0.150 Angle : 0.491 6.657 12060 Z= 0.255 Chirality : 0.041 0.227 1353 Planarity : 0.003 0.044 1546 Dihedral : 3.836 47.174 1225 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.02 % Allowed : 17.06 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1112 helix: 1.94 (0.26), residues: 406 sheet: -0.68 (0.34), residues: 220 loop : -0.55 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP R 241 HIS 0.002 0.000 HIS R 44 PHE 0.011 0.001 PHE N 108 TYR 0.018 0.001 TYR A 360 ARG 0.010 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.017 Fit side-chains REVERT: B 130 GLU cc_start: 0.7348 (mp0) cc_final: 0.7046 (mp0) REVERT: E 11 SER cc_start: 0.8690 (t) cc_final: 0.8405 (p) REVERT: R 355 ILE cc_start: 0.8994 (mt) cc_final: 0.8647 (mt) REVERT: R 378 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.4269 (ppt170) outliers start: 18 outliers final: 11 residues processed: 141 average time/residue: 0.1961 time to fit residues: 39.1695 Evaluate side-chains 129 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain R residue 378 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8892 Z= 0.175 Angle : 0.502 8.197 12060 Z= 0.259 Chirality : 0.041 0.204 1353 Planarity : 0.003 0.034 1546 Dihedral : 3.803 40.480 1225 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.36 % Allowed : 18.07 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1112 helix: 1.95 (0.27), residues: 407 sheet: -0.66 (0.34), residues: 220 loop : -0.55 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP R 241 HIS 0.002 0.000 HIS R 44 PHE 0.012 0.001 PHE N 108 TYR 0.018 0.001 TYR A 360 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.022 Fit side-chains REVERT: B 130 GLU cc_start: 0.7350 (mp0) cc_final: 0.7068 (mp0) REVERT: E 11 SER cc_start: 0.8677 (t) cc_final: 0.8408 (p) REVERT: N 73 ASP cc_start: 0.8895 (t70) cc_final: 0.8532 (t0) REVERT: R 201 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7801 (tpt-90) REVERT: R 355 ILE cc_start: 0.8972 (mt) cc_final: 0.8633 (mt) REVERT: R 378 ARG cc_start: 0.6131 (OUTLIER) cc_final: 0.4328 (ppt170) outliers start: 21 outliers final: 12 residues processed: 141 average time/residue: 0.1999 time to fit residues: 39.3801 Evaluate side-chains 132 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 201 ARG Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain R residue 378 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 chunk 77 optimal weight: 0.0370 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8892 Z= 0.135 Angle : 0.500 10.509 12060 Z= 0.256 Chirality : 0.041 0.212 1353 Planarity : 0.003 0.034 1546 Dihedral : 3.657 34.842 1225 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.68 % Allowed : 18.97 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1112 helix: 1.97 (0.27), residues: 407 sheet: -0.52 (0.35), residues: 218 loop : -0.55 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP R 241 HIS 0.002 0.000 HIS R 361 PHE 0.011 0.001 PHE R 312 TYR 0.017 0.001 TYR A 360 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.107 Fit side-chains REVERT: B 130 GLU cc_start: 0.7321 (mp0) cc_final: 0.7045 (mp0) REVERT: E 11 SER cc_start: 0.8684 (t) cc_final: 0.8433 (p) REVERT: N 73 ASP cc_start: 0.8891 (t70) cc_final: 0.8525 (t0) REVERT: R 290 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7864 (mm-30) REVERT: R 355 ILE cc_start: 0.8876 (mt) cc_final: 0.8549 (mt) REVERT: R 378 ARG cc_start: 0.6049 (OUTLIER) cc_final: 0.4333 (ppt170) outliers start: 15 outliers final: 11 residues processed: 140 average time/residue: 0.1940 time to fit residues: 38.3768 Evaluate side-chains 133 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain R residue 378 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 0.0970 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 20.0000 chunk 95 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8892 Z= 0.144 Angle : 0.503 10.785 12060 Z= 0.255 Chirality : 0.041 0.164 1353 Planarity : 0.003 0.035 1546 Dihedral : 3.598 30.417 1225 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.35 % Allowed : 20.20 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1112 helix: 2.00 (0.27), residues: 407 sheet: -0.51 (0.35), residues: 218 loop : -0.57 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 241 HIS 0.002 0.000 HIS R 361 PHE 0.011 0.001 PHE R 312 TYR 0.017 0.001 TYR A 360 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.016 Fit side-chains REVERT: B 130 GLU cc_start: 0.7290 (mp0) cc_final: 0.7040 (mp0) REVERT: E 11 SER cc_start: 0.8696 (t) cc_final: 0.8429 (p) REVERT: N 73 ASP cc_start: 0.8879 (t70) cc_final: 0.8498 (t0) REVERT: R 290 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7885 (mm-30) REVERT: R 355 ILE cc_start: 0.8866 (mt) cc_final: 0.8544 (mt) outliers start: 12 outliers final: 11 residues processed: 131 average time/residue: 0.1994 time to fit residues: 37.0432 Evaluate side-chains 130 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 376 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 76 optimal weight: 50.0000 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8892 Z= 0.187 Angle : 0.534 12.148 12060 Z= 0.268 Chirality : 0.041 0.159 1353 Planarity : 0.003 0.035 1546 Dihedral : 3.621 20.423 1221 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.02 % Allowed : 20.65 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1112 helix: 1.99 (0.27), residues: 407 sheet: -0.60 (0.34), residues: 220 loop : -0.54 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 241 HIS 0.002 0.000 HIS R 361 PHE 0.015 0.001 PHE N 108 TYR 0.016 0.001 TYR A 360 ARG 0.004 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.126 Fit side-chains REVERT: B 130 GLU cc_start: 0.7320 (mp0) cc_final: 0.7079 (mp0) REVERT: E 11 SER cc_start: 0.8715 (t) cc_final: 0.8436 (p) REVERT: N 73 ASP cc_start: 0.8876 (t70) cc_final: 0.8479 (t0) REVERT: R 290 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7920 (mm-30) REVERT: R 355 ILE cc_start: 0.8906 (mt) cc_final: 0.8574 (mt) outliers start: 18 outliers final: 14 residues processed: 132 average time/residue: 0.1954 time to fit residues: 36.9968 Evaluate side-chains 133 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 338 MET Chi-restraints excluded: chain R residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 0.1980 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8892 Z= 0.209 Angle : 0.554 11.964 12060 Z= 0.277 Chirality : 0.041 0.156 1353 Planarity : 0.003 0.035 1546 Dihedral : 3.702 22.610 1221 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.80 % Allowed : 21.10 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1112 helix: 1.96 (0.26), residues: 407 sheet: -0.61 (0.35), residues: 220 loop : -0.51 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP R 241 HIS 0.002 0.001 HIS R 44 PHE 0.017 0.001 PHE N 108 TYR 0.017 0.001 TYR A 360 ARG 0.004 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.964 Fit side-chains REVERT: B 130 GLU cc_start: 0.7359 (mp0) cc_final: 0.7065 (mp0) REVERT: E 11 SER cc_start: 0.8705 (t) cc_final: 0.8437 (p) REVERT: N 73 ASP cc_start: 0.8877 (t70) cc_final: 0.8485 (t0) REVERT: R 290 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7946 (mm-30) REVERT: R 355 ILE cc_start: 0.8921 (mt) cc_final: 0.8551 (mt) outliers start: 16 outliers final: 14 residues processed: 132 average time/residue: 0.1903 time to fit residues: 35.7789 Evaluate side-chains 134 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 338 MET Chi-restraints excluded: chain R residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 50.0000 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 4 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** 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 = 0.4003 r_free = 0.4003 target = 0.124330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.086543 restraints weight = 17422.014| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.42 r_work: 0.3234 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8892 Z= 0.175 Angle : 0.545 11.903 12060 Z= 0.272 Chirality : 0.041 0.157 1353 Planarity : 0.003 0.035 1546 Dihedral : 3.636 20.629 1221 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.46 % Allowed : 21.55 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1112 helix: 1.98 (0.26), residues: 407 sheet: -0.57 (0.34), residues: 219 loop : -0.50 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP R 241 HIS 0.002 0.000 HIS R 44 PHE 0.014 0.001 PHE N 108 TYR 0.017 0.001 TYR A 360 ARG 0.004 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2055.99 seconds wall clock time: 38 minutes 7.30 seconds (2287.30 seconds total)