Starting phenix.real_space_refine on Fri Jun 6 13:55:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u02_41776/06_2025/8u02_41776.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u02_41776/06_2025/8u02_41776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u02_41776/06_2025/8u02_41776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u02_41776/06_2025/8u02_41776.map" model { file = "/net/cci-nas-00/data/ceres_data/8u02_41776/06_2025/8u02_41776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u02_41776/06_2025/8u02_41776.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 59 5.16 5 C 4956 2.51 5 N 1299 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7774 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2136 Classifications: {'peptide': 272} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2657 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 336} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2544 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 426 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.95, per 1000 atoms: 0.77 Number of scatterers: 7774 At special positions: 0 Unit cell: (83.904, 101.384, 130.226, 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 59 16.00 O 1460 8.00 N 1299 7.00 C 4956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 182 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.2 seconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 50.9% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'R' and resid 37 through 40 Processing helix chain 'R' and resid 41 through 61 Processing helix chain 'R' and resid 67 through 87 Processing helix chain 'R' and resid 87 through 97 Processing helix chain 'R' and resid 103 through 138 Processing helix chain 'R' and resid 138 through 143 removed outlier: 3.503A pdb=" N TYR R 142 " --> pdb=" O MET R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 168 Processing helix chain 'R' and resid 169 through 172 removed outlier: 3.600A pdb=" N PHE R 172 " --> pdb=" O PRO R 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 169 through 172' Processing helix chain 'R' and resid 186 through 198 removed outlier: 4.166A pdb=" N TYR R 192 " --> pdb=" O ALA R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 224 removed outlier: 3.555A pdb=" N ARG R 222 " --> pdb=" O ARG R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 399 removed outlier: 4.356A pdb=" N ALA R 376 " --> pdb=" O THR R 372 " (cutoff:3.500A) Proline residue: R 388 - end of helix removed outlier: 4.208A pdb=" N ILE R 397 " --> pdb=" O HIS R 393 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 428 removed outlier: 3.521A pdb=" N TYR R 416 " --> pdb=" O THR R 412 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 430 through 441 Processing helix chain 'B' and resid 7 through 32 removed outlier: 4.006A pdb=" N LYS B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 69 through 92 Processing helix chain 'B' and resid 98 through 113 removed outlier: 4.208A pdb=" N ALA B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 103 " --> pdb=" O GLU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 134 through 143 removed outlier: 3.697A pdb=" N GLN B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 159 Processing helix chain 'B' and resid 159 through 166 Processing helix chain 'B' and resid 208 through 214 removed outlier: 3.731A pdb=" N TRP B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 229 through 233 removed outlier: 4.028A pdb=" N ASP B 232 " --> pdb=" O SER B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 242 through 256 Processing helix chain 'B' and resid 271 through 279 Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 331 through 352 Processing helix chain 'A' and resid 3 through 24 Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.742A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 192 removed outlier: 6.518A pdb=" N VAL B 34 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE B 200 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU B 36 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS B 35 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE B 223 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU B 37 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N CYS B 225 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B 39 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N ALA B 227 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 51 removed outlier: 6.902A pdb=" N ILE A 338 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N THR A 50 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 336 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 63 removed outlier: 3.913A pdb=" N SER A 74 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 79 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA A 92 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 81 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 105 removed outlier: 6.991A pdb=" N GLY A 115 " --> pdb=" O MET A 101 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS A 103 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA A 113 " --> pdb=" O CYS A 103 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR A 105 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR A 111 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N CYS A 121 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU A 138 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 123 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG A 134 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 153 removed outlier: 3.727A pdb=" N CYS A 148 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLN A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASP A 170 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN A 176 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 187 through 192 removed outlier: 3.698A pdb=" N SER A 189 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP A 212 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N CYS A 218 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 229 through 234 removed outlier: 3.527A pdb=" N ALA A 231 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS A 250 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR A 263 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 252 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 273 through 278 removed outlier: 3.848A pdb=" N SER A 275 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS A 294 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL A 307 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 296 " --> pdb=" O ALA A 305 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1281 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: 4.24 Time building geometry restraints manager: 2.47 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: 2510 1.34 - 1.46: 1767 1.46 - 1.58: 3559 1.58 - 1.70: 0 1.70 - 1.83: 85 Bond restraints: 7921 Sorted by residual: bond pdb=" N ILE B 213 " pdb=" CA ILE B 213 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N ILE B 286 " pdb=" CA ILE B 286 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.22e+00 bond pdb=" N TRP B 212 " pdb=" CA TRP B 212 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.35e-02 5.49e+03 8.05e+00 bond pdb=" N THR R 205 " pdb=" CA THR R 205 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.41e+00 bond pdb=" N CYS B 287 " pdb=" CA CYS B 287 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.28e-02 6.10e+03 7.34e+00 ... (remaining 7916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 9806 1.63 - 3.26: 805 3.26 - 4.89: 126 4.89 - 6.52: 19 6.52 - 8.15: 8 Bond angle restraints: 10764 Sorted by residual: angle pdb=" N GLU B 43 " pdb=" CA GLU B 43 " pdb=" C GLU B 43 " ideal model delta sigma weight residual 111.69 103.54 8.15 1.23e+00 6.61e-01 4.40e+01 angle pdb=" N ARG B 179 " pdb=" CA ARG B 179 " pdb=" C ARG B 179 " ideal model delta sigma weight residual 112.24 105.31 6.93 1.28e+00 6.10e-01 2.93e+01 angle pdb=" N ILE R 212 " pdb=" CA ILE R 212 " pdb=" C ILE R 212 " ideal model delta sigma weight residual 110.62 105.51 5.11 1.02e+00 9.61e-01 2.51e+01 angle pdb=" CA LEU B 353 " pdb=" C LEU B 353 " pdb=" O LEU B 353 " ideal model delta sigma weight residual 121.16 115.77 5.39 1.12e+00 7.97e-01 2.32e+01 angle pdb=" N LEU B 353 " pdb=" CA LEU B 353 " pdb=" C LEU B 353 " ideal model delta sigma weight residual 110.28 103.22 7.06 1.48e+00 4.57e-01 2.27e+01 ... (remaining 10759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 4531 16.95 - 33.89: 124 33.89 - 50.84: 40 50.84 - 67.78: 9 67.78 - 84.73: 6 Dihedral angle restraints: 4710 sinusoidal: 1746 harmonic: 2964 Sorted by residual: dihedral pdb=" CD ARG B 209 " pdb=" NE ARG B 209 " pdb=" CZ ARG B 209 " pdb=" NH1 ARG B 209 " ideal model delta sinusoidal sigma weight residual 0.00 -84.73 84.73 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CD ARG A 129 " pdb=" NE ARG A 129 " pdb=" CZ ARG A 129 " pdb=" NH1 ARG A 129 " ideal model delta sinusoidal sigma weight residual 0.00 40.13 -40.13 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" C ASP A 205 " pdb=" N ASP A 205 " pdb=" CA ASP A 205 " pdb=" CB ASP A 205 " ideal model delta harmonic sigma weight residual -122.60 -113.37 -9.23 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 4707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 931 0.055 - 0.110: 257 0.110 - 0.165: 65 0.165 - 0.220: 14 0.220 - 0.274: 2 Chirality restraints: 1269 Sorted by residual: chirality pdb=" CA ASP A 205 " pdb=" N ASP A 205 " pdb=" C ASP A 205 " pdb=" CB ASP A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA LEU B 353 " pdb=" N LEU B 353 " pdb=" C LEU B 353 " pdb=" CB LEU B 353 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ILE R 212 " pdb=" N ILE R 212 " pdb=" C ILE R 212 " pdb=" CB ILE R 212 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1266 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 209 " -0.967 9.50e-02 1.11e+02 4.34e-01 1.22e+02 pdb=" NE ARG B 209 " 0.077 2.00e-02 2.50e+03 pdb=" CZ ARG B 209 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG B 209 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 209 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 129 " -0.704 9.50e-02 1.11e+02 3.16e-01 6.07e+01 pdb=" NE ARG A 129 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG A 129 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 129 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 129 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 382 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C PHE R 382 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE R 382 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE R 383 " 0.024 2.00e-02 2.50e+03 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1281 2.76 - 3.29: 8013 3.29 - 3.83: 13215 3.83 - 4.36: 16249 4.36 - 4.90: 26749 Nonbonded interactions: 65507 Sorted by model distance: nonbonded pdb=" O PRO R 423 " pdb=" OG1 THR R 427 " model vdw 2.222 3.040 nonbonded pdb=" OG SER B 126 " pdb=" NH1 ARG B 130 " model vdw 2.258 3.120 nonbonded pdb=" CD1 LEU R 216 " pdb=" OH TYR B 354 " model vdw 2.274 3.460 nonbonded pdb=" O CYS B 255 " pdb=" NZ LYS B 317 " model vdw 2.278 3.120 nonbonded pdb=" OE1 GLU B 217 " pdb=" NZ LYS A 57 " model vdw 2.279 3.120 ... (remaining 65502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.150 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 0.005 0.041 7922 Z= 0.307 Angle : 0.977 8.155 10766 Z= 0.649 Chirality : 0.056 0.274 1269 Planarity : 0.016 0.434 1360 Dihedral : 10.236 84.730 2785 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.61 % Allowed : 1.33 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1001 helix: 0.46 (0.21), residues: 465 sheet: 1.39 (0.38), residues: 172 loop : 0.13 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 63 HIS 0.010 0.002 HIS R 393 PHE 0.027 0.003 PHE A 234 TYR 0.040 0.003 TYR B 69 ARG 0.049 0.002 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.15352 ( 438) hydrogen bonds : angle 6.48093 ( 1281) SS BOND : bond 0.00149 ( 1) SS BOND : angle 2.97066 ( 2) covalent geometry : bond 0.00517 ( 7921) covalent geometry : angle 0.97657 (10764) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 267 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 218 ASP cc_start: 0.8420 (p0) cc_final: 0.8028 (p0) REVERT: B 263 THR cc_start: 0.8988 (m) cc_final: 0.8754 (p) REVERT: B 307 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8298 (mm110) REVERT: A 14 LEU cc_start: 0.9348 (mt) cc_final: 0.9041 (mt) REVERT: A 59 TYR cc_start: 0.8269 (m-80) cc_final: 0.8019 (m-80) outliers start: 5 outliers final: 1 residues processed: 270 average time/residue: 0.2470 time to fit residues: 85.6318 Evaluate side-chains 163 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 208 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 0.0470 chunk 41 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 418 ASN B 173 GLN B 196 HIS B 214 HIS A 62 HIS A 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.108102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.075276 restraints weight = 19255.843| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 4.22 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 7922 Z= 0.157 Angle : 0.675 8.822 10766 Z= 0.356 Chirality : 0.044 0.219 1269 Planarity : 0.004 0.038 1360 Dihedral : 4.585 44.389 1086 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.31 % Allowed : 11.89 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.26), residues: 1001 helix: 1.57 (0.23), residues: 479 sheet: 1.18 (0.37), residues: 180 loop : 0.09 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 169 HIS 0.005 0.001 HIS R 393 PHE 0.030 0.002 PHE A 241 TYR 0.027 0.002 TYR B 69 ARG 0.006 0.001 ARG R 219 Details of bonding type rmsd hydrogen bonds : bond 0.04732 ( 438) hydrogen bonds : angle 4.54977 ( 1281) SS BOND : bond 0.00058 ( 1) SS BOND : angle 2.20157 ( 2) covalent geometry : bond 0.00352 ( 7921) covalent geometry : angle 0.67422 (10764) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 95 GLU cc_start: 0.9127 (tp30) cc_final: 0.8922 (tp30) REVERT: R 131 ASP cc_start: 0.8585 (t70) cc_final: 0.8233 (t70) REVERT: R 369 LYS cc_start: 0.9361 (mttt) cc_final: 0.9041 (mttt) REVERT: R 373 GLN cc_start: 0.8735 (tt0) cc_final: 0.8228 (pp30) REVERT: R 394 ILE cc_start: 0.9010 (pt) cc_final: 0.8656 (mm) REVERT: B 20 GLU cc_start: 0.9312 (tp30) cc_final: 0.8932 (tp30) REVERT: B 189 HIS cc_start: 0.7747 (m170) cc_final: 0.7535 (m90) REVERT: A 127 LYS cc_start: 0.9017 (mmmm) cc_final: 0.8808 (mmmt) REVERT: A 217 MET cc_start: 0.8512 (ppp) cc_final: 0.8135 (ppp) REVERT: A 228 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7283 (m-30) REVERT: A 280 LYS cc_start: 0.8854 (tmtt) cc_final: 0.8496 (tmtt) REVERT: A 317 CYS cc_start: 0.7769 (m) cc_final: 0.7076 (p) REVERT: C 21 MET cc_start: 0.8515 (tmm) cc_final: 0.8042 (tmm) outliers start: 19 outliers final: 7 residues processed: 186 average time/residue: 0.2361 time to fit residues: 59.5517 Evaluate side-chains 152 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 294 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 65 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 75 GLN A 268 ASN C 44 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.103646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.071678 restraints weight = 19859.027| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 4.13 r_work: 0.3007 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7922 Z= 0.205 Angle : 0.646 10.941 10766 Z= 0.343 Chirality : 0.045 0.155 1269 Planarity : 0.004 0.046 1360 Dihedral : 4.603 47.476 1085 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.16 % Allowed : 12.14 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.27), residues: 1001 helix: 1.68 (0.23), residues: 480 sheet: 1.10 (0.37), residues: 184 loop : -0.15 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 90 HIS 0.010 0.001 HIS B 322 PHE 0.027 0.002 PHE A 241 TYR 0.022 0.002 TYR B 69 ARG 0.007 0.001 ARG R 61 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 438) hydrogen bonds : angle 4.47040 ( 1281) SS BOND : bond 0.00405 ( 1) SS BOND : angle 1.89942 ( 2) covalent geometry : bond 0.00454 ( 7921) covalent geometry : angle 0.64556 (10764) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 80 ASP cc_start: 0.9172 (OUTLIER) cc_final: 0.8854 (t0) REVERT: R 131 ASP cc_start: 0.9038 (t70) cc_final: 0.8767 (t70) REVERT: R 369 LYS cc_start: 0.9345 (mttt) cc_final: 0.8982 (pttp) REVERT: R 373 GLN cc_start: 0.8884 (tt0) cc_final: 0.8545 (pp30) REVERT: R 394 ILE cc_start: 0.9000 (pt) cc_final: 0.8764 (mm) REVERT: B 128 MET cc_start: 0.8858 (mtp) cc_final: 0.8342 (mtp) REVERT: B 189 HIS cc_start: 0.8142 (m170) cc_final: 0.7924 (m90) REVERT: B 217 GLU cc_start: 0.9343 (pt0) cc_final: 0.9124 (pt0) REVERT: B 255 CYS cc_start: 0.9272 (t) cc_final: 0.9066 (p) REVERT: B 308 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8474 (m-10) REVERT: A 13 GLN cc_start: 0.9454 (pp30) cc_final: 0.9161 (pp30) REVERT: A 61 MET cc_start: 0.9014 (tmm) cc_final: 0.8626 (tmm) REVERT: A 317 CYS cc_start: 0.8152 (m) cc_final: 0.7221 (p) REVERT: C 38 MET cc_start: 0.8804 (mtp) cc_final: 0.8407 (ptp) REVERT: C 41 CYS cc_start: 0.8280 (m) cc_final: 0.8071 (p) outliers start: 26 outliers final: 15 residues processed: 170 average time/residue: 0.3129 time to fit residues: 71.8491 Evaluate side-chains 147 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 421 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 18 optimal weight: 6.9990 chunk 42 optimal weight: 0.0670 chunk 34 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS A 75 GLN A 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.106792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.073686 restraints weight = 19718.443| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 4.35 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7922 Z= 0.136 Angle : 0.610 11.314 10766 Z= 0.313 Chirality : 0.043 0.164 1269 Planarity : 0.003 0.047 1360 Dihedral : 4.427 46.733 1085 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.06 % Allowed : 13.83 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.27), residues: 1001 helix: 1.81 (0.24), residues: 480 sheet: 1.13 (0.37), residues: 181 loop : -0.20 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 169 HIS 0.006 0.001 HIS B 322 PHE 0.022 0.002 PHE A 241 TYR 0.018 0.001 TYR B 69 ARG 0.003 0.000 ARG R 219 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 438) hydrogen bonds : angle 4.28619 ( 1281) SS BOND : bond 0.00027 ( 1) SS BOND : angle 1.63036 ( 2) covalent geometry : bond 0.00298 ( 7921) covalent geometry : angle 0.61015 (10764) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 80 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8877 (t0) REVERT: R 131 ASP cc_start: 0.8757 (t70) cc_final: 0.8491 (t70) REVERT: R 164 PHE cc_start: 0.8866 (t80) cc_final: 0.8637 (t80) REVERT: R 369 LYS cc_start: 0.9332 (mttt) cc_final: 0.8929 (pttp) REVERT: R 373 GLN cc_start: 0.8754 (tt0) cc_final: 0.8412 (pp30) REVERT: R 394 ILE cc_start: 0.8900 (pt) cc_final: 0.8698 (mm) REVERT: B 88 MET cc_start: 0.4549 (tpt) cc_final: 0.4216 (mmm) REVERT: B 189 HIS cc_start: 0.7920 (m170) cc_final: 0.7621 (m90) REVERT: B 217 GLU cc_start: 0.8991 (pt0) cc_final: 0.8717 (pt0) REVERT: B 307 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8256 (tp-100) REVERT: B 308 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8345 (m-10) REVERT: B 322 HIS cc_start: 0.8188 (t-90) cc_final: 0.7846 (t-90) REVERT: A 61 MET cc_start: 0.8444 (tmm) cc_final: 0.8156 (tmm) REVERT: A 175 GLN cc_start: 0.8346 (pm20) cc_final: 0.8110 (pm20) REVERT: A 246 ASP cc_start: 0.8607 (m-30) cc_final: 0.8205 (m-30) REVERT: A 280 LYS cc_start: 0.8924 (tmtt) cc_final: 0.8377 (tmmt) REVERT: A 301 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8258 (mmtt) REVERT: C 48 ASP cc_start: 0.8479 (t70) cc_final: 0.8014 (t0) outliers start: 17 outliers final: 11 residues processed: 158 average time/residue: 0.1932 time to fit residues: 41.5983 Evaluate side-chains 148 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 43 optimal weight: 0.0670 chunk 31 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.107109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074040 restraints weight = 19759.022| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 4.38 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7922 Z= 0.123 Angle : 0.603 11.097 10766 Z= 0.306 Chirality : 0.042 0.148 1269 Planarity : 0.003 0.047 1360 Dihedral : 4.307 44.352 1085 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.67 % Allowed : 14.81 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1001 helix: 1.76 (0.23), residues: 481 sheet: 1.15 (0.36), residues: 178 loop : -0.38 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 169 HIS 0.004 0.001 HIS R 393 PHE 0.020 0.001 PHE A 241 TYR 0.016 0.001 TYR B 69 ARG 0.004 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 438) hydrogen bonds : angle 4.19993 ( 1281) SS BOND : bond 0.00151 ( 1) SS BOND : angle 1.26212 ( 2) covalent geometry : bond 0.00271 ( 7921) covalent geometry : angle 0.60312 (10764) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 80 ASP cc_start: 0.9130 (OUTLIER) cc_final: 0.8872 (t0) REVERT: R 131 ASP cc_start: 0.8805 (t70) cc_final: 0.8568 (t70) REVERT: R 369 LYS cc_start: 0.9310 (mttt) cc_final: 0.8889 (pttp) REVERT: R 373 GLN cc_start: 0.8754 (tt0) cc_final: 0.8416 (pp30) REVERT: B 114 MET cc_start: 0.5105 (mtm) cc_final: 0.4901 (mtm) REVERT: B 189 HIS cc_start: 0.7983 (m170) cc_final: 0.7678 (m90) REVERT: B 217 GLU cc_start: 0.8972 (pt0) cc_final: 0.8697 (pt0) REVERT: B 278 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8180 (ttmt) REVERT: B 307 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8281 (tp-100) REVERT: B 322 HIS cc_start: 0.8163 (t-90) cc_final: 0.7780 (t-90) REVERT: A 61 MET cc_start: 0.8486 (tmm) cc_final: 0.7990 (tmm) REVERT: A 175 GLN cc_start: 0.8389 (pm20) cc_final: 0.8038 (pm20) REVERT: A 228 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7157 (m-30) REVERT: A 280 LYS cc_start: 0.8940 (tmtt) cc_final: 0.8350 (tmmt) REVERT: A 317 CYS cc_start: 0.7694 (m) cc_final: 0.6795 (p) REVERT: C 26 ASP cc_start: 0.8845 (m-30) cc_final: 0.8529 (t0) REVERT: C 38 MET cc_start: 0.8448 (mtp) cc_final: 0.8019 (mtp) REVERT: C 41 CYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7645 (p) REVERT: C 42 GLU cc_start: 0.9083 (pp20) cc_final: 0.8839 (mm-30) REVERT: C 48 ASP cc_start: 0.8464 (t70) cc_final: 0.7625 (t0) outliers start: 22 outliers final: 11 residues processed: 181 average time/residue: 0.2758 time to fit residues: 64.9024 Evaluate side-chains 156 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.0980 chunk 65 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS A 44 GLN A 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.106441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.073764 restraints weight = 19712.255| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.35 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7922 Z= 0.128 Angle : 0.630 12.082 10766 Z= 0.313 Chirality : 0.042 0.167 1269 Planarity : 0.004 0.047 1360 Dihedral : 4.240 41.087 1085 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.67 % Allowed : 15.78 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.26), residues: 1001 helix: 1.75 (0.24), residues: 480 sheet: 1.12 (0.35), residues: 176 loop : -0.44 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 169 HIS 0.004 0.001 HIS R 393 PHE 0.019 0.001 PHE A 241 TYR 0.028 0.001 TYR B 69 ARG 0.006 0.000 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 438) hydrogen bonds : angle 4.24844 ( 1281) SS BOND : bond 0.00103 ( 1) SS BOND : angle 1.04903 ( 2) covalent geometry : bond 0.00282 ( 7921) covalent geometry : angle 0.63013 (10764) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 80 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8836 (t0) REVERT: R 131 ASP cc_start: 0.8775 (t70) cc_final: 0.8568 (t70) REVERT: R 369 LYS cc_start: 0.9327 (mttt) cc_final: 0.8785 (pttp) REVERT: B 106 MET cc_start: 0.8729 (mmm) cc_final: 0.8392 (tpp) REVERT: B 109 ASP cc_start: 0.9406 (m-30) cc_final: 0.9168 (t0) REVERT: B 189 HIS cc_start: 0.7980 (m170) cc_final: 0.7683 (m90) REVERT: B 217 GLU cc_start: 0.8980 (pt0) cc_final: 0.8708 (pt0) REVERT: B 278 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8211 (ttmt) REVERT: B 307 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8258 (tp-100) REVERT: B 322 HIS cc_start: 0.8270 (t-90) cc_final: 0.7462 (t-90) REVERT: A 13 GLN cc_start: 0.9428 (pp30) cc_final: 0.9162 (pp30) REVERT: A 61 MET cc_start: 0.8542 (tmm) cc_final: 0.8023 (tmm) REVERT: A 175 GLN cc_start: 0.8433 (pm20) cc_final: 0.8032 (pm20) REVERT: A 280 LYS cc_start: 0.8969 (tmtt) cc_final: 0.8361 (tmtt) REVERT: A 317 CYS cc_start: 0.7737 (m) cc_final: 0.6794 (p) REVERT: C 26 ASP cc_start: 0.8843 (m-30) cc_final: 0.8572 (t0) REVERT: C 48 ASP cc_start: 0.8577 (t70) cc_final: 0.7865 (t0) outliers start: 22 outliers final: 15 residues processed: 160 average time/residue: 0.2482 time to fit residues: 53.8928 Evaluate side-chains 156 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 85 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS A 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.105367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.072393 restraints weight = 19825.676| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 4.35 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7922 Z= 0.158 Angle : 0.667 16.297 10766 Z= 0.325 Chirality : 0.043 0.213 1269 Planarity : 0.004 0.048 1360 Dihedral : 4.332 46.159 1085 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.43 % Allowed : 17.84 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.27), residues: 1001 helix: 1.72 (0.24), residues: 481 sheet: 0.95 (0.35), residues: 178 loop : -0.52 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 82 HIS 0.004 0.001 HIS R 393 PHE 0.019 0.002 PHE A 241 TYR 0.022 0.001 TYR B 69 ARG 0.005 0.000 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 438) hydrogen bonds : angle 4.31425 ( 1281) SS BOND : bond 0.00257 ( 1) SS BOND : angle 1.15153 ( 2) covalent geometry : bond 0.00350 ( 7921) covalent geometry : angle 0.66670 (10764) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 80 ASP cc_start: 0.9190 (OUTLIER) cc_final: 0.8892 (t0) REVERT: R 131 ASP cc_start: 0.8840 (t70) cc_final: 0.8533 (t0) REVERT: R 369 LYS cc_start: 0.9304 (mttt) cc_final: 0.8844 (ptmt) REVERT: B 106 MET cc_start: 0.8752 (mmm) cc_final: 0.8410 (tpp) REVERT: B 109 ASP cc_start: 0.9406 (m-30) cc_final: 0.9127 (t0) REVERT: B 189 HIS cc_start: 0.8035 (m170) cc_final: 0.7746 (m90) REVERT: B 217 GLU cc_start: 0.8990 (pt0) cc_final: 0.8730 (pt0) REVERT: B 278 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8209 (ttmt) REVERT: B 322 HIS cc_start: 0.8358 (t-90) cc_final: 0.7564 (t-90) REVERT: B 323 MET cc_start: 0.8368 (mmm) cc_final: 0.7557 (mmm) REVERT: A 34 THR cc_start: 0.8437 (t) cc_final: 0.7907 (t) REVERT: A 61 MET cc_start: 0.8545 (tmm) cc_final: 0.7546 (tmm) REVERT: A 172 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8739 (tm-30) REVERT: A 175 GLN cc_start: 0.8575 (pm20) cc_final: 0.8123 (pm20) REVERT: A 280 LYS cc_start: 0.9032 (tmtt) cc_final: 0.8413 (tmtt) REVERT: A 317 CYS cc_start: 0.7770 (m) cc_final: 0.6803 (p) REVERT: C 26 ASP cc_start: 0.9012 (m-30) cc_final: 0.8642 (t0) REVERT: C 38 MET cc_start: 0.8534 (mtp) cc_final: 0.8174 (mpp) REVERT: C 48 ASP cc_start: 0.8617 (t70) cc_final: 0.7726 (t0) outliers start: 20 outliers final: 17 residues processed: 157 average time/residue: 0.1927 time to fit residues: 41.2437 Evaluate side-chains 157 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 418 ASN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 30 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS A 32 GLN A 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.107583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.074631 restraints weight = 19761.948| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 4.21 r_work: 0.3018 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7922 Z= 0.135 Angle : 0.663 16.995 10766 Z= 0.320 Chirality : 0.043 0.250 1269 Planarity : 0.004 0.048 1360 Dihedral : 4.279 43.882 1085 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.79 % Allowed : 17.35 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.26), residues: 1001 helix: 1.75 (0.24), residues: 481 sheet: 0.88 (0.36), residues: 169 loop : -0.51 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 169 HIS 0.004 0.001 HIS R 393 PHE 0.017 0.001 PHE A 241 TYR 0.020 0.001 TYR B 69 ARG 0.004 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 438) hydrogen bonds : angle 4.23294 ( 1281) SS BOND : bond 0.00132 ( 1) SS BOND : angle 1.06482 ( 2) covalent geometry : bond 0.00299 ( 7921) covalent geometry : angle 0.66255 (10764) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 62 GLU cc_start: 0.7693 (mp0) cc_final: 0.7358 (mp0) REVERT: R 80 ASP cc_start: 0.9113 (OUTLIER) cc_final: 0.8867 (t0) REVERT: R 149 LYS cc_start: 0.8702 (mmmm) cc_final: 0.8395 (mmmm) REVERT: R 369 LYS cc_start: 0.9273 (mttt) cc_final: 0.8814 (ptmt) REVERT: B 106 MET cc_start: 0.8826 (mmm) cc_final: 0.8521 (tpp) REVERT: B 109 ASP cc_start: 0.9437 (m-30) cc_final: 0.9148 (t0) REVERT: B 189 HIS cc_start: 0.8099 (m170) cc_final: 0.7836 (m90) REVERT: B 278 LYS cc_start: 0.8629 (mtpt) cc_final: 0.8258 (ttmt) REVERT: B 322 HIS cc_start: 0.8675 (t-90) cc_final: 0.7956 (t-90) REVERT: B 323 MET cc_start: 0.8586 (mmm) cc_final: 0.7877 (mmm) REVERT: A 61 MET cc_start: 0.8980 (tmm) cc_final: 0.8086 (tmm) REVERT: A 172 GLU cc_start: 0.9296 (mt-10) cc_final: 0.8866 (tm-30) REVERT: A 175 GLN cc_start: 0.8725 (pm20) cc_final: 0.8302 (pm20) REVERT: A 280 LYS cc_start: 0.9006 (tmtt) cc_final: 0.8497 (tmtt) REVERT: A 317 CYS cc_start: 0.8103 (m) cc_final: 0.7002 (p) REVERT: C 26 ASP cc_start: 0.9000 (m-30) cc_final: 0.8753 (t0) REVERT: C 48 ASP cc_start: 0.8713 (t70) cc_final: 0.8002 (t70) outliers start: 23 outliers final: 18 residues processed: 157 average time/residue: 0.1923 time to fit residues: 41.5046 Evaluate side-chains 163 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 385 CYS Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 56 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 75 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.111958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.079192 restraints weight = 20197.779| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 4.14 r_work: 0.3237 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7922 Z= 0.112 Angle : 0.681 17.255 10766 Z= 0.323 Chirality : 0.043 0.232 1269 Planarity : 0.003 0.047 1360 Dihedral : 4.125 36.401 1085 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.18 % Allowed : 18.20 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1001 helix: 1.76 (0.24), residues: 482 sheet: 0.95 (0.37), residues: 168 loop : -0.54 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 169 HIS 0.004 0.001 HIS R 393 PHE 0.017 0.001 PHE A 241 TYR 0.018 0.001 TYR B 69 ARG 0.004 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 438) hydrogen bonds : angle 4.12497 ( 1281) SS BOND : bond 0.00016 ( 1) SS BOND : angle 0.91137 ( 2) covalent geometry : bond 0.00240 ( 7921) covalent geometry : angle 0.68053 (10764) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 62 GLU cc_start: 0.8068 (mp0) cc_final: 0.7244 (mp0) REVERT: R 80 ASP cc_start: 0.9198 (OUTLIER) cc_final: 0.8986 (t0) REVERT: R 82 LEU cc_start: 0.9015 (mt) cc_final: 0.8790 (mp) REVERT: R 116 MET cc_start: 0.7522 (ttt) cc_final: 0.7281 (ttm) REVERT: R 149 LYS cc_start: 0.8868 (mmmm) cc_final: 0.8507 (mmmm) REVERT: R 174 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7225 (pp) REVERT: R 369 LYS cc_start: 0.9324 (mttt) cc_final: 0.8837 (ptmt) REVERT: B 106 MET cc_start: 0.9028 (mmm) cc_final: 0.8770 (tpp) REVERT: B 109 ASP cc_start: 0.9443 (m-30) cc_final: 0.9200 (t0) REVERT: B 114 MET cc_start: 0.6683 (ttm) cc_final: 0.6425 (ttm) REVERT: B 189 HIS cc_start: 0.8314 (m170) cc_final: 0.8101 (m90) REVERT: B 278 LYS cc_start: 0.8809 (mtpt) cc_final: 0.8527 (ttmt) REVERT: B 322 HIS cc_start: 0.8794 (t-90) cc_final: 0.8296 (t-90) REVERT: B 323 MET cc_start: 0.8532 (mmm) cc_final: 0.7918 (mmm) REVERT: A 61 MET cc_start: 0.8838 (tmm) cc_final: 0.8445 (tmm) REVERT: A 127 LYS cc_start: 0.9171 (mmmt) cc_final: 0.8824 (mmmm) REVERT: A 172 GLU cc_start: 0.9309 (mt-10) cc_final: 0.9021 (tm-30) REVERT: A 175 GLN cc_start: 0.9071 (pm20) cc_final: 0.8712 (pm20) REVERT: A 246 ASP cc_start: 0.8660 (m-30) cc_final: 0.8458 (m-30) REVERT: A 264 TYR cc_start: 0.8982 (m-10) cc_final: 0.8754 (m-10) REVERT: A 280 LYS cc_start: 0.9175 (tmtt) cc_final: 0.8636 (tmtt) REVERT: A 317 CYS cc_start: 0.8117 (m) cc_final: 0.7633 (p) REVERT: C 26 ASP cc_start: 0.9101 (m-30) cc_final: 0.8795 (t0) REVERT: C 48 ASP cc_start: 0.8691 (t70) cc_final: 0.7747 (t0) outliers start: 18 outliers final: 13 residues processed: 168 average time/residue: 0.2278 time to fit residues: 52.0190 Evaluate side-chains 166 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 70 optimal weight: 0.0870 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.110460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.077579 restraints weight = 20053.217| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 4.09 r_work: 0.3215 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7922 Z= 0.134 Angle : 0.699 17.343 10766 Z= 0.336 Chirality : 0.043 0.220 1269 Planarity : 0.003 0.047 1360 Dihedral : 4.146 36.962 1085 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.94 % Allowed : 19.42 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.27), residues: 1001 helix: 1.70 (0.24), residues: 481 sheet: 0.76 (0.36), residues: 173 loop : -0.50 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 90 HIS 0.004 0.001 HIS R 393 PHE 0.017 0.001 PHE A 241 TYR 0.019 0.001 TYR B 69 ARG 0.005 0.000 ARG R 222 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 438) hydrogen bonds : angle 4.22413 ( 1281) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.87274 ( 2) covalent geometry : bond 0.00300 ( 7921) covalent geometry : angle 0.69882 (10764) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 90 TRP cc_start: 0.8774 (m-90) cc_final: 0.8565 (m-90) REVERT: R 116 MET cc_start: 0.7553 (ttt) cc_final: 0.7314 (ttm) REVERT: R 149 LYS cc_start: 0.8785 (mmmm) cc_final: 0.8446 (mmmm) REVERT: R 174 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7253 (pp) REVERT: R 369 LYS cc_start: 0.9334 (mttt) cc_final: 0.8856 (ptmt) REVERT: B 106 MET cc_start: 0.9098 (mmm) cc_final: 0.8889 (tpp) REVERT: B 109 ASP cc_start: 0.9468 (m-30) cc_final: 0.9264 (t0) REVERT: B 189 HIS cc_start: 0.8328 (m170) cc_final: 0.8106 (m90) REVERT: B 278 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8453 (ttmt) REVERT: B 322 HIS cc_start: 0.8795 (t-90) cc_final: 0.8286 (t-90) REVERT: B 323 MET cc_start: 0.8555 (mmm) cc_final: 0.7949 (mmm) REVERT: A 61 MET cc_start: 0.8853 (tmm) cc_final: 0.8138 (tmm) REVERT: A 127 LYS cc_start: 0.9206 (mmmt) cc_final: 0.8989 (mmmt) REVERT: A 172 GLU cc_start: 0.9307 (mt-10) cc_final: 0.9040 (tm-30) REVERT: A 175 GLN cc_start: 0.9079 (pm20) cc_final: 0.8715 (pm20) REVERT: A 280 LYS cc_start: 0.9185 (tmtt) cc_final: 0.8737 (tmmt) REVERT: A 292 PHE cc_start: 0.9257 (m-80) cc_final: 0.9036 (m-80) REVERT: A 317 CYS cc_start: 0.8163 (m) cc_final: 0.7587 (p) REVERT: C 26 ASP cc_start: 0.9123 (m-30) cc_final: 0.8850 (t0) REVERT: C 48 ASP cc_start: 0.8703 (t70) cc_final: 0.8081 (t70) outliers start: 16 outliers final: 13 residues processed: 163 average time/residue: 0.2033 time to fit residues: 46.1751 Evaluate side-chains 160 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 385 CYS Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 3 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 39 optimal weight: 0.0170 chunk 90 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS A 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.110048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.077233 restraints weight = 19953.702| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.06 r_work: 0.3207 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7922 Z= 0.139 Angle : 0.727 17.169 10766 Z= 0.347 Chirality : 0.044 0.252 1269 Planarity : 0.003 0.047 1360 Dihedral : 4.163 35.864 1085 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.82 % Allowed : 20.02 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.27), residues: 1001 helix: 1.68 (0.24), residues: 482 sheet: 0.79 (0.37), residues: 171 loop : -0.44 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 90 HIS 0.004 0.001 HIS R 393 PHE 0.017 0.001 PHE A 241 TYR 0.018 0.001 TYR B 69 ARG 0.005 0.000 ARG R 222 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 438) hydrogen bonds : angle 4.21429 ( 1281) SS BOND : bond 0.00174 ( 1) SS BOND : angle 0.91923 ( 2) covalent geometry : bond 0.00314 ( 7921) covalent geometry : angle 0.72679 (10764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4557.01 seconds wall clock time: 81 minutes 39.17 seconds (4899.17 seconds total)