Starting phenix.real_space_refine on Thu Mar 14 22:06:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3q_0336/03_2024/6n3q_0336.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3q_0336/03_2024/6n3q_0336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3q_0336/03_2024/6n3q_0336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3q_0336/03_2024/6n3q_0336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3q_0336/03_2024/6n3q_0336.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3q_0336/03_2024/6n3q_0336.pdb" } resolution = 3.68 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= 0.010 sd= 0.066 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 38 5.16 5 C 6495 2.51 5 N 1678 2.21 5 O 1720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 186": "NH1" <-> "NH2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 185": "NH1" <-> "NH2" 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: 9931 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 2960 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 3 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 435 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 229 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 3779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3779 Classifications: {'peptide': 487} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 28, 'TRANS': 458} Chain breaks: 4 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 17, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 124 Chain: "E" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1095 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 132} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1433 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 182} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 5.35, per 1000 atoms: 0.54 Number of scatterers: 9931 At special positions: 0 Unit cell: (105.56, 126.44, 127.6, 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 38 16.00 O 1720 8.00 N 1678 7.00 C 6495 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: 3.87 Conformation dependent library (CDL) restraints added in 1.8 seconds 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2432 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 67.2% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 28 through 48 removed outlier: 3.806A pdb=" N ILE A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 99 Processing helix chain 'A' and resid 107 through 137 Processing helix chain 'A' and resid 148 through 173 Processing helix chain 'A' and resid 179 through 199 Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.545A pdb=" N ALA A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 243 through 261 Processing helix chain 'A' and resid 291 through 310 removed outlier: 3.803A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 385 removed outlier: 4.202A pdb=" N GLU A 382 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 408 through 440 Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 444 through 466 Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.883A pdb=" N LYS C 38 " --> pdb=" O GLN C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 79 removed outlier: 3.839A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix Processing helix chain 'B' and resid 53 through 82 Processing helix chain 'D' and resid 13 through 36 removed outlier: 3.705A pdb=" N ILE D 18 " --> pdb=" O TRP D 14 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Proline residue: D 28 - end of helix Processing helix chain 'D' and resid 58 through 67 removed outlier: 3.877A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 Processing helix chain 'D' and resid 94 through 113 removed outlier: 3.646A pdb=" N ASN D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 249 removed outlier: 4.449A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) Proline residue: D 236 - end of helix removed outlier: 3.541A pdb=" N TYR D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.777A pdb=" N ASN D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 285 Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.750A pdb=" N LYS D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.739A pdb=" N LYS D 304 " --> pdb=" O THR D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 343 removed outlier: 4.606A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 362 removed outlier: 3.672A pdb=" N ALA D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 372 removed outlier: 3.708A pdb=" N ILE D 371 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 Processing helix chain 'D' and resid 391 through 396 Processing helix chain 'D' and resid 401 through 408 removed outlier: 4.301A pdb=" N GLU D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 406 " --> pdb=" O LYS D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 424 removed outlier: 3.686A pdb=" N HIS D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 485 Processing helix chain 'D' and resid 487 through 493 removed outlier: 3.998A pdb=" N MET D 491 " --> pdb=" O PRO D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 545 Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.591A pdb=" N TYR E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 124 removed outlier: 3.746A pdb=" N LEU E 96 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU E 97 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 127 through 156 removed outlier: 3.543A pdb=" N TRP E 131 " --> pdb=" O GLY E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 182 removed outlier: 4.177A pdb=" N MET E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'F' and resid 21 through 42 removed outlier: 3.526A pdb=" N ASN F 27 " --> pdb=" O SER F 23 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 71 Processing helix chain 'F' and resid 73 through 91 Processing helix chain 'F' and resid 97 through 120 Proline residue: F 103 - end of helix removed outlier: 3.712A pdb=" N ILE F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 136 removed outlier: 3.646A pdb=" N ALA F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 153 removed outlier: 3.551A pdb=" N PHE F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 168 removed outlier: 3.592A pdb=" N ALA F 161 " --> pdb=" O GLU F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 192 removed outlier: 3.812A pdb=" N ARG F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA F 178 " --> pdb=" O MET F 174 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 211 removed outlier: 3.832A pdb=" N ASN A 204 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER D 205 " --> pdb=" O ASN A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 281 removed outlier: 3.627A pdb=" N GLY A 279 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 281 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 267 " --> pdb=" O TYR A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 430 through 436 removed outlier: 4.910A pdb=" N LYS D 432 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D 454 " --> pdb=" O LYS D 432 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP D 434 " --> pdb=" O SER D 452 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.863A pdb=" N GLY D 584 " --> pdb=" O VAL D 610 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL D 610 " --> pdb=" O GLY D 584 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE D 586 " --> pdb=" O MET D 608 " (cutoff:3.500A) 631 hydrogen bonds defined for protein. 1866 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: 2.53 Time building geometry restraints manager: 4.21 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: 2909 1.34 - 1.46: 1541 1.46 - 1.57: 5620 1.57 - 1.69: 0 1.69 - 1.81: 59 Bond restraints: 10129 Sorted by residual: bond pdb=" C LEU D 235 " pdb=" N PRO D 236 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.20e-02 6.94e+03 1.26e+01 bond pdb=" C THR A 291 " pdb=" N PRO A 292 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.34e+00 bond pdb=" CB CYS E 167 " pdb=" SG CYS E 167 " ideal model delta sigma weight residual 1.808 1.740 0.068 3.30e-02 9.18e+02 4.29e+00 bond pdb=" CG1 ILE D 280 " pdb=" CD1 ILE D 280 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.68e+00 bond pdb=" C ALA E 114 " pdb=" N PRO E 115 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.45e+00 ... (remaining 10124 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.17: 251 106.17 - 113.15: 5617 113.15 - 120.13: 3545 120.13 - 127.11: 4216 127.11 - 134.09: 109 Bond angle restraints: 13738 Sorted by residual: angle pdb=" C THR A 98 " pdb=" N GLN A 99 " pdb=" CA GLN A 99 " ideal model delta sigma weight residual 122.74 129.32 -6.58 1.44e+00 4.82e-01 2.09e+01 angle pdb=" C ILE A 417 " pdb=" N ILE A 418 " pdb=" CA ILE A 418 " ideal model delta sigma weight residual 120.33 123.96 -3.63 8.00e-01 1.56e+00 2.05e+01 angle pdb=" C ILE C 79 " pdb=" N VAL C 80 " pdb=" CA VAL C 80 " ideal model delta sigma weight residual 121.70 128.70 -7.00 1.80e+00 3.09e-01 1.51e+01 angle pdb=" CA GLY A 178 " pdb=" C GLY A 178 " pdb=" O GLY A 178 " ideal model delta sigma weight residual 122.22 119.78 2.44 6.50e-01 2.37e+00 1.41e+01 angle pdb=" N GLN A 99 " pdb=" CA GLN A 99 " pdb=" C GLN A 99 " ideal model delta sigma weight residual 112.58 108.19 4.39 1.22e+00 6.72e-01 1.30e+01 ... (remaining 13733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.28: 5657 15.28 - 30.55: 318 30.55 - 45.83: 93 45.83 - 61.11: 2 61.11 - 76.38: 6 Dihedral angle restraints: 6076 sinusoidal: 2332 harmonic: 3744 Sorted by residual: dihedral pdb=" CA LEU F 137 " pdb=" C LEU F 137 " pdb=" N ILE F 138 " pdb=" CA ILE F 138 " ideal model delta harmonic sigma weight residual -180.00 -143.35 -36.65 0 5.00e+00 4.00e-02 5.37e+01 dihedral pdb=" CA PHE D 501 " pdb=" C PHE D 501 " pdb=" N ALA D 502 " pdb=" CA ALA D 502 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA PRO D 463 " pdb=" C PRO D 463 " pdb=" N LEU D 464 " pdb=" CA LEU D 464 " ideal model delta harmonic sigma weight residual 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 6073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1062 0.044 - 0.089: 418 0.089 - 0.133: 126 0.133 - 0.177: 28 0.177 - 0.222: 9 Chirality restraints: 1643 Sorted by residual: chirality pdb=" CB ILE A 49 " pdb=" CA ILE A 49 " pdb=" CG1 ILE A 49 " pdb=" CG2 ILE A 49 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LEU D 235 " pdb=" N LEU D 235 " pdb=" C LEU D 235 " pdb=" CB LEU D 235 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CB THR A 453 " pdb=" CA THR A 453 " pdb=" OG1 THR A 453 " pdb=" CG2 THR A 453 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 1640 not shown) Planarity restraints: 1703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 137 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C LEU F 137 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU F 137 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE F 138 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO F 48 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 141 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO A 142 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.036 5.00e-02 4.00e+02 ... (remaining 1700 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2967 2.83 - 3.34: 9609 3.34 - 3.86: 16151 3.86 - 4.38: 16894 4.38 - 4.90: 29885 Nonbonded interactions: 75506 Sorted by model distance: nonbonded pdb=" O SER D 512 " pdb=" OG1 THR D 595 " model vdw 2.308 2.440 nonbonded pdb=" O GLY D 27 " pdb=" OG1 THR D 30 " model vdw 2.309 2.440 nonbonded pdb=" OD1 ASN A 204 " pdb=" OG SER D 205 " model vdw 2.318 2.440 nonbonded pdb=" O LYS E 79 " pdb=" OG SER E 82 " model vdw 2.320 2.440 nonbonded pdb=" O PHE A 198 " pdb=" OH TYR C 66 " model vdw 2.334 2.440 ... (remaining 75501 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 group one per residue 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: 4.030 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.920 Find NCS groups from input model: 0.250 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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 : 0.006 0.068 10129 Z= 0.359 Angle : 1.032 10.714 13738 Z= 0.547 Chirality : 0.053 0.222 1643 Planarity : 0.008 0.060 1703 Dihedral : 10.912 76.383 3644 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.67 % Allowed : 5.47 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.32 (0.18), residues: 1264 helix: -1.92 (0.13), residues: 817 sheet: -2.55 (0.56), residues: 64 loop : -2.34 (0.27), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 242 HIS 0.008 0.002 HIS C 72 PHE 0.029 0.003 PHE D 290 TYR 0.026 0.002 TYR A 175 ARG 0.017 0.001 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 342 time to evaluate : 1.142 Fit side-chains REVERT: A 30 ASN cc_start: 0.8289 (t0) cc_final: 0.8071 (t0) REVERT: A 45 ILE cc_start: 0.8985 (tt) cc_final: 0.8781 (tt) REVERT: A 162 LEU cc_start: 0.9112 (tm) cc_final: 0.8889 (tp) REVERT: A 168 ASP cc_start: 0.8373 (t0) cc_final: 0.7936 (t0) REVERT: A 188 ASN cc_start: 0.8384 (t0) cc_final: 0.8125 (t0) REVERT: A 212 GLU cc_start: 0.7937 (tt0) cc_final: 0.7262 (mt-10) REVERT: A 244 MET cc_start: 0.7318 (tmm) cc_final: 0.7072 (ttp) REVERT: A 376 PHE cc_start: 0.7766 (m-80) cc_final: 0.7215 (m-10) REVERT: A 424 PHE cc_start: 0.8019 (t80) cc_final: 0.7808 (t80) REVERT: C 30 ARG cc_start: 0.7156 (ttm-80) cc_final: 0.6643 (mmm-85) REVERT: C 38 LYS cc_start: 0.8650 (mtmp) cc_final: 0.8237 (mttp) REVERT: C 52 LYS cc_start: 0.7668 (ttmt) cc_final: 0.7269 (ttmt) REVERT: D 16 SER cc_start: 0.8921 (m) cc_final: 0.8609 (t) REVERT: D 100 TRP cc_start: 0.7541 (m100) cc_final: 0.7200 (m100) REVERT: D 222 LEU cc_start: 0.8266 (tp) cc_final: 0.7523 (mm) REVERT: D 272 SER cc_start: 0.8517 (m) cc_final: 0.8164 (p) REVERT: D 282 HIS cc_start: 0.8258 (t70) cc_final: 0.7903 (t70) REVERT: D 444 THR cc_start: 0.9188 (t) cc_final: 0.8892 (p) REVERT: E 146 LYS cc_start: 0.8398 (ttmt) cc_final: 0.8169 (tptt) REVERT: E 147 ASP cc_start: 0.8891 (t0) cc_final: 0.8658 (t0) REVERT: E 148 THR cc_start: 0.9156 (p) cc_final: 0.8801 (p) REVERT: E 150 GLN cc_start: 0.7871 (tt0) cc_final: 0.7044 (tm-30) REVERT: E 165 MET cc_start: 0.7251 (tpt) cc_final: 0.6980 (tpp) REVERT: F 10 SER cc_start: 0.8787 (t) cc_final: 0.8429 (p) REVERT: F 49 GLN cc_start: 0.8762 (pp30) cc_final: 0.8520 (pp30) REVERT: F 91 LYS cc_start: 0.8858 (mmtp) cc_final: 0.8625 (mmmm) REVERT: F 108 MET cc_start: 0.8502 (mtm) cc_final: 0.8089 (mtt) REVERT: F 112 LYS cc_start: 0.9223 (tttt) cc_final: 0.8940 (tttp) outliers start: 7 outliers final: 1 residues processed: 346 average time/residue: 0.2344 time to fit residues: 109.2725 Evaluate side-chains 196 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 0.0070 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 192 GLN A 204 ASN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 ASN D 494 GLN D 539 ASN ** D 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 ASN ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 GLN F 80 ASN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10129 Z= 0.210 Angle : 0.647 8.315 13738 Z= 0.323 Chirality : 0.041 0.249 1643 Planarity : 0.005 0.047 1703 Dihedral : 4.875 22.381 1364 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.03 % Allowed : 13.53 % Favored : 82.44 % 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: -0.78 (0.22), residues: 1264 helix: 0.24 (0.17), residues: 817 sheet: -1.89 (0.58), residues: 69 loop : -1.76 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 35 HIS 0.008 0.001 HIS D 288 PHE 0.031 0.002 PHE A 16 TYR 0.023 0.002 TYR A 237 ARG 0.008 0.001 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 233 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: A 30 ASN cc_start: 0.8357 (t0) cc_final: 0.8153 (t0) REVERT: A 41 LEU cc_start: 0.8446 (tp) cc_final: 0.8174 (tt) REVERT: A 188 ASN cc_start: 0.8439 (t0) cc_final: 0.8035 (t0) REVERT: A 424 PHE cc_start: 0.8066 (t80) cc_final: 0.7834 (t80) REVERT: A 447 SER cc_start: 0.8685 (m) cc_final: 0.8402 (p) REVERT: C 30 ARG cc_start: 0.7290 (ttm-80) cc_final: 0.6743 (mmm-85) REVERT: C 38 LYS cc_start: 0.8588 (mtmp) cc_final: 0.8101 (mttp) REVERT: C 52 LYS cc_start: 0.7492 (ttmt) cc_final: 0.7177 (ttmt) REVERT: D 100 TRP cc_start: 0.7343 (m100) cc_final: 0.7010 (m100) REVERT: D 222 LEU cc_start: 0.8238 (tp) cc_final: 0.7676 (mm) REVERT: D 272 SER cc_start: 0.8606 (m) cc_final: 0.8376 (p) REVERT: D 288 HIS cc_start: 0.7944 (t70) cc_final: 0.7701 (t70) REVERT: D 444 THR cc_start: 0.9156 (t) cc_final: 0.8955 (p) REVERT: E 146 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7881 (tptp) REVERT: E 147 ASP cc_start: 0.8935 (t0) cc_final: 0.8670 (t0) REVERT: E 150 GLN cc_start: 0.7542 (tt0) cc_final: 0.6946 (tm-30) REVERT: E 153 GLU cc_start: 0.7862 (tp30) cc_final: 0.7187 (tt0) REVERT: E 165 MET cc_start: 0.7244 (tpt) cc_final: 0.6981 (tpp) REVERT: F 49 GLN cc_start: 0.8868 (pp30) cc_final: 0.8522 (pp30) REVERT: F 71 GLN cc_start: 0.9065 (mt0) cc_final: 0.8038 (tm-30) REVERT: F 86 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8578 (tp30) REVERT: F 90 ARG cc_start: 0.8247 (tpp80) cc_final: 0.8004 (tpp80) REVERT: F 91 LYS cc_start: 0.8871 (mmtp) cc_final: 0.8556 (mmmm) REVERT: F 108 MET cc_start: 0.8518 (mtm) cc_final: 0.7987 (mtt) REVERT: F 124 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7889 (tm-30) REVERT: F 152 LYS cc_start: 0.8959 (tppt) cc_final: 0.8197 (tmtt) outliers start: 42 outliers final: 25 residues processed: 263 average time/residue: 0.1900 time to fit residues: 71.8187 Evaluate side-chains 217 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 181 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 92 optimal weight: 0.4980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN E 98 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10129 Z= 0.365 Angle : 0.714 9.364 13738 Z= 0.357 Chirality : 0.043 0.181 1643 Planarity : 0.004 0.047 1703 Dihedral : 4.754 21.588 1363 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 7.20 % Allowed : 14.88 % Favored : 77.93 % 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: 0.05 (0.23), residues: 1264 helix: 0.93 (0.18), residues: 816 sheet: -1.55 (0.61), residues: 69 loop : -1.54 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 14 HIS 0.007 0.002 HIS D 288 PHE 0.021 0.002 PHE D 74 TYR 0.024 0.002 TYR F 190 ARG 0.005 0.001 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 202 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 30 ASN cc_start: 0.8408 (t0) cc_final: 0.8193 (t0) REVERT: A 188 ASN cc_start: 0.8484 (t0) cc_final: 0.8077 (t0) REVERT: A 212 GLU cc_start: 0.7994 (tt0) cc_final: 0.7353 (mt-10) REVERT: A 244 MET cc_start: 0.8095 (ttp) cc_final: 0.7481 (ttp) REVERT: A 376 PHE cc_start: 0.7919 (m-80) cc_final: 0.7018 (m-10) REVERT: A 382 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7186 (mm-30) REVERT: A 400 MET cc_start: 0.7673 (mtm) cc_final: 0.7466 (mtt) REVERT: A 447 SER cc_start: 0.9021 (m) cc_final: 0.8455 (p) REVERT: C 30 ARG cc_start: 0.7314 (ttm-80) cc_final: 0.6819 (mmm-85) REVERT: C 38 LYS cc_start: 0.8652 (mtmp) cc_final: 0.8434 (mtmm) REVERT: C 46 GLU cc_start: 0.8688 (tp30) cc_final: 0.8454 (tp30) REVERT: D 66 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7350 (m-10) REVERT: D 100 TRP cc_start: 0.7442 (m100) cc_final: 0.7199 (m100) REVERT: D 222 LEU cc_start: 0.8374 (tp) cc_final: 0.7791 (mm) REVERT: D 272 SER cc_start: 0.8739 (m) cc_final: 0.8476 (p) REVERT: E 146 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7898 (tptp) REVERT: E 147 ASP cc_start: 0.9007 (t0) cc_final: 0.8735 (t0) REVERT: E 150 GLN cc_start: 0.7834 (tt0) cc_final: 0.7137 (tm-30) REVERT: E 165 MET cc_start: 0.7348 (tpt) cc_final: 0.7071 (tpp) REVERT: F 49 GLN cc_start: 0.8793 (pp30) cc_final: 0.8537 (pp30) REVERT: F 71 GLN cc_start: 0.9130 (mt0) cc_final: 0.8040 (tm-30) REVERT: F 90 ARG cc_start: 0.8303 (tpp80) cc_final: 0.7943 (mmt90) REVERT: F 91 LYS cc_start: 0.8926 (mmtp) cc_final: 0.8642 (mmmm) REVERT: F 107 PHE cc_start: 0.8394 (t80) cc_final: 0.7920 (t80) REVERT: F 124 GLU cc_start: 0.8606 (tm-30) cc_final: 0.7953 (tm-30) REVERT: F 152 LYS cc_start: 0.9166 (tppt) cc_final: 0.8365 (tmtt) outliers start: 75 outliers final: 45 residues processed: 256 average time/residue: 0.1781 time to fit residues: 66.5615 Evaluate side-chains 225 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 179 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 181 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10129 Z= 0.219 Angle : 0.641 10.232 13738 Z= 0.311 Chirality : 0.041 0.189 1643 Planarity : 0.004 0.044 1703 Dihedral : 4.458 20.343 1363 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.95 % Allowed : 18.33 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.24), residues: 1264 helix: 1.34 (0.18), residues: 815 sheet: -1.43 (0.60), residues: 73 loop : -1.34 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 35 HIS 0.003 0.001 HIS D 288 PHE 0.016 0.001 PHE D 290 TYR 0.020 0.001 TYR A 237 ARG 0.003 0.000 ARG E 179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 209 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 30 ASN cc_start: 0.8382 (t0) cc_final: 0.8135 (t0) REVERT: A 156 GLN cc_start: 0.7391 (tp-100) cc_final: 0.7082 (mm-40) REVERT: A 188 ASN cc_start: 0.8455 (t0) cc_final: 0.8073 (t0) REVERT: A 212 GLU cc_start: 0.7941 (tt0) cc_final: 0.7311 (mt-10) REVERT: A 244 MET cc_start: 0.7928 (ttp) cc_final: 0.7392 (ttp) REVERT: A 376 PHE cc_start: 0.7841 (m-80) cc_final: 0.6935 (m-10) REVERT: A 400 MET cc_start: 0.7571 (mtm) cc_final: 0.7360 (mtt) REVERT: A 447 SER cc_start: 0.9006 (m) cc_final: 0.8566 (p) REVERT: C 30 ARG cc_start: 0.7339 (ttm-80) cc_final: 0.6815 (mmm-85) REVERT: C 31 GLU cc_start: 0.8804 (tp30) cc_final: 0.8565 (tp30) REVERT: C 38 LYS cc_start: 0.8644 (mtmp) cc_final: 0.8110 (mttp) REVERT: C 40 LYS cc_start: 0.7458 (tmtt) cc_final: 0.6800 (tmtt) REVERT: C 46 GLU cc_start: 0.8635 (tp30) cc_final: 0.8259 (tp30) REVERT: D 66 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7010 (m-10) REVERT: D 100 TRP cc_start: 0.7488 (m100) cc_final: 0.7189 (m100) REVERT: D 222 LEU cc_start: 0.8374 (tp) cc_final: 0.7821 (mm) REVERT: D 272 SER cc_start: 0.8775 (m) cc_final: 0.8449 (p) REVERT: E 130 TYR cc_start: 0.8635 (t80) cc_final: 0.8348 (t80) REVERT: E 146 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7793 (tptp) REVERT: E 150 GLN cc_start: 0.7686 (tt0) cc_final: 0.7055 (tm-30) REVERT: E 165 MET cc_start: 0.7229 (tpt) cc_final: 0.6972 (tpp) REVERT: F 25 GLU cc_start: 0.9146 (tp30) cc_final: 0.8814 (tp30) REVERT: F 49 GLN cc_start: 0.8693 (pp30) cc_final: 0.8476 (pp30) REVERT: F 71 GLN cc_start: 0.9101 (mt0) cc_final: 0.8079 (tm-30) REVERT: F 90 ARG cc_start: 0.8285 (tpp80) cc_final: 0.7975 (mmt90) REVERT: F 91 LYS cc_start: 0.8869 (mmtp) cc_final: 0.8581 (mmmm) REVERT: F 107 PHE cc_start: 0.8402 (t80) cc_final: 0.7924 (t80) REVERT: F 124 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8056 (tm-30) REVERT: F 152 LYS cc_start: 0.9080 (tppt) cc_final: 0.8305 (tmtt) outliers start: 62 outliers final: 40 residues processed: 255 average time/residue: 0.2081 time to fit residues: 74.3769 Evaluate side-chains 221 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 180 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 181 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 104 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10129 Z= 0.212 Angle : 0.646 15.129 13738 Z= 0.305 Chirality : 0.040 0.201 1643 Planarity : 0.004 0.042 1703 Dihedral : 4.288 19.965 1363 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.76 % Allowed : 20.83 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.24), residues: 1264 helix: 1.53 (0.18), residues: 815 sheet: -1.39 (0.60), residues: 73 loop : -1.27 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 35 HIS 0.002 0.001 HIS D 288 PHE 0.013 0.001 PHE D 290 TYR 0.019 0.001 TYR A 237 ARG 0.007 0.001 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 190 time to evaluate : 1.139 Fit side-chains REVERT: A 30 ASN cc_start: 0.8396 (t0) cc_final: 0.8156 (t0) REVERT: A 149 ILE cc_start: 0.7980 (mt) cc_final: 0.7737 (tt) REVERT: A 188 ASN cc_start: 0.8420 (t0) cc_final: 0.8036 (t0) REVERT: A 244 MET cc_start: 0.7950 (ttp) cc_final: 0.7382 (ttp) REVERT: A 376 PHE cc_start: 0.7915 (m-80) cc_final: 0.7035 (m-10) REVERT: A 400 MET cc_start: 0.7551 (mtm) cc_final: 0.7337 (mtt) REVERT: A 447 SER cc_start: 0.9005 (m) cc_final: 0.8316 (p) REVERT: C 30 ARG cc_start: 0.7343 (ttm-80) cc_final: 0.6810 (mmm-85) REVERT: C 31 GLU cc_start: 0.8768 (tp30) cc_final: 0.8528 (tp30) REVERT: C 38 LYS cc_start: 0.8671 (mtmp) cc_final: 0.8125 (mttp) REVERT: C 40 LYS cc_start: 0.7706 (tmtt) cc_final: 0.7431 (tmtt) REVERT: C 46 GLU cc_start: 0.8685 (tp30) cc_final: 0.8378 (tp30) REVERT: D 66 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7166 (m-10) REVERT: D 100 TRP cc_start: 0.7466 (m100) cc_final: 0.7173 (m100) REVERT: D 272 SER cc_start: 0.8762 (m) cc_final: 0.8438 (p) REVERT: E 146 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7764 (tptp) REVERT: E 150 GLN cc_start: 0.7687 (tt0) cc_final: 0.7072 (tm-30) REVERT: E 165 MET cc_start: 0.7241 (tpt) cc_final: 0.6977 (tpp) REVERT: F 25 GLU cc_start: 0.9187 (tp30) cc_final: 0.8837 (tp30) REVERT: F 49 GLN cc_start: 0.8622 (pp30) cc_final: 0.8391 (pp30) REVERT: F 71 GLN cc_start: 0.9085 (mt0) cc_final: 0.8076 (tm-30) REVERT: F 90 ARG cc_start: 0.8249 (tpp80) cc_final: 0.7955 (mmt90) REVERT: F 91 LYS cc_start: 0.8877 (mmtp) cc_final: 0.8605 (mmmm) REVERT: F 107 PHE cc_start: 0.8363 (t80) cc_final: 0.7944 (t80) REVERT: F 124 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8005 (tm-30) REVERT: F 152 LYS cc_start: 0.9102 (tppt) cc_final: 0.8317 (tmtt) REVERT: F 182 GLU cc_start: 0.8154 (tp30) cc_final: 0.7854 (tm-30) outliers start: 60 outliers final: 43 residues processed: 234 average time/residue: 0.1838 time to fit residues: 62.9161 Evaluate side-chains 221 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 177 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 181 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.2980 chunk 64 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10129 Z= 0.185 Angle : 0.635 13.887 13738 Z= 0.297 Chirality : 0.040 0.206 1643 Planarity : 0.004 0.041 1703 Dihedral : 4.175 19.187 1363 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.89 % Allowed : 22.46 % Favored : 72.65 % 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: 1.00 (0.24), residues: 1264 helix: 1.71 (0.18), residues: 816 sheet: -1.24 (0.62), residues: 73 loop : -1.27 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 35 HIS 0.002 0.001 HIS F 122 PHE 0.028 0.001 PHE F 62 TYR 0.018 0.001 TYR A 237 ARG 0.004 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 193 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8660 (mp) cc_final: 0.8297 (tt) REVERT: A 149 ILE cc_start: 0.7953 (mt) cc_final: 0.7707 (tt) REVERT: A 188 ASN cc_start: 0.8351 (t0) cc_final: 0.7958 (t0) REVERT: A 212 GLU cc_start: 0.7871 (tt0) cc_final: 0.7277 (mt-10) REVERT: A 244 MET cc_start: 0.7907 (ttp) cc_final: 0.7251 (ttp) REVERT: A 376 PHE cc_start: 0.7851 (m-80) cc_final: 0.7058 (m-10) REVERT: A 400 MET cc_start: 0.7523 (mtm) cc_final: 0.7304 (mtt) REVERT: A 447 SER cc_start: 0.8717 (m) cc_final: 0.8353 (p) REVERT: C 30 ARG cc_start: 0.7338 (ttm-80) cc_final: 0.6806 (mmm-85) REVERT: C 31 GLU cc_start: 0.8720 (tp30) cc_final: 0.8465 (tp30) REVERT: C 38 LYS cc_start: 0.8657 (mtmp) cc_final: 0.8114 (mttp) REVERT: C 40 LYS cc_start: 0.7684 (tmtt) cc_final: 0.7462 (tmtt) REVERT: C 46 GLU cc_start: 0.8699 (tp30) cc_final: 0.8380 (tp30) REVERT: D 66 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: D 100 TRP cc_start: 0.7536 (m100) cc_final: 0.7163 (m100) REVERT: D 272 SER cc_start: 0.8715 (m) cc_final: 0.8396 (p) REVERT: E 146 LYS cc_start: 0.8263 (ttmt) cc_final: 0.7771 (tptp) REVERT: E 150 GLN cc_start: 0.7678 (tt0) cc_final: 0.7083 (tm-30) REVERT: E 165 MET cc_start: 0.7237 (tpt) cc_final: 0.6989 (tpp) REVERT: F 25 GLU cc_start: 0.9180 (tp30) cc_final: 0.8848 (tp30) REVERT: F 49 GLN cc_start: 0.8588 (pp30) cc_final: 0.8368 (pp30) REVERT: F 71 GLN cc_start: 0.9081 (mt0) cc_final: 0.8092 (tm-30) REVERT: F 79 LYS cc_start: 0.9036 (tppt) cc_final: 0.8701 (tptp) REVERT: F 90 ARG cc_start: 0.8368 (tpp80) cc_final: 0.8069 (mmt90) REVERT: F 91 LYS cc_start: 0.8795 (mmtp) cc_final: 0.8519 (mmmm) REVERT: F 107 PHE cc_start: 0.8370 (t80) cc_final: 0.7994 (t80) REVERT: F 124 GLU cc_start: 0.8677 (tm-30) cc_final: 0.7893 (tm-30) REVERT: F 152 LYS cc_start: 0.9060 (tppt) cc_final: 0.8180 (tptt) REVERT: F 182 GLU cc_start: 0.8075 (tp30) cc_final: 0.7870 (tm-30) outliers start: 51 outliers final: 40 residues processed: 233 average time/residue: 0.1907 time to fit residues: 64.4631 Evaluate side-chains 217 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 176 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 167 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10129 Z= 0.206 Angle : 0.638 13.102 13738 Z= 0.300 Chirality : 0.040 0.216 1643 Planarity : 0.004 0.041 1703 Dihedral : 4.087 19.468 1363 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.76 % Allowed : 22.07 % Favored : 72.17 % 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: 1.07 (0.25), residues: 1264 helix: 1.73 (0.18), residues: 821 sheet: -1.11 (0.63), residues: 73 loop : -1.24 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 35 HIS 0.002 0.001 HIS F 122 PHE 0.011 0.001 PHE D 481 TYR 0.015 0.001 TYR A 237 ARG 0.005 0.000 ARG F 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 180 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 30 ASN cc_start: 0.8316 (t0) cc_final: 0.7951 (t0) REVERT: A 100 LEU cc_start: 0.8650 (mp) cc_final: 0.8273 (tt) REVERT: A 149 ILE cc_start: 0.7963 (mt) cc_final: 0.7726 (tt) REVERT: A 188 ASN cc_start: 0.8328 (t0) cc_final: 0.7870 (t0) REVERT: A 244 MET cc_start: 0.7920 (ttp) cc_final: 0.7350 (ttp) REVERT: A 376 PHE cc_start: 0.7875 (m-80) cc_final: 0.7139 (m-10) REVERT: A 400 MET cc_start: 0.7556 (mtm) cc_final: 0.7314 (mtt) REVERT: C 30 ARG cc_start: 0.7351 (ttm-80) cc_final: 0.6814 (mmm-85) REVERT: C 31 GLU cc_start: 0.8736 (tp30) cc_final: 0.8486 (tp30) REVERT: C 38 LYS cc_start: 0.8660 (mtmp) cc_final: 0.8102 (mttp) REVERT: C 46 GLU cc_start: 0.8728 (tp30) cc_final: 0.8406 (tp30) REVERT: D 66 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7329 (m-10) REVERT: D 100 TRP cc_start: 0.7557 (m100) cc_final: 0.7168 (m100) REVERT: D 272 SER cc_start: 0.8733 (m) cc_final: 0.8411 (p) REVERT: D 336 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8334 (tt) REVERT: D 474 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7856 (p0) REVERT: E 146 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7777 (tptp) REVERT: E 150 GLN cc_start: 0.7753 (tt0) cc_final: 0.7122 (tm-30) REVERT: E 165 MET cc_start: 0.7225 (tpt) cc_final: 0.6959 (tpp) REVERT: F 25 GLU cc_start: 0.9204 (tp30) cc_final: 0.8825 (tp30) REVERT: F 49 GLN cc_start: 0.8564 (pp30) cc_final: 0.8341 (pp30) REVERT: F 63 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8626 (mp0) REVERT: F 71 GLN cc_start: 0.9075 (mt0) cc_final: 0.8072 (tm-30) REVERT: F 91 LYS cc_start: 0.8802 (mmtp) cc_final: 0.8553 (mmmm) REVERT: F 107 PHE cc_start: 0.8316 (t80) cc_final: 0.8041 (t80) REVERT: F 124 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8119 (tm-30) REVERT: F 152 LYS cc_start: 0.9053 (tppt) cc_final: 0.8163 (tptt) REVERT: F 157 GLU cc_start: 0.8142 (tp30) cc_final: 0.7917 (tp30) REVERT: F 182 GLU cc_start: 0.8128 (tp30) cc_final: 0.7924 (tm-30) outliers start: 60 outliers final: 47 residues processed: 227 average time/residue: 0.1875 time to fit residues: 62.0727 Evaluate side-chains 224 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 174 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 474 ASN Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 181 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 0.0570 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 77 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 0.0870 chunk 96 optimal weight: 0.6980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 HIS ** D 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10129 Z= 0.174 Angle : 0.652 12.590 13738 Z= 0.304 Chirality : 0.040 0.231 1643 Planarity : 0.004 0.040 1703 Dihedral : 4.011 18.287 1363 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.09 % Allowed : 23.61 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1264 helix: 1.83 (0.18), residues: 823 sheet: -1.07 (0.59), residues: 83 loop : -1.27 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 35 HIS 0.003 0.001 HIS F 122 PHE 0.010 0.001 PHE E 134 TYR 0.015 0.001 TYR A 237 ARG 0.007 0.000 ARG F 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 195 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8640 (mp) cc_final: 0.8251 (tt) REVERT: A 149 ILE cc_start: 0.7878 (mt) cc_final: 0.7633 (tt) REVERT: A 192 GLN cc_start: 0.8271 (tp-100) cc_final: 0.7720 (tp-100) REVERT: A 212 GLU cc_start: 0.7827 (tt0) cc_final: 0.7242 (mt-10) REVERT: A 244 MET cc_start: 0.7825 (ttp) cc_final: 0.7275 (ttp) REVERT: A 260 LEU cc_start: 0.8858 (tp) cc_final: 0.8569 (tp) REVERT: A 376 PHE cc_start: 0.7854 (m-80) cc_final: 0.7198 (m-10) REVERT: A 400 MET cc_start: 0.7526 (mtm) cc_final: 0.7295 (mtt) REVERT: C 30 ARG cc_start: 0.7370 (ttm-80) cc_final: 0.6836 (mmm-85) REVERT: C 38 LYS cc_start: 0.8653 (mtmp) cc_final: 0.8129 (mttp) REVERT: C 46 GLU cc_start: 0.8743 (tp30) cc_final: 0.8426 (tp30) REVERT: D 100 TRP cc_start: 0.7440 (m100) cc_final: 0.6977 (m100) REVERT: D 272 SER cc_start: 0.8685 (m) cc_final: 0.8382 (p) REVERT: D 336 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8273 (tt) REVERT: E 146 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7808 (tptp) REVERT: E 150 GLN cc_start: 0.7697 (tt0) cc_final: 0.7053 (tm-30) REVERT: F 25 GLU cc_start: 0.9174 (tp30) cc_final: 0.8894 (tp30) REVERT: F 49 GLN cc_start: 0.8517 (pp30) cc_final: 0.8310 (pp30) REVERT: F 71 GLN cc_start: 0.8984 (mt0) cc_final: 0.8008 (tm-30) REVERT: F 79 LYS cc_start: 0.9024 (tppt) cc_final: 0.8673 (tptp) REVERT: F 91 LYS cc_start: 0.8770 (mmtp) cc_final: 0.8529 (mmmm) REVERT: F 107 PHE cc_start: 0.8377 (t80) cc_final: 0.8096 (t80) REVERT: F 124 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8145 (tm-30) REVERT: F 152 LYS cc_start: 0.9093 (tppt) cc_final: 0.8172 (tptt) REVERT: F 157 GLU cc_start: 0.8195 (tp30) cc_final: 0.7955 (tp30) outliers start: 53 outliers final: 41 residues processed: 233 average time/residue: 0.1954 time to fit residues: 65.1420 Evaluate side-chains 218 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 118 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 0.0070 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10129 Z= 0.295 Angle : 0.702 12.313 13738 Z= 0.334 Chirality : 0.042 0.228 1643 Planarity : 0.004 0.040 1703 Dihedral : 4.093 19.838 1363 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.76 % Allowed : 22.55 % Favored : 71.69 % 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: 1.12 (0.25), residues: 1264 helix: 1.77 (0.18), residues: 822 sheet: -1.21 (0.57), residues: 84 loop : -1.20 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 35 HIS 0.003 0.001 HIS D 255 PHE 0.015 0.002 PHE D 74 TYR 0.020 0.002 TYR D 597 ARG 0.006 0.001 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 174 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8670 (mp) cc_final: 0.8293 (tt) REVERT: A 149 ILE cc_start: 0.7963 (mt) cc_final: 0.7722 (tt) REVERT: A 192 GLN cc_start: 0.8325 (tp-100) cc_final: 0.7873 (tp-100) REVERT: A 212 GLU cc_start: 0.7810 (tt0) cc_final: 0.7268 (mt-10) REVERT: A 244 MET cc_start: 0.7974 (ttp) cc_final: 0.7374 (ttp) REVERT: A 260 LEU cc_start: 0.8921 (tp) cc_final: 0.8611 (tp) REVERT: A 376 PHE cc_start: 0.7942 (m-80) cc_final: 0.7245 (m-10) REVERT: C 30 ARG cc_start: 0.7373 (ttm-80) cc_final: 0.6840 (mmm-85) REVERT: C 31 GLU cc_start: 0.8850 (tp30) cc_final: 0.8565 (tp30) REVERT: C 38 LYS cc_start: 0.8676 (mtmp) cc_final: 0.8116 (mttp) REVERT: C 46 GLU cc_start: 0.8744 (tp30) cc_final: 0.8411 (tp30) REVERT: D 66 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7143 (m-10) REVERT: D 100 TRP cc_start: 0.7615 (m100) cc_final: 0.7238 (m100) REVERT: D 272 SER cc_start: 0.8811 (m) cc_final: 0.8466 (p) REVERT: D 336 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8403 (tp) REVERT: D 376 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7652 (p0) REVERT: E 146 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7737 (tptp) REVERT: E 150 GLN cc_start: 0.7866 (tt0) cc_final: 0.7186 (tm-30) REVERT: E 165 MET cc_start: 0.7193 (tpt) cc_final: 0.6925 (tpp) REVERT: F 25 GLU cc_start: 0.9212 (tp30) cc_final: 0.8819 (tp30) REVERT: F 49 GLN cc_start: 0.8551 (pp30) cc_final: 0.8342 (pp30) REVERT: F 63 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8642 (mm-30) REVERT: F 71 GLN cc_start: 0.9046 (mt0) cc_final: 0.8011 (tm-30) REVERT: F 79 LYS cc_start: 0.9048 (tppt) cc_final: 0.8674 (tptp) REVERT: F 90 ARG cc_start: 0.8374 (tpp80) cc_final: 0.8149 (mmt90) REVERT: F 91 LYS cc_start: 0.8806 (mmtp) cc_final: 0.8558 (mmmm) REVERT: F 124 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8218 (tm-30) REVERT: F 152 LYS cc_start: 0.9195 (tppt) cc_final: 0.8193 (tptt) outliers start: 60 outliers final: 49 residues processed: 218 average time/residue: 0.1921 time to fit residues: 60.7297 Evaluate side-chains 220 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 168 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 162 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 83 optimal weight: 0.0980 chunk 126 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 77 optimal weight: 0.1980 chunk 61 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 HIS ** D 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10129 Z= 0.195 Angle : 0.688 12.355 13738 Z= 0.321 Chirality : 0.040 0.236 1643 Planarity : 0.004 0.040 1703 Dihedral : 4.035 19.859 1363 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.51 % Allowed : 23.99 % Favored : 71.50 % 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: 1.24 (0.25), residues: 1264 helix: 1.89 (0.18), residues: 822 sheet: -1.25 (0.57), residues: 84 loop : -1.19 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 35 HIS 0.002 0.001 HIS D 255 PHE 0.011 0.001 PHE E 134 TYR 0.015 0.001 TYR A 237 ARG 0.007 0.001 ARG F 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 181 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8657 (mp) cc_final: 0.8267 (tt) REVERT: A 149 ILE cc_start: 0.7861 (mt) cc_final: 0.7613 (tt) REVERT: A 192 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7739 (tp-100) REVERT: A 212 GLU cc_start: 0.7777 (tt0) cc_final: 0.7238 (mt-10) REVERT: A 244 MET cc_start: 0.7854 (ttp) cc_final: 0.7273 (ttp) REVERT: A 260 LEU cc_start: 0.8907 (tp) cc_final: 0.8620 (tp) REVERT: A 376 PHE cc_start: 0.7913 (m-80) cc_final: 0.7239 (m-10) REVERT: C 30 ARG cc_start: 0.7405 (ttm-80) cc_final: 0.6851 (mmm-85) REVERT: C 31 GLU cc_start: 0.8814 (tp30) cc_final: 0.8551 (tp30) REVERT: C 38 LYS cc_start: 0.8646 (mtmp) cc_final: 0.8085 (mttp) REVERT: C 46 GLU cc_start: 0.8705 (tp30) cc_final: 0.8354 (tp30) REVERT: D 100 TRP cc_start: 0.7553 (m100) cc_final: 0.7146 (m100) REVERT: D 272 SER cc_start: 0.8737 (m) cc_final: 0.8424 (p) REVERT: D 336 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8301 (tt) REVERT: E 146 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7758 (tptp) REVERT: E 150 GLN cc_start: 0.7739 (tt0) cc_final: 0.7056 (tm-30) REVERT: F 25 GLU cc_start: 0.9179 (tp30) cc_final: 0.8872 (tp30) REVERT: F 62 PHE cc_start: 0.7192 (t80) cc_final: 0.6519 (t80) REVERT: F 71 GLN cc_start: 0.9026 (mt0) cc_final: 0.7973 (tm-30) REVERT: F 79 LYS cc_start: 0.9006 (tppt) cc_final: 0.8648 (tptp) REVERT: F 90 ARG cc_start: 0.8357 (tpp80) cc_final: 0.8094 (mmt90) REVERT: F 91 LYS cc_start: 0.8774 (mmtp) cc_final: 0.8543 (mmmm) REVERT: F 108 MET cc_start: 0.8829 (mmm) cc_final: 0.8577 (mmm) REVERT: F 124 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8157 (tm-30) REVERT: F 152 LYS cc_start: 0.9193 (tppt) cc_final: 0.8178 (tptm) outliers start: 47 outliers final: 42 residues processed: 217 average time/residue: 0.2001 time to fit residues: 62.8002 Evaluate side-chains 215 residues out of total 1130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 172 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 ASN ** D 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.098295 restraints weight = 18903.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099963 restraints weight = 12331.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.101612 restraints weight = 8238.351| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 10129 Z= 0.386 Angle : 0.778 12.737 13738 Z= 0.377 Chirality : 0.045 0.219 1643 Planarity : 0.005 0.040 1703 Dihedral : 4.339 20.981 1363 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.37 % Allowed : 23.42 % Favored : 71.21 % 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: 0.91 (0.24), residues: 1264 helix: 1.62 (0.18), residues: 816 sheet: -1.40 (0.57), residues: 86 loop : -1.21 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 35 HIS 0.003 0.001 HIS D 309 PHE 0.020 0.002 PHE D 74 TYR 0.026 0.002 TYR D 597 ARG 0.007 0.001 ARG F 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2128.84 seconds wall clock time: 39 minutes 9.61 seconds (2349.61 seconds total)