Starting phenix.real_space_refine on Wed Sep 17 16:58:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n3q_0336/09_2025/6n3q_0336.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n3q_0336/09_2025/6n3q_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 { model { file = "/net/cci-nas-00/data/ceres_data/6n3q_0336/09_2025/6n3q_0336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n3q_0336/09_2025/6n3q_0336.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n3q_0336/09_2025/6n3q_0336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n3q_0336/09_2025/6n3q_0336.map" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'PHE:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP: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: {'ASP:plan': 1, 'PHE: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: {'ASN:plan1': 1, 'GLU:plan': 17, 'ASP:plan': 13, 'GLN:plan1': 2, 'PHE:plan': 1} 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: {'GLU:plan': 4, 'GLN:plan1': 1, '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: 2.08, per 1000 atoms: 0.21 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 363.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.28 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: 1.49 Time building geometry restraints manager: 1.09 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: 0.00 - 2.14: 13110 2.14 - 4.29: 507 4.29 - 6.43: 73 6.43 - 8.57: 39 8.57 - 10.71: 9 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 3.040 nonbonded pdb=" O GLY D 27 " pdb=" OG1 THR D 30 " model vdw 2.309 3.040 nonbonded pdb=" OD1 ASN A 204 " pdb=" OG SER D 205 " model vdw 2.318 3.040 nonbonded pdb=" O LYS E 79 " pdb=" OG SER E 82 " model vdw 2.320 3.040 nonbonded pdb=" O PHE A 198 " pdb=" OH TYR C 66 " model vdw 2.334 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.490 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.650 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.720 ------------------------------------------------------------------------------- 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= 0.253 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.017 0.001 ARG E 99 TYR 0.026 0.002 TYR A 175 PHE 0.029 0.003 PHE D 290 TRP 0.030 0.003 TRP D 242 HIS 0.008 0.002 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00563 (10129) covalent geometry : angle 1.03208 (13738) hydrogen bonds : bond 0.13132 ( 631) hydrogen bonds : angle 6.34952 ( 1866) *********************** 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 to be fit. rotamer outliers: 7 poor density : 342 time to evaluate : 0.279 Fit side-chains revert: symmetry clash 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: 0.8862 (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: 0.7263 (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: 0.7809 (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: 0.7268 (ttmt) REVERT: D 16 SER cc_start: 0.8921 (m) cc_final: 0.8610 (t) REVERT: D 100 TRP cc_start: 0.7541 (m100) cc_final: 0.7201 (m100) REVERT: D 222 LEU cc_start: 0.8266 (tp) cc_final: 0.7522 (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: 0.8802 (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: 0.6979 (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: 0.8624 (mmmm) REVERT: F 108 MET cc_start: 0.8502 (mtm) cc_final: 0.8087 (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: 0.1016 time to fit residues: 47.6554 Evaluate side-chains 197 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 108 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 D 309 HIS D 345 ASN D 494 GLN ** D 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 174 GLN F 30 GLN F 71 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.134080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.117783 restraints weight = 19312.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.120606 restraints weight = 9842.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.122289 restraints weight = 6169.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.123557 restraints weight = 4545.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.124304 restraints weight = 3623.692| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10129 Z= 0.159 Angle : 0.665 8.909 13738 Z= 0.335 Chirality : 0.042 0.283 1643 Planarity : 0.005 0.048 1703 Dihedral : 4.905 22.700 1364 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.03 % Allowed : 13.82 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.22), residues: 1264 helix: 0.26 (0.17), residues: 816 sheet: -1.91 (0.56), residues: 74 loop : -1.70 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 177 TYR 0.024 0.002 TYR A 237 PHE 0.031 0.002 PHE A 16 TRP 0.012 0.002 TRP A 35 HIS 0.012 0.002 HIS D 558 Details of bonding type rmsd covalent geometry : bond 0.00361 (10129) covalent geometry : angle 0.66523 (13738) hydrogen bonds : bond 0.04364 ( 631) hydrogen bonds : angle 4.49703 ( 1866) *********************** 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 to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 41 LEU cc_start: 0.8807 (tp) cc_final: 0.8495 (tt) REVERT: A 100 LEU cc_start: 0.8337 (mt) cc_final: 0.8135 (tt) REVERT: A 162 LEU cc_start: 0.9354 (tm) cc_final: 0.9122 (tp) REVERT: A 188 ASN cc_start: 0.8720 (t0) cc_final: 0.8272 (t0) REVERT: A 447 SER cc_start: 0.8582 (m) cc_final: 0.8362 (p) REVERT: C 30 ARG cc_start: 0.6884 (ttm-80) cc_final: 0.6471 (mmm-85) REVERT: C 38 LYS cc_start: 0.8378 (mtmp) cc_final: 0.8076 (mttp) REVERT: C 52 LYS cc_start: 0.7891 (ttmt) cc_final: 0.7559 (ttmt) REVERT: D 222 LEU cc_start: 0.8039 (tp) cc_final: 0.7593 (mm) REVERT: E 150 GLN cc_start: 0.7111 (tt0) cc_final: 0.6888 (tm-30) REVERT: E 153 GLU cc_start: 0.7312 (tp30) cc_final: 0.6967 (tt0) REVERT: F 71 GLN cc_start: 0.8464 (mt0) cc_final: 0.7891 (tm-30) REVERT: F 86 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8136 (tp30) REVERT: F 108 MET cc_start: 0.8134 (mtm) cc_final: 0.7563 (mtt) REVERT: F 124 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7661 (tm-30) REVERT: F 152 LYS cc_start: 0.8848 (tppt) cc_final: 0.8188 (tptt) outliers start: 42 outliers final: 24 residues processed: 262 average time/residue: 0.0884 time to fit residues: 33.3698 Evaluate side-chains 211 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 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 314 ASP Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 366 THR 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 110 LEU 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 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 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 0.0070 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.3404 ------------------------------------------------------------------------------- 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** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.124978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.105011 restraints weight = 20019.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.108056 restraints weight = 10218.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.110044 restraints weight = 6479.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.111212 restraints weight = 4739.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.112151 restraints weight = 3878.175| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10129 Z= 0.192 Angle : 0.674 9.856 13738 Z= 0.336 Chirality : 0.042 0.193 1643 Planarity : 0.004 0.045 1703 Dihedral : 4.633 20.626 1363 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 6.14 % Allowed : 16.22 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.23), residues: 1264 helix: 0.95 (0.18), residues: 815 sheet: -1.53 (0.62), residues: 69 loop : -1.54 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 90 TYR 0.022 0.002 TYR A 237 PHE 0.018 0.002 PHE D 290 TRP 0.013 0.002 TRP D 14 HIS 0.003 0.001 HIS D 424 Details of bonding type rmsd covalent geometry : bond 0.00444 (10129) covalent geometry : angle 0.67388 (13738) hydrogen bonds : bond 0.04274 ( 631) hydrogen bonds : angle 4.31080 ( 1866) *********************** 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 269 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 205 time to evaluate : 0.388 Fit side-chains REVERT: A 188 ASN cc_start: 0.8686 (t0) cc_final: 0.8262 (t0) REVERT: A 212 GLU cc_start: 0.7925 (tt0) cc_final: 0.7350 (mt-10) REVERT: A 244 MET cc_start: 0.7936 (ttp) cc_final: 0.7456 (ttp) REVERT: A 376 PHE cc_start: 0.7793 (m-80) cc_final: 0.6947 (m-10) REVERT: A 447 SER cc_start: 0.8876 (m) cc_final: 0.8324 (p) REVERT: C 30 ARG cc_start: 0.7142 (ttm-80) cc_final: 0.6614 (mmm-85) REVERT: C 38 LYS cc_start: 0.8516 (mtmp) cc_final: 0.8112 (mttp) REVERT: C 46 GLU cc_start: 0.8366 (tp30) cc_final: 0.8147 (tp30) REVERT: D 222 LEU cc_start: 0.8128 (tp) cc_final: 0.7658 (mm) REVERT: D 288 HIS cc_start: 0.8208 (t70) cc_final: 0.7993 (t70) REVERT: E 130 TYR cc_start: 0.8810 (t80) cc_final: 0.8558 (t80) REVERT: E 150 GLN cc_start: 0.7530 (tt0) cc_final: 0.6986 (tm-30) REVERT: F 71 GLN cc_start: 0.8654 (mt0) cc_final: 0.7881 (tm-30) REVERT: F 124 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7761 (tm-30) REVERT: F 152 LYS cc_start: 0.8982 (tppt) cc_final: 0.8385 (tmtt) outliers start: 64 outliers final: 43 residues processed: 250 average time/residue: 0.0851 time to fit residues: 31.2616 Evaluate side-chains 217 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 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 274 VAL 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 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 16 SER Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 272 SER 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 419 LEU Chi-restraints excluded: chain D residue 425 ILE 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 110 LEU Chi-restraints excluded: chain E residue 123 ASN 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 57 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 HIS ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.103933 restraints weight = 18779.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105290 restraints weight = 12135.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107208 restraints weight = 8235.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.107557 restraints weight = 6354.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107636 restraints weight = 5267.574| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10129 Z= 0.143 Angle : 0.654 10.496 13738 Z= 0.315 Chirality : 0.041 0.209 1643 Planarity : 0.004 0.041 1703 Dihedral : 4.406 20.523 1363 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.47 % Allowed : 18.43 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.24), residues: 1264 helix: 1.31 (0.18), residues: 814 sheet: -1.40 (0.64), residues: 69 loop : -1.33 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 90 TYR 0.019 0.001 TYR A 237 PHE 0.015 0.001 PHE D 290 TRP 0.020 0.002 TRP A 35 HIS 0.002 0.001 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00326 (10129) covalent geometry : angle 0.65413 (13738) hydrogen bonds : bond 0.03957 ( 631) hydrogen bonds : angle 4.10361 ( 1866) *********************** 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 253 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 0.335 Fit side-chains REVERT: A 41 LEU cc_start: 0.8984 (tp) cc_final: 0.8772 (tt) REVERT: A 188 ASN cc_start: 0.8775 (t0) cc_final: 0.8372 (t0) REVERT: A 244 MET cc_start: 0.7776 (ttp) cc_final: 0.7294 (ttp) REVERT: A 376 PHE cc_start: 0.7488 (m-80) cc_final: 0.6746 (m-10) REVERT: A 447 SER cc_start: 0.8758 (m) cc_final: 0.8421 (p) REVERT: C 30 ARG cc_start: 0.6843 (ttm-80) cc_final: 0.6473 (mmm-85) REVERT: C 38 LYS cc_start: 0.8281 (mtmp) cc_final: 0.7990 (mttp) REVERT: C 46 GLU cc_start: 0.7909 (tp30) cc_final: 0.7611 (tp30) REVERT: D 222 LEU cc_start: 0.7825 (tp) cc_final: 0.7482 (mm) REVERT: E 150 GLN cc_start: 0.7092 (tt0) cc_final: 0.6829 (tm-30) REVERT: E 193 GLU cc_start: 0.8194 (tp30) cc_final: 0.7785 (tp30) REVERT: F 71 GLN cc_start: 0.8228 (mt0) cc_final: 0.7785 (tm-30) REVERT: F 124 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7605 (tm-30) REVERT: F 152 LYS cc_start: 0.8681 (tppt) cc_final: 0.8423 (tmtt) outliers start: 57 outliers final: 35 residues processed: 236 average time/residue: 0.0817 time to fit residues: 28.3104 Evaluate side-chains 213 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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 274 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 310 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 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 272 SER 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 425 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 110 LEU 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 138 ILE Chi-restraints excluded: chain F residue 162 THR 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 23 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 156 GLN ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.118395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.103713 restraints weight = 18839.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.105456 restraints weight = 12329.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.106987 restraints weight = 7966.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.107304 restraints weight = 6582.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.107500 restraints weight = 5594.634| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3725 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= 0.142 Angle : 0.653 15.543 13738 Z= 0.309 Chirality : 0.041 0.201 1643 Planarity : 0.004 0.041 1703 Dihedral : 4.260 19.758 1363 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.28 % Allowed : 20.44 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.24), residues: 1264 helix: 1.50 (0.18), residues: 817 sheet: -1.24 (0.62), residues: 73 loop : -1.29 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 90 TYR 0.018 0.001 TYR A 237 PHE 0.013 0.001 PHE D 290 TRP 0.026 0.002 TRP A 35 HIS 0.003 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00325 (10129) covalent geometry : angle 0.65303 (13738) hydrogen bonds : bond 0.03862 ( 631) hydrogen bonds : angle 3.99439 ( 1866) *********************** 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 256 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.8973 (tp) cc_final: 0.8760 (tt) REVERT: A 100 LEU cc_start: 0.8139 (mp) cc_final: 0.7745 (tt) REVERT: A 188 ASN cc_start: 0.8692 (t0) cc_final: 0.8305 (t0) REVERT: A 212 GLU cc_start: 0.7791 (tt0) cc_final: 0.7395 (mt-10) REVERT: A 244 MET cc_start: 0.7732 (ttp) cc_final: 0.7307 (ttp) REVERT: A 376 PHE cc_start: 0.7578 (m-80) cc_final: 0.6817 (m-10) REVERT: A 447 SER cc_start: 0.8703 (m) cc_final: 0.8148 (p) REVERT: C 30 ARG cc_start: 0.6884 (ttm-80) cc_final: 0.6506 (mmm-85) REVERT: C 38 LYS cc_start: 0.8310 (mtmp) cc_final: 0.8011 (mttp) REVERT: C 46 GLU cc_start: 0.7900 (tp30) cc_final: 0.7590 (tp30) REVERT: D 222 LEU cc_start: 0.7923 (tp) cc_final: 0.7545 (mm) REVERT: E 150 GLN cc_start: 0.7130 (tt0) cc_final: 0.6872 (tm-30) REVERT: E 165 MET cc_start: 0.6660 (tpp) cc_final: 0.6431 (tpt) REVERT: E 193 GLU cc_start: 0.8244 (tp30) cc_final: 0.7834 (tp30) REVERT: F 25 GLU cc_start: 0.8698 (tp30) cc_final: 0.8433 (tp30) REVERT: F 62 PHE cc_start: 0.8193 (t80) cc_final: 0.7928 (t80) REVERT: F 71 GLN cc_start: 0.8309 (mt0) cc_final: 0.7789 (tm-30) REVERT: F 107 PHE cc_start: 0.8151 (t80) cc_final: 0.7861 (t80) REVERT: F 124 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7633 (tm-30) REVERT: F 152 LYS cc_start: 0.8735 (tppt) cc_final: 0.8457 (tmtt) REVERT: F 175 LYS cc_start: 0.7803 (ptmm) cc_final: 0.7547 (ptmm) outliers start: 55 outliers final: 44 residues processed: 241 average time/residue: 0.0771 time to fit residues: 27.4210 Evaluate side-chains 220 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 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 274 VAL Chi-restraints excluded: chain A residue 293 ILE 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 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 100 TRP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 272 SER 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 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 497 VAL Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 594 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 110 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 181 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 83 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 370 GLN ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102517 restraints weight = 18926.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104145 restraints weight = 12601.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.105829 restraints weight = 8187.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106123 restraints weight = 6586.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.106236 restraints weight = 5663.943| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10129 Z= 0.157 Angle : 0.661 14.158 13738 Z= 0.316 Chirality : 0.041 0.214 1643 Planarity : 0.004 0.041 1703 Dihedral : 4.209 19.796 1363 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.47 % Allowed : 21.02 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.24), residues: 1264 helix: 1.60 (0.18), residues: 818 sheet: -1.22 (0.62), residues: 74 loop : -1.29 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 154 TYR 0.017 0.001 TYR F 190 PHE 0.013 0.001 PHE D 435 TRP 0.033 0.002 TRP A 35 HIS 0.002 0.001 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00367 (10129) covalent geometry : angle 0.66107 (13738) hydrogen bonds : bond 0.03837 ( 631) hydrogen bonds : angle 3.97349 ( 1866) *********************** 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 249 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 192 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9010 (tp) cc_final: 0.8767 (tt) REVERT: A 100 LEU cc_start: 0.8110 (mp) cc_final: 0.7715 (tt) REVERT: A 188 ASN cc_start: 0.8480 (t0) cc_final: 0.8165 (t0) REVERT: A 244 MET cc_start: 0.7734 (ttp) cc_final: 0.7387 (ttp) REVERT: A 376 PHE cc_start: 0.7493 (m-80) cc_final: 0.6820 (m-10) REVERT: C 30 ARG cc_start: 0.6853 (ttm-80) cc_final: 0.6529 (mmm-85) REVERT: C 38 LYS cc_start: 0.8301 (mtmp) cc_final: 0.7993 (mttp) REVERT: C 40 LYS cc_start: 0.7650 (tmtt) cc_final: 0.7361 (tmtt) REVERT: C 46 GLU cc_start: 0.7890 (tp30) cc_final: 0.7652 (tp30) REVERT: D 336 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8739 (tp) REVERT: E 150 GLN cc_start: 0.7130 (tt0) cc_final: 0.6905 (tm-30) REVERT: E 193 GLU cc_start: 0.8167 (tp30) cc_final: 0.7814 (tp30) REVERT: F 71 GLN cc_start: 0.8264 (mt0) cc_final: 0.7786 (tm-30) REVERT: F 107 PHE cc_start: 0.8132 (t80) cc_final: 0.7850 (t80) REVERT: F 124 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7652 (tm-30) REVERT: F 152 LYS cc_start: 0.8658 (tppt) cc_final: 0.8415 (tmtt) outliers start: 57 outliers final: 47 residues processed: 236 average time/residue: 0.0861 time to fit residues: 28.3031 Evaluate side-chains 222 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 133 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 179 SER 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 274 VAL Chi-restraints excluded: chain A residue 293 ILE 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 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 18 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 272 SER 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 366 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 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 110 LEU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 181 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 82 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 96 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 123 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.117358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102830 restraints weight = 18887.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.104574 restraints weight = 12299.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106056 restraints weight = 7937.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.106345 restraints weight = 6582.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.106458 restraints weight = 5584.635| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10129 Z= 0.147 Angle : 0.660 13.299 13738 Z= 0.314 Chirality : 0.041 0.225 1643 Planarity : 0.004 0.041 1703 Dihedral : 4.161 20.146 1363 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 6.33 % Allowed : 20.54 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.25), residues: 1264 helix: 1.65 (0.18), residues: 818 sheet: -1.27 (0.62), residues: 74 loop : -1.19 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 264 TYR 0.016 0.001 TYR A 237 PHE 0.033 0.001 PHE F 62 TRP 0.033 0.002 TRP A 35 HIS 0.002 0.001 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00343 (10129) covalent geometry : angle 0.65979 (13738) hydrogen bonds : bond 0.03785 ( 631) hydrogen bonds : angle 3.92099 ( 1866) *********************** 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 255 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 189 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8053 (mp) cc_final: 0.7690 (tt) REVERT: A 188 ASN cc_start: 0.8506 (t0) cc_final: 0.8066 (t0) REVERT: A 192 GLN cc_start: 0.8257 (tp40) cc_final: 0.8001 (tp-100) REVERT: A 212 GLU cc_start: 0.7711 (tt0) cc_final: 0.7326 (mt-10) REVERT: A 244 MET cc_start: 0.7711 (ttp) cc_final: 0.7326 (ttp) REVERT: A 376 PHE cc_start: 0.7439 (m-80) cc_final: 0.6848 (m-10) REVERT: C 30 ARG cc_start: 0.6858 (ttm-80) cc_final: 0.6534 (mmm-85) REVERT: C 38 LYS cc_start: 0.8315 (mtmp) cc_final: 0.7996 (mttp) REVERT: D 336 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8627 (tt) REVERT: E 150 GLN cc_start: 0.7109 (tt0) cc_final: 0.6887 (tm-30) REVERT: E 193 GLU cc_start: 0.7958 (tp30) cc_final: 0.7742 (tp30) REVERT: F 71 GLN cc_start: 0.8141 (mt0) cc_final: 0.7902 (tm-30) REVERT: F 107 PHE cc_start: 0.8167 (t80) cc_final: 0.7900 (t80) REVERT: F 124 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7624 (tm-30) REVERT: F 152 LYS cc_start: 0.8729 (tppt) cc_final: 0.8382 (tptt) outliers start: 66 outliers final: 52 residues processed: 234 average time/residue: 0.0783 time to fit residues: 27.1491 Evaluate side-chains 226 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 173 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 179 SER 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 274 VAL Chi-restraints excluded: chain A residue 293 ILE 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 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 14 TRP Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 272 SER 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 366 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 497 VAL Chi-restraints excluded: chain D residue 514 CYS 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 D residue 594 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 149 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102014 restraints weight = 18659.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103766 restraints weight = 12291.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.104917 restraints weight = 7931.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105299 restraints weight = 6670.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.105434 restraints weight = 5859.885| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10129 Z= 0.172 Angle : 0.700 12.930 13738 Z= 0.333 Chirality : 0.042 0.224 1643 Planarity : 0.004 0.041 1703 Dihedral : 4.174 19.866 1363 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 6.05 % Allowed : 21.11 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.25), residues: 1264 helix: 1.66 (0.18), residues: 817 sheet: -1.39 (0.57), residues: 84 loop : -1.21 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 264 TYR 0.018 0.002 TYR F 190 PHE 0.013 0.001 PHE D 74 TRP 0.033 0.002 TRP A 35 HIS 0.002 0.001 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00408 (10129) covalent geometry : angle 0.70026 (13738) hydrogen bonds : bond 0.03860 ( 631) hydrogen bonds : angle 3.95816 ( 1866) *********************** 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 251 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 188 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8101 (mp) cc_final: 0.7683 (tt) REVERT: A 192 GLN cc_start: 0.8301 (tp40) cc_final: 0.7892 (tp-100) REVERT: A 212 GLU cc_start: 0.7728 (tt0) cc_final: 0.7357 (mt-10) REVERT: A 244 MET cc_start: 0.7772 (ttp) cc_final: 0.7404 (ttp) REVERT: A 376 PHE cc_start: 0.7515 (m-80) cc_final: 0.6889 (m-10) REVERT: C 30 ARG cc_start: 0.6921 (ttm-80) cc_final: 0.6575 (mmm-85) REVERT: C 38 LYS cc_start: 0.8421 (mtmp) cc_final: 0.8085 (mttp) REVERT: D 336 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8734 (tp) REVERT: E 150 GLN cc_start: 0.7154 (tt0) cc_final: 0.6919 (tm-30) REVERT: E 193 GLU cc_start: 0.8041 (tp30) cc_final: 0.7816 (tp30) REVERT: F 71 GLN cc_start: 0.8246 (mt0) cc_final: 0.7722 (tm-30) REVERT: F 107 PHE cc_start: 0.8196 (t80) cc_final: 0.7953 (t80) REVERT: F 152 LYS cc_start: 0.8759 (tppt) cc_final: 0.8473 (tmtt) outliers start: 63 outliers final: 54 residues processed: 230 average time/residue: 0.0751 time to fit residues: 25.3021 Evaluate side-chains 224 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 169 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 179 SER 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 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 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 14 TRP Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 272 SER 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 366 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 497 VAL Chi-restraints excluded: chain D residue 514 CYS 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 D residue 594 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain F residue 13 ILE Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 162 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 109 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 91 optimal weight: 0.3980 chunk 72 optimal weight: 0.0870 chunk 70 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.105325 restraints weight = 18595.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.107255 restraints weight = 12085.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108352 restraints weight = 7667.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.108767 restraints weight = 6415.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108942 restraints weight = 5616.319| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10129 Z= 0.129 Angle : 0.690 13.892 13738 Z= 0.320 Chirality : 0.041 0.239 1643 Planarity : 0.004 0.043 1703 Dihedral : 4.103 20.878 1363 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.09 % Allowed : 22.94 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.25), residues: 1264 helix: 1.74 (0.18), residues: 821 sheet: -1.43 (0.58), residues: 84 loop : -1.18 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 264 TYR 0.015 0.001 TYR E 121 PHE 0.011 0.001 PHE F 98 TRP 0.037 0.002 TRP A 35 HIS 0.003 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00297 (10129) covalent geometry : angle 0.69038 (13738) hydrogen bonds : bond 0.03631 ( 631) hydrogen bonds : angle 3.85861 ( 1866) *********************** 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 241 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8033 (mp) cc_final: 0.7649 (tt) REVERT: A 192 GLN cc_start: 0.8141 (tp40) cc_final: 0.7562 (tp-100) REVERT: A 244 MET cc_start: 0.7677 (ttp) cc_final: 0.7333 (ttp) REVERT: A 376 PHE cc_start: 0.7415 (m-80) cc_final: 0.6856 (m-10) REVERT: C 30 ARG cc_start: 0.6879 (ttm-80) cc_final: 0.6529 (mmm-85) REVERT: C 38 LYS cc_start: 0.8377 (mtmp) cc_final: 0.8073 (mttp) REVERT: D 336 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8400 (tt) REVERT: D 567 GLU cc_start: 0.6555 (tt0) cc_final: 0.6347 (tt0) REVERT: E 150 GLN cc_start: 0.7053 (tt0) cc_final: 0.6823 (tm-30) REVERT: F 63 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8134 (mm-30) REVERT: F 71 GLN cc_start: 0.8216 (mt0) cc_final: 0.7838 (tm-30) REVERT: F 152 LYS cc_start: 0.8709 (tppt) cc_final: 0.8365 (tptt) REVERT: F 177 ARG cc_start: 0.8904 (mtp85) cc_final: 0.8632 (mtt-85) outliers start: 53 outliers final: 46 residues processed: 223 average time/residue: 0.0841 time to fit residues: 27.4035 Evaluate side-chains 224 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 179 SER 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 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 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 79 ILE Chi-restraints excluded: chain D residue 14 TRP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 100 TRP 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 366 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 497 VAL Chi-restraints excluded: chain D residue 514 CYS 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 D residue 594 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 113 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 93 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 HIS ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 123 ASN F 30 GLN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.119590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105210 restraints weight = 18595.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.106968 restraints weight = 12053.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.108610 restraints weight = 7851.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108933 restraints weight = 6147.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108982 restraints weight = 5253.440| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10129 Z= 0.148 Angle : 0.723 13.112 13738 Z= 0.341 Chirality : 0.041 0.245 1643 Planarity : 0.004 0.041 1703 Dihedral : 4.080 20.605 1363 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.09 % Allowed : 23.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.24), residues: 1264 helix: 1.72 (0.18), residues: 818 sheet: -1.44 (0.57), residues: 84 loop : -1.14 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 264 TYR 0.016 0.001 TYR F 190 PHE 0.010 0.001 PHE F 98 TRP 0.054 0.002 TRP A 35 HIS 0.002 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00349 (10129) covalent geometry : angle 0.72265 (13738) hydrogen bonds : bond 0.03722 ( 631) hydrogen bonds : angle 3.91328 ( 1866) ********************** 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 229 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 176 time to evaluate : 0.409 Fit side-chains REVERT: A 100 LEU cc_start: 0.8051 (mp) cc_final: 0.7667 (tt) REVERT: A 192 GLN cc_start: 0.8112 (tp40) cc_final: 0.7565 (tp-100) REVERT: A 244 MET cc_start: 0.7722 (ttp) cc_final: 0.7375 (ttp) REVERT: A 376 PHE cc_start: 0.7415 (m-80) cc_final: 0.6889 (m-10) REVERT: C 30 ARG cc_start: 0.6892 (ttm-80) cc_final: 0.6555 (mmm-85) REVERT: C 38 LYS cc_start: 0.8406 (mtmp) cc_final: 0.8111 (mttp) REVERT: D 336 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8441 (tt) REVERT: E 150 GLN cc_start: 0.7049 (tt0) cc_final: 0.6835 (tm-30) REVERT: F 29 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7812 (t70) REVERT: F 67 LYS cc_start: 0.8369 (mtmm) cc_final: 0.8111 (mtmm) REVERT: F 71 GLN cc_start: 0.8147 (mt0) cc_final: 0.7825 (tm-30) REVERT: F 152 LYS cc_start: 0.8738 (tppt) cc_final: 0.8269 (tptt) REVERT: F 177 ARG cc_start: 0.8876 (mtp85) cc_final: 0.8629 (mtt-85) outliers start: 53 outliers final: 46 residues processed: 215 average time/residue: 0.0785 time to fit residues: 25.2070 Evaluate side-chains 216 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 179 SER 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 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 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 79 ILE Chi-restraints excluded: chain D residue 14 TRP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 100 TRP 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 366 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 497 VAL Chi-restraints excluded: chain D residue 514 CYS 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 D residue 594 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 113 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 5 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 92 optimal weight: 0.3980 chunk 36 optimal weight: 0.0470 chunk 55 optimal weight: 0.0040 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 75 optimal weight: 0.0010 chunk 120 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.1696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.123174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109027 restraints weight = 18646.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.110841 restraints weight = 11888.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.112689 restraints weight = 7737.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113035 restraints weight = 5856.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113052 restraints weight = 4980.348| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10129 Z= 0.129 Angle : 0.720 13.617 13738 Z= 0.336 Chirality : 0.040 0.244 1643 Planarity : 0.004 0.042 1703 Dihedral : 4.055 20.915 1363 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.89 % Allowed : 23.22 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.25), residues: 1264 helix: 1.78 (0.18), residues: 822 sheet: -1.33 (0.59), residues: 83 loop : -1.12 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 485 TYR 0.016 0.001 TYR E 121 PHE 0.013 0.001 PHE E 134 TRP 0.049 0.002 TRP A 35 HIS 0.002 0.001 HIS D 334 Details of bonding type rmsd covalent geometry : bond 0.00284 (10129) covalent geometry : angle 0.71962 (13738) hydrogen bonds : bond 0.03615 ( 631) hydrogen bonds : angle 3.80543 ( 1866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1585.34 seconds wall clock time: 28 minutes 10.42 seconds (1690.42 seconds total)