Starting phenix.real_space_refine on Sun Jul 27 00:10:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uun_20883/07_2025/6uun_20883.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uun_20883/07_2025/6uun_20883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uun_20883/07_2025/6uun_20883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uun_20883/07_2025/6uun_20883.map" model { file = "/net/cci-nas-00/data/ceres_data/6uun_20883/07_2025/6uun_20883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uun_20883/07_2025/6uun_20883.cif" } resolution = 3.0 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= 0.004 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 64 5.16 5 C 5693 2.51 5 N 1580 2.21 5 O 1643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8980 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1604 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain breaks: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 627 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 98} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 195 Chain: "G" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 380 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 260 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 36} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2565 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 10, 'TRANS': 343} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 342 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 5, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 232 Time building chain proxies: 5.47, per 1000 atoms: 0.61 Number of scatterers: 8980 At special positions: 0 Unit cell: (84.66, 95.45, 160.19, 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 64 16.00 O 1643 8.00 N 1580 7.00 C 5693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS P 16 " - pdb=" SG CYS P 21 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 65 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 282 " 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: 2.83 Conformation dependent library (CDL) restraints added in 1.2 seconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 13 sheets defined 41.1% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 17 through 39 removed outlier: 3.668A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.905A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.572A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.933A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'E' and resid 78 through 83 removed outlier: 4.542A pdb=" N LYS E 81 " --> pdb=" O PRO E 78 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP E 83 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 106 removed outlier: 3.508A pdb=" N TYR E 93 " --> pdb=" O ILE E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 126 removed outlier: 3.638A pdb=" N ILE E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 155 Proline residue: E 153 - end of helix Processing helix chain 'E' and resid 156 through 167 removed outlier: 3.610A pdb=" N LEU E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 22 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.593A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'P' and resid 20 through 22 No H-bonds generated for 'chain 'P' and resid 20 through 22' Processing helix chain 'P' and resid 23 through 34 removed outlier: 4.326A pdb=" N GLN P 32 " --> pdb=" O HIS P 28 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 48 Processing helix chain 'R' and resid 36 through 55 removed outlier: 3.708A pdb=" N ASP R 55 " --> pdb=" O LYS R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 167 removed outlier: 3.955A pdb=" N ASN R 128 " --> pdb=" O TYR R 124 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS R 132 " --> pdb=" O ASN R 128 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU R 133 " --> pdb=" O VAL R 129 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS R 136 " --> pdb=" O HIS R 132 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR R 137 " --> pdb=" O GLU R 133 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS R 167 " --> pdb=" O PHE R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 196 Processing helix chain 'R' and resid 201 through 208 Processing helix chain 'R' and resid 209 through 242 removed outlier: 3.515A pdb=" N LYS R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR R 227 " --> pdb=" O MET R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 261 Processing helix chain 'R' and resid 263 through 279 removed outlier: 3.570A pdb=" N ALA R 267 " --> pdb=" O PRO R 263 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN R 279 " --> pdb=" O SER R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 284 Processing helix chain 'R' and resid 290 through 294 Processing helix chain 'R' and resid 296 through 321 Processing helix chain 'R' and resid 333 through 345 Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 364 through 375 Processing helix chain 'R' and resid 375 through 385 Processing helix chain 'R' and resid 388 through 400 removed outlier: 4.056A pdb=" N ASN R 400 " --> pdb=" O ARG R 396 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.110A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.757A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.543A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.056A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.556A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.516A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.708A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.517A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.544A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 64 through 65 Processing sheet with id=AB3, first strand: chain 'R' and resid 68 through 69 Processing sheet with id=AB4, first strand: chain 'R' and resid 82 through 87 removed outlier: 4.095A pdb=" N THR R 82 " --> pdb=" O CYS R 105 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS R 105 " --> pdb=" O THR R 82 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 3.31 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: 2765 1.34 - 1.45: 1409 1.45 - 1.57: 4896 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 9154 Sorted by residual: bond pdb=" N VAL R 198 " pdb=" CA VAL R 198 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 8.99e+00 bond pdb=" N HIS B 311 " pdb=" CA HIS B 311 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.21e-02 6.83e+03 8.94e+00 bond pdb=" N ILE B 80 " pdb=" CA ILE B 80 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.17e-02 7.31e+03 8.67e+00 bond pdb=" N VAL R 214 " pdb=" CA VAL R 214 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.62e+00 bond pdb=" N VAL R 135 " pdb=" CA VAL R 135 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.27e+00 ... (remaining 9149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 11731 1.53 - 3.06: 621 3.06 - 4.59: 72 4.59 - 6.13: 12 6.13 - 7.66: 3 Bond angle restraints: 12439 Sorted by residual: angle pdb=" N HIS R 289 " pdb=" CA HIS R 289 " pdb=" C HIS R 289 " ideal model delta sigma weight residual 112.72 105.06 7.66 1.14e+00 7.69e-01 4.51e+01 angle pdb=" C LEU E 156 " pdb=" N ILE E 157 " pdb=" CA ILE E 157 " ideal model delta sigma weight residual 120.33 123.99 -3.66 8.00e-01 1.56e+00 2.09e+01 angle pdb=" N TRP B 332 " pdb=" CA TRP B 332 " pdb=" C TRP B 332 " ideal model delta sigma weight residual 113.01 107.74 5.27 1.20e+00 6.94e-01 1.93e+01 angle pdb=" CA ASN R 281 " pdb=" C ASN R 281 " pdb=" O ASN R 281 " ideal model delta sigma weight residual 121.54 117.06 4.48 1.16e+00 7.43e-01 1.49e+01 angle pdb=" N CYS R 282 " pdb=" CA CYS R 282 " pdb=" C CYS R 282 " ideal model delta sigma weight residual 113.56 108.68 4.88 1.39e+00 5.18e-01 1.23e+01 ... (remaining 12434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5073 17.66 - 35.32: 292 35.32 - 52.97: 51 52.97 - 70.63: 13 70.63 - 88.29: 5 Dihedral angle restraints: 5434 sinusoidal: 1935 harmonic: 3499 Sorted by residual: dihedral pdb=" CB CYS E 68 " pdb=" SG CYS E 68 " pdb=" SG CYS E 99 " pdb=" CB CYS E 99 " ideal model delta sinusoidal sigma weight residual -86.00 -139.41 53.41 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS R 212 " pdb=" SG CYS R 212 " pdb=" SG CYS R 282 " pdb=" CB CYS R 282 " ideal model delta sinusoidal sigma weight residual 93.00 142.77 -49.77 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CB CYS P 16 " pdb=" SG CYS P 16 " pdb=" SG CYS P 21 " pdb=" CB CYS P 21 " ideal model delta sinusoidal sigma weight residual -86.00 -43.45 -42.55 1 1.00e+01 1.00e-02 2.53e+01 ... (remaining 5431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1102 0.055 - 0.111: 258 0.111 - 0.166: 54 0.166 - 0.221: 18 0.221 - 0.277: 6 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA LYS B 57 " pdb=" N LYS B 57 " pdb=" C LYS B 57 " pdb=" CB LYS B 57 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1435 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 196 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C THR R 196 " -0.025 2.00e-02 2.50e+03 pdb=" O THR R 196 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA R 197 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO G 55 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 52 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C ARG B 52 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG B 52 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY B 53 " -0.008 2.00e-02 2.50e+03 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1423 2.76 - 3.30: 8778 3.30 - 3.83: 14872 3.83 - 4.37: 18007 4.37 - 4.90: 30630 Nonbonded interactions: 73710 Sorted by model distance: nonbonded pdb=" O ASN R 398 " pdb=" ND2 ASN R 398 " model vdw 2.226 3.120 nonbonded pdb=" OG SER B 227 " pdb=" O PRO N 100 " model vdw 2.270 3.040 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.275 3.120 nonbonded pdb=" O SER N 52 " pdb=" NH1 ARG N 72 " model vdw 2.282 3.120 nonbonded pdb=" OD1 ASP A 274 " pdb=" ND2 ASN A 278 " model vdw 2.283 3.120 ... (remaining 73705 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: 1.780 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.400 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 0.039 9163 Z= 0.366 Angle : 0.730 7.657 12457 Z= 0.515 Chirality : 0.055 0.277 1438 Planarity : 0.003 0.036 1597 Dihedral : 11.918 88.291 3135 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.45 % Allowed : 4.20 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.59 (0.23), residues: 1176 helix: 0.35 (0.25), residues: 433 sheet: -1.39 (0.32), residues: 223 loop : -2.11 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.009 0.001 TYR P 31 ARG 0.002 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.15150 ( 453) hydrogen bonds : angle 6.35703 ( 1287) SS BOND : bond 0.00162 ( 9) SS BOND : angle 1.25497 ( 18) covalent geometry : bond 0.00524 ( 9154) covalent geometry : angle 0.72871 (12439) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 183 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7834 (mt0) cc_final: 0.7143 (tp-100) REVERT: A 34 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7979 (ttmm) REVERT: A 274 ASP cc_start: 0.7228 (t0) cc_final: 0.6908 (t70) REVERT: B 111 TYR cc_start: 0.8834 (m-80) cc_final: 0.8547 (m-80) REVERT: B 124 TYR cc_start: 0.8821 (m-80) cc_final: 0.8550 (m-80) REVERT: B 325 MET cc_start: 0.8077 (tpp) cc_final: 0.7685 (tpt) REVERT: E 167 ARG cc_start: 0.4151 (mpt180) cc_final: 0.3350 (mmm-85) REVERT: G 42 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6530 (mm-30) REVERT: N 80 TYR cc_start: 0.8083 (m-80) cc_final: 0.7666 (m-80) REVERT: N 87 LYS cc_start: 0.7990 (mttp) cc_final: 0.7278 (mtpm) REVERT: R 134 LYS cc_start: 0.6307 (ttpt) cc_final: 0.6106 (mmtt) REVERT: R 139 LEU cc_start: 0.6457 (mm) cc_final: 0.6232 (mm) REVERT: R 213 LYS cc_start: 0.6557 (mtmt) cc_final: 0.6256 (mttt) REVERT: R 332 MET cc_start: 0.6557 (mmp) cc_final: 0.6302 (pmm) REVERT: R 381 SER cc_start: 0.7836 (t) cc_final: 0.7489 (m) outliers start: 4 outliers final: 3 residues processed: 185 average time/residue: 1.2914 time to fit residues: 254.1408 Evaluate side-chains 135 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 127 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.2980 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 29 GLN A 31 GLN A 35 GLN A 262 GLN A 377 ASN A 390 GLN B 6 GLN B 32 GLN B 175 GLN B 237 ASN B 340 ASN N 31 ASN N 35 ASN N 74 ASN N 120 GLN P 24 GLN R 172 GLN R 179 ASN R 219 HIS R 281 ASN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 398 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.177489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119402 restraints weight = 10224.499| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.80 r_work: 0.3237 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9163 Z= 0.163 Angle : 0.558 6.399 12457 Z= 0.298 Chirality : 0.043 0.166 1438 Planarity : 0.004 0.039 1597 Dihedral : 4.638 59.637 1290 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.30 % Allowed : 12.16 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.66 (0.24), residues: 1176 helix: 1.21 (0.25), residues: 458 sheet: -1.17 (0.32), residues: 220 loop : -1.65 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.016 0.001 TYR R 277 ARG 0.006 0.001 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 453) hydrogen bonds : angle 4.63037 ( 1287) SS BOND : bond 0.00197 ( 9) SS BOND : angle 0.88710 ( 18) covalent geometry : bond 0.00369 ( 9154) covalent geometry : angle 0.55704 (12439) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8320 (mt0) cc_final: 0.7444 (tp-100) REVERT: A 34 LYS cc_start: 0.8488 (ttpt) cc_final: 0.8267 (ttmm) REVERT: A 223 ASP cc_start: 0.7881 (p0) cc_final: 0.7649 (t70) REVERT: B 17 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7505 (tt0) REVERT: B 97 SER cc_start: 0.8101 (p) cc_final: 0.7655 (t) REVERT: B 124 TYR cc_start: 0.9010 (m-80) cc_final: 0.8725 (m-80) REVERT: B 127 LYS cc_start: 0.8736 (mmpt) cc_final: 0.8460 (mmtm) REVERT: B 325 MET cc_start: 0.8445 (tpp) cc_final: 0.8051 (tpt) REVERT: E 167 ARG cc_start: 0.4575 (mpt180) cc_final: 0.3655 (mmm-85) REVERT: N 65 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8327 (ttpt) REVERT: N 80 TYR cc_start: 0.8516 (m-80) cc_final: 0.8251 (m-80) REVERT: R 134 LYS cc_start: 0.5982 (ttpt) cc_final: 0.5774 (mmtt) REVERT: R 139 LEU cc_start: 0.6577 (mm) cc_final: 0.6300 (mm) REVERT: R 182 PHE cc_start: 0.7343 (t80) cc_final: 0.6821 (t80) REVERT: R 213 LYS cc_start: 0.6865 (mtmt) cc_final: 0.6459 (mttt) REVERT: R 253 MET cc_start: 0.8053 (ttt) cc_final: 0.7703 (ttp) REVERT: R 269 ILE cc_start: 0.7995 (mm) cc_final: 0.7766 (mp) REVERT: R 332 MET cc_start: 0.6754 (mmp) cc_final: 0.6452 (pmm) REVERT: R 381 SER cc_start: 0.8063 (t) cc_final: 0.7700 (m) outliers start: 29 outliers final: 11 residues processed: 155 average time/residue: 1.2804 time to fit residues: 211.3577 Evaluate side-chains 142 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 215 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 88 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 98 optimal weight: 20.0000 chunk 52 optimal weight: 0.1980 chunk 111 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN N 31 ASN R 370 HIS R 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.179157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123769 restraints weight = 10358.967| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.03 r_work: 0.3247 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9163 Z= 0.154 Angle : 0.522 6.332 12457 Z= 0.279 Chirality : 0.042 0.146 1438 Planarity : 0.003 0.039 1597 Dihedral : 4.600 56.799 1290 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.64 % Allowed : 13.86 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.32 (0.24), residues: 1176 helix: 1.45 (0.25), residues: 466 sheet: -1.02 (0.32), residues: 216 loop : -1.45 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS R 270 PHE 0.014 0.001 PHE A 212 TYR 0.014 0.001 TYR B 105 ARG 0.004 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 453) hydrogen bonds : angle 4.38116 ( 1287) SS BOND : bond 0.00222 ( 9) SS BOND : angle 0.77686 ( 18) covalent geometry : bond 0.00349 ( 9154) covalent geometry : angle 0.52123 (12439) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.926 Fit side-chains REVERT: A 21 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: A 31 GLN cc_start: 0.8297 (mt0) cc_final: 0.7444 (tp-100) REVERT: A 34 LYS cc_start: 0.8491 (ttpt) cc_final: 0.8288 (ttmt) REVERT: A 223 ASP cc_start: 0.8064 (p0) cc_final: 0.7837 (t70) REVERT: A 266 LEU cc_start: 0.8731 (tp) cc_final: 0.8380 (tp) REVERT: B 17 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7493 (tt0) REVERT: B 97 SER cc_start: 0.8213 (p) cc_final: 0.7784 (t) REVERT: B 127 LYS cc_start: 0.8791 (mmpt) cc_final: 0.8524 (mmtm) REVERT: B 325 MET cc_start: 0.8412 (tpp) cc_final: 0.7949 (tpt) REVERT: E 167 ARG cc_start: 0.4823 (mpt180) cc_final: 0.3863 (mmm-85) REVERT: N 65 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8213 (ttpt) REVERT: N 73 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7265 (t0) REVERT: N 80 TYR cc_start: 0.8563 (m-80) cc_final: 0.8242 (m-80) REVERT: N 105 ARG cc_start: 0.7931 (ttp-170) cc_final: 0.7645 (ttp-110) REVERT: N 106 ASP cc_start: 0.8854 (p0) cc_final: 0.8630 (p0) REVERT: R 127 CYS cc_start: 0.4791 (OUTLIER) cc_final: 0.4177 (p) REVERT: R 134 LYS cc_start: 0.6256 (ttpt) cc_final: 0.6002 (mmtt) REVERT: R 165 TYR cc_start: 0.6393 (t80) cc_final: 0.6106 (t80) REVERT: R 213 LYS cc_start: 0.6931 (mtmt) cc_final: 0.6520 (mttt) REVERT: R 253 MET cc_start: 0.8035 (ttt) cc_final: 0.7689 (ttp) REVERT: R 332 MET cc_start: 0.6905 (mmp) cc_final: 0.6405 (pmm) REVERT: R 370 HIS cc_start: 0.6567 (m-70) cc_final: 0.6159 (m90) REVERT: R 381 SER cc_start: 0.8099 (t) cc_final: 0.7716 (m) outliers start: 32 outliers final: 14 residues processed: 151 average time/residue: 1.1829 time to fit residues: 190.5083 Evaluate side-chains 147 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 91 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.178580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.123531 restraints weight = 10345.253| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.11 r_work: 0.3236 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9163 Z= 0.153 Angle : 0.525 6.349 12457 Z= 0.280 Chirality : 0.042 0.159 1438 Planarity : 0.003 0.037 1597 Dihedral : 4.600 56.385 1290 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.98 % Allowed : 14.66 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.17 (0.24), residues: 1176 helix: 1.59 (0.25), residues: 466 sheet: -1.07 (0.32), residues: 219 loop : -1.31 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 99 HIS 0.005 0.001 HIS R 270 PHE 0.014 0.001 PHE R 228 TYR 0.013 0.001 TYR B 105 ARG 0.003 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 453) hydrogen bonds : angle 4.28856 ( 1287) SS BOND : bond 0.00205 ( 9) SS BOND : angle 0.81644 ( 18) covalent geometry : bond 0.00347 ( 9154) covalent geometry : angle 0.52469 (12439) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 1.008 Fit side-chains REVERT: A 17 LYS cc_start: 0.7611 (mmmm) cc_final: 0.7379 (mmmm) REVERT: A 21 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: A 31 GLN cc_start: 0.8301 (mt0) cc_final: 0.7453 (tp-100) REVERT: A 34 LYS cc_start: 0.8504 (ttpt) cc_final: 0.8254 (ttmt) REVERT: A 223 ASP cc_start: 0.8110 (p0) cc_final: 0.7901 (t70) REVERT: A 266 LEU cc_start: 0.8738 (tp) cc_final: 0.8410 (tp) REVERT: A 333 ARG cc_start: 0.5783 (OUTLIER) cc_final: 0.3505 (ttt180) REVERT: B 17 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7503 (tt0) REVERT: B 97 SER cc_start: 0.8211 (p) cc_final: 0.7785 (t) REVERT: B 127 LYS cc_start: 0.8773 (mmpt) cc_final: 0.8521 (mmtm) REVERT: B 325 MET cc_start: 0.8425 (tpp) cc_final: 0.7873 (tpt) REVERT: E 167 ARG cc_start: 0.4849 (mpt180) cc_final: 0.3754 (mmm-85) REVERT: N 5 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7340 (tp40) REVERT: N 65 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8143 (ttpt) REVERT: N 73 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7274 (t0) REVERT: N 80 TYR cc_start: 0.8599 (m-80) cc_final: 0.8329 (m-80) REVERT: N 105 ARG cc_start: 0.7918 (ttp-170) cc_final: 0.7658 (ttp-110) REVERT: R 127 CYS cc_start: 0.4414 (OUTLIER) cc_final: 0.3889 (p) REVERT: R 134 LYS cc_start: 0.6317 (ttpt) cc_final: 0.6055 (mmtt) REVERT: R 165 TYR cc_start: 0.6338 (t80) cc_final: 0.6044 (t80) REVERT: R 213 LYS cc_start: 0.7027 (mtmt) cc_final: 0.6557 (mttt) REVERT: R 253 MET cc_start: 0.8026 (ttt) cc_final: 0.7694 (ttp) REVERT: R 332 MET cc_start: 0.6895 (mmp) cc_final: 0.6270 (pmm) REVERT: R 370 HIS cc_start: 0.6564 (m-70) cc_final: 0.6156 (m90) REVERT: R 381 SER cc_start: 0.8095 (t) cc_final: 0.7694 (m) outliers start: 35 outliers final: 18 residues processed: 153 average time/residue: 1.2757 time to fit residues: 208.5208 Evaluate side-chains 153 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 45 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.0670 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.180695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138074 restraints weight = 10324.702| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.32 r_work: 0.3261 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9163 Z= 0.108 Angle : 0.488 6.463 12457 Z= 0.260 Chirality : 0.041 0.177 1438 Planarity : 0.003 0.034 1597 Dihedral : 4.410 54.952 1290 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.32 % Allowed : 15.11 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1176 helix: 1.74 (0.25), residues: 466 sheet: -0.91 (0.32), residues: 218 loop : -1.18 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 99 HIS 0.004 0.001 HIS R 270 PHE 0.015 0.001 PHE R 228 TYR 0.010 0.001 TYR R 278 ARG 0.002 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 453) hydrogen bonds : angle 4.14069 ( 1287) SS BOND : bond 0.00176 ( 9) SS BOND : angle 0.62069 ( 18) covalent geometry : bond 0.00234 ( 9154) covalent geometry : angle 0.48775 (12439) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: A 31 GLN cc_start: 0.8373 (mt0) cc_final: 0.7545 (tp-100) REVERT: A 266 LEU cc_start: 0.8693 (tp) cc_final: 0.8364 (tp) REVERT: A 333 ARG cc_start: 0.5916 (OUTLIER) cc_final: 0.3581 (ttt180) REVERT: B 97 SER cc_start: 0.8198 (p) cc_final: 0.7847 (t) REVERT: B 127 LYS cc_start: 0.8796 (mmpt) cc_final: 0.8562 (mmtm) REVERT: B 325 MET cc_start: 0.8405 (tpp) cc_final: 0.7873 (tpt) REVERT: E 167 ARG cc_start: 0.4898 (mpt180) cc_final: 0.3877 (mmm-85) REVERT: N 5 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7195 (tp40) REVERT: N 65 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8157 (ttpt) REVERT: N 73 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7255 (t0) REVERT: N 80 TYR cc_start: 0.8619 (m-80) cc_final: 0.8375 (m-80) REVERT: N 89 GLU cc_start: 0.7439 (pt0) cc_final: 0.6921 (pp20) REVERT: N 105 ARG cc_start: 0.7811 (ttp-170) cc_final: 0.7551 (ttp-110) REVERT: P 31 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.6172 (t80) REVERT: R 127 CYS cc_start: 0.4355 (OUTLIER) cc_final: 0.3859 (p) REVERT: R 134 LYS cc_start: 0.6368 (ttpt) cc_final: 0.6083 (mmtt) REVERT: R 213 LYS cc_start: 0.7136 (mtmt) cc_final: 0.6634 (mttt) REVERT: R 253 MET cc_start: 0.8011 (ttt) cc_final: 0.7699 (ttp) REVERT: R 332 MET cc_start: 0.6814 (mmp) cc_final: 0.6263 (pmm) REVERT: R 370 HIS cc_start: 0.6640 (m-70) cc_final: 0.6286 (m90) REVERT: R 381 SER cc_start: 0.8094 (t) cc_final: 0.7725 (m) outliers start: 38 outliers final: 19 residues processed: 159 average time/residue: 1.1596 time to fit residues: 197.2733 Evaluate side-chains 153 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN N 39 GLN R 281 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.177110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.133619 restraints weight = 10298.673| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.40 r_work: 0.3208 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9163 Z= 0.195 Angle : 0.563 7.609 12457 Z= 0.298 Chirality : 0.044 0.208 1438 Planarity : 0.004 0.031 1597 Dihedral : 4.650 54.529 1290 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.86 % Allowed : 16.59 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.00 (0.24), residues: 1176 helix: 1.69 (0.25), residues: 466 sheet: -1.08 (0.31), residues: 217 loop : -1.12 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 99 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.002 PHE A 212 TYR 0.018 0.001 TYR B 105 ARG 0.002 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 453) hydrogen bonds : angle 4.25445 ( 1287) SS BOND : bond 0.00197 ( 9) SS BOND : angle 0.76595 ( 18) covalent geometry : bond 0.00454 ( 9154) covalent geometry : angle 0.56290 (12439) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: A 31 GLN cc_start: 0.8342 (mt0) cc_final: 0.7528 (tp-100) REVERT: A 266 LEU cc_start: 0.8731 (tp) cc_final: 0.8418 (tp) REVERT: A 333 ARG cc_start: 0.5824 (OUTLIER) cc_final: 0.3521 (ttt180) REVERT: B 127 LYS cc_start: 0.8774 (mmpt) cc_final: 0.8543 (mmtm) REVERT: B 325 MET cc_start: 0.8433 (tpp) cc_final: 0.7929 (tpt) REVERT: E 151 ILE cc_start: 0.5294 (OUTLIER) cc_final: 0.5055 (mt) REVERT: E 167 ARG cc_start: 0.4866 (mpt180) cc_final: 0.3786 (mmm-85) REVERT: G 47 GLU cc_start: 0.8409 (pt0) cc_final: 0.8191 (pt0) REVERT: N 5 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7323 (tp40) REVERT: N 80 TYR cc_start: 0.8666 (m-80) cc_final: 0.8424 (m-80) REVERT: N 89 GLU cc_start: 0.7465 (pt0) cc_final: 0.6938 (pp20) REVERT: R 127 CYS cc_start: 0.4184 (OUTLIER) cc_final: 0.3817 (p) REVERT: R 134 LYS cc_start: 0.6433 (ttpt) cc_final: 0.6141 (mmtt) REVERT: R 165 TYR cc_start: 0.6411 (t80) cc_final: 0.6073 (t80) REVERT: R 213 LYS cc_start: 0.7128 (mtmt) cc_final: 0.6617 (mttt) REVERT: R 253 MET cc_start: 0.8021 (ttt) cc_final: 0.7798 (ttt) REVERT: R 332 MET cc_start: 0.6890 (mmp) cc_final: 0.6237 (pmm) REVERT: R 370 HIS cc_start: 0.6638 (m-70) cc_final: 0.6257 (m90) REVERT: R 381 SER cc_start: 0.8194 (t) cc_final: 0.7780 (m) outliers start: 34 outliers final: 22 residues processed: 154 average time/residue: 1.1334 time to fit residues: 186.9118 Evaluate side-chains 151 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.176095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132790 restraints weight = 10382.158| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.61 r_work: 0.3189 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9163 Z= 0.216 Angle : 0.581 6.771 12457 Z= 0.309 Chirality : 0.045 0.232 1438 Planarity : 0.004 0.030 1597 Dihedral : 4.802 54.629 1290 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.43 % Allowed : 17.50 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.07 (0.24), residues: 1176 helix: 1.59 (0.25), residues: 467 sheet: -1.15 (0.31), residues: 217 loop : -1.09 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 99 HIS 0.005 0.001 HIS A 220 PHE 0.016 0.002 PHE R 228 TYR 0.017 0.002 TYR B 105 ARG 0.002 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 453) hydrogen bonds : angle 4.34870 ( 1287) SS BOND : bond 0.00243 ( 9) SS BOND : angle 0.80883 ( 18) covalent geometry : bond 0.00507 ( 9154) covalent geometry : angle 0.58032 (12439) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.933 Fit side-chains REVERT: A 17 LYS cc_start: 0.7485 (mmmm) cc_final: 0.7208 (mmmm) REVERT: A 21 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: A 31 GLN cc_start: 0.8350 (mt0) cc_final: 0.7527 (tp-100) REVERT: A 209 GLU cc_start: 0.8038 (mp0) cc_final: 0.7792 (mp0) REVERT: A 211 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7689 (mmmt) REVERT: A 266 LEU cc_start: 0.8742 (tp) cc_final: 0.8447 (tp) REVERT: A 333 ARG cc_start: 0.5776 (OUTLIER) cc_final: 0.3521 (ttt180) REVERT: B 97 SER cc_start: 0.8319 (p) cc_final: 0.7987 (t) REVERT: B 127 LYS cc_start: 0.8767 (mmpt) cc_final: 0.8538 (mmtm) REVERT: B 325 MET cc_start: 0.8454 (tpp) cc_final: 0.7930 (tpt) REVERT: E 151 ILE cc_start: 0.5266 (OUTLIER) cc_final: 0.5009 (mt) REVERT: E 167 ARG cc_start: 0.4883 (mpt180) cc_final: 0.3808 (mmm-85) REVERT: G 47 GLU cc_start: 0.8402 (pt0) cc_final: 0.8114 (pt0) REVERT: N 5 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7301 (tp40) REVERT: N 73 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7325 (t0) REVERT: N 80 TYR cc_start: 0.8670 (m-80) cc_final: 0.8423 (m-80) REVERT: N 89 GLU cc_start: 0.7447 (pt0) cc_final: 0.6945 (pp20) REVERT: R 127 CYS cc_start: 0.4153 (OUTLIER) cc_final: 0.3759 (p) REVERT: R 134 LYS cc_start: 0.6369 (ttpt) cc_final: 0.6096 (mmtt) REVERT: R 165 TYR cc_start: 0.6472 (t80) cc_final: 0.6153 (t80) REVERT: R 182 PHE cc_start: 0.7660 (t80) cc_final: 0.7202 (t80) REVERT: R 202 GLN cc_start: 0.6164 (tp40) cc_final: 0.5743 (mm-40) REVERT: R 213 LYS cc_start: 0.7087 (mtmt) cc_final: 0.6584 (mttt) REVERT: R 253 MET cc_start: 0.8070 (ttt) cc_final: 0.7860 (ttt) REVERT: R 370 HIS cc_start: 0.6602 (m-70) cc_final: 0.6211 (m90) REVERT: R 381 SER cc_start: 0.8184 (t) cc_final: 0.7777 (m) outliers start: 39 outliers final: 19 residues processed: 149 average time/residue: 1.2001 time to fit residues: 191.7854 Evaluate side-chains 145 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 50 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 281 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.178735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.136820 restraints weight = 10521.536| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.36 r_work: 0.3232 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9163 Z= 0.122 Angle : 0.513 6.654 12457 Z= 0.272 Chirality : 0.042 0.180 1438 Planarity : 0.003 0.031 1597 Dihedral : 4.533 53.826 1290 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.07 % Allowed : 18.86 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.16 (0.25), residues: 1176 helix: 1.81 (0.25), residues: 463 sheet: -1.01 (0.31), residues: 216 loop : -0.99 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 99 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.001 PHE R 228 TYR 0.019 0.001 TYR P 31 ARG 0.002 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 453) hydrogen bonds : angle 4.23158 ( 1287) SS BOND : bond 0.00191 ( 9) SS BOND : angle 0.71619 ( 18) covalent geometry : bond 0.00276 ( 9154) covalent geometry : angle 0.51271 (12439) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.944 Fit side-chains REVERT: A 17 LYS cc_start: 0.7394 (mmmm) cc_final: 0.7084 (mmmm) REVERT: A 21 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: A 31 GLN cc_start: 0.8313 (mt0) cc_final: 0.7522 (tp-100) REVERT: A 333 ARG cc_start: 0.5897 (OUTLIER) cc_final: 0.3579 (ttt180) REVERT: B 127 LYS cc_start: 0.8758 (mmpt) cc_final: 0.8549 (mmtm) REVERT: B 325 MET cc_start: 0.8436 (tpp) cc_final: 0.7902 (tpt) REVERT: E 167 ARG cc_start: 0.4791 (mpt180) cc_final: 0.3734 (mmm-85) REVERT: G 47 GLU cc_start: 0.8316 (pt0) cc_final: 0.8014 (pt0) REVERT: N 73 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7289 (t0) REVERT: N 89 GLU cc_start: 0.7446 (pt0) cc_final: 0.6924 (pp20) REVERT: R 127 CYS cc_start: 0.3969 (OUTLIER) cc_final: 0.3642 (p) REVERT: R 134 LYS cc_start: 0.6384 (ttpt) cc_final: 0.6084 (mmtt) REVERT: R 165 TYR cc_start: 0.6382 (t80) cc_final: 0.6107 (t80) REVERT: R 182 PHE cc_start: 0.7674 (t80) cc_final: 0.7204 (t80) REVERT: R 202 GLN cc_start: 0.6382 (tp40) cc_final: 0.5804 (mm-40) REVERT: R 213 LYS cc_start: 0.7179 (mtmt) cc_final: 0.6657 (mttt) REVERT: R 215 SER cc_start: 0.6432 (OUTLIER) cc_final: 0.5915 (p) REVERT: R 253 MET cc_start: 0.8013 (ttt) cc_final: 0.7812 (ttt) REVERT: R 370 HIS cc_start: 0.6605 (m-70) cc_final: 0.6242 (m90) REVERT: R 381 SER cc_start: 0.8151 (t) cc_final: 0.7756 (m) outliers start: 27 outliers final: 17 residues processed: 150 average time/residue: 1.1403 time to fit residues: 183.1728 Evaluate side-chains 153 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 108 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN G 59 ASN ** R 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 281 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.177965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121749 restraints weight = 10293.481| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.89 r_work: 0.3253 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9163 Z= 0.147 Angle : 0.539 7.003 12457 Z= 0.285 Chirality : 0.042 0.157 1438 Planarity : 0.003 0.030 1597 Dihedral : 4.569 54.305 1290 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.41 % Allowed : 18.75 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.19 (0.25), residues: 1176 helix: 1.80 (0.25), residues: 464 sheet: -0.99 (0.32), residues: 216 loop : -0.95 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 99 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE R 228 TYR 0.020 0.001 TYR P 31 ARG 0.002 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 453) hydrogen bonds : angle 4.23603 ( 1287) SS BOND : bond 0.00203 ( 9) SS BOND : angle 0.93934 ( 18) covalent geometry : bond 0.00340 ( 9154) covalent geometry : angle 0.53867 (12439) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.004 Fit side-chains REVERT: A 17 LYS cc_start: 0.7321 (mmmm) cc_final: 0.7030 (mmmm) REVERT: A 21 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: A 31 GLN cc_start: 0.8288 (mt0) cc_final: 0.7467 (tp-100) REVERT: A 266 LEU cc_start: 0.8637 (tp) cc_final: 0.8270 (tp) REVERT: A 333 ARG cc_start: 0.5803 (OUTLIER) cc_final: 0.3511 (ttt180) REVERT: B 127 LYS cc_start: 0.8725 (mmpt) cc_final: 0.8520 (mmtm) REVERT: B 325 MET cc_start: 0.8395 (tpp) cc_final: 0.7866 (tpt) REVERT: E 151 ILE cc_start: 0.5518 (OUTLIER) cc_final: 0.5222 (OUTLIER) REVERT: E 167 ARG cc_start: 0.4766 (mpt180) cc_final: 0.3815 (mmm-85) REVERT: G 47 GLU cc_start: 0.8329 (pt0) cc_final: 0.8040 (pt0) REVERT: N 65 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8127 (ttpt) REVERT: N 73 ASP cc_start: 0.7630 (t70) cc_final: 0.7219 (t0) REVERT: N 89 GLU cc_start: 0.7380 (pt0) cc_final: 0.6879 (pp20) REVERT: N 105 ARG cc_start: 0.7753 (ttp-170) cc_final: 0.7530 (ttp-110) REVERT: R 127 CYS cc_start: 0.3985 (OUTLIER) cc_final: 0.3650 (p) REVERT: R 134 LYS cc_start: 0.6327 (ttpt) cc_final: 0.6005 (mmtt) REVERT: R 165 TYR cc_start: 0.6360 (t80) cc_final: 0.6083 (t80) REVERT: R 182 PHE cc_start: 0.7611 (t80) cc_final: 0.7124 (t80) REVERT: R 202 GLN cc_start: 0.6429 (tp40) cc_final: 0.5811 (mm-40) REVERT: R 213 LYS cc_start: 0.7153 (mtmt) cc_final: 0.6640 (mttt) REVERT: R 215 SER cc_start: 0.6406 (OUTLIER) cc_final: 0.5893 (p) REVERT: R 253 MET cc_start: 0.7965 (ttt) cc_final: 0.7763 (ttt) REVERT: R 370 HIS cc_start: 0.6550 (m-70) cc_final: 0.6178 (m90) REVERT: R 373 MET cc_start: 0.7276 (ttp) cc_final: 0.6942 (ttp) REVERT: R 381 SER cc_start: 0.8125 (t) cc_final: 0.7695 (m) outliers start: 30 outliers final: 21 residues processed: 150 average time/residue: 1.1908 time to fit residues: 190.8725 Evaluate side-chains 153 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 113 optimal weight: 0.0970 chunk 40 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 8 optimal weight: 0.0770 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN G 59 ASN R 281 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.178501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.135016 restraints weight = 10502.630| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.18 r_work: 0.3239 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9163 Z= 0.106 Angle : 0.507 7.439 12457 Z= 0.269 Chirality : 0.041 0.151 1438 Planarity : 0.003 0.031 1597 Dihedral : 4.375 52.715 1290 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.84 % Allowed : 19.43 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1176 helix: 2.04 (0.25), residues: 458 sheet: -0.79 (0.32), residues: 212 loop : -0.87 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 99 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE R 228 TYR 0.024 0.001 TYR P 31 ARG 0.003 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03009 ( 453) hydrogen bonds : angle 4.11069 ( 1287) SS BOND : bond 0.00153 ( 9) SS BOND : angle 0.71009 ( 18) covalent geometry : bond 0.00233 ( 9154) covalent geometry : angle 0.50697 (12439) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7181 (mmmm) cc_final: 0.6949 (mmmm) REVERT: A 21 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: A 31 GLN cc_start: 0.8330 (mt0) cc_final: 0.7541 (tp-100) REVERT: A 230 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8085 (mt-10) REVERT: A 333 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.3521 (ttt180) REVERT: B 127 LYS cc_start: 0.8738 (mmpt) cc_final: 0.8523 (mmtm) REVERT: B 325 MET cc_start: 0.8439 (tpp) cc_final: 0.7885 (tpt) REVERT: E 151 ILE cc_start: 0.5494 (OUTLIER) cc_final: 0.5194 (mt) REVERT: E 167 ARG cc_start: 0.4688 (mpt180) cc_final: 0.3767 (mmm-85) REVERT: G 47 GLU cc_start: 0.8292 (pt0) cc_final: 0.7999 (pt0) REVERT: N 73 ASP cc_start: 0.7628 (t70) cc_final: 0.7199 (t0) REVERT: N 89 GLU cc_start: 0.7413 (pt0) cc_final: 0.6894 (pp20) REVERT: R 127 CYS cc_start: 0.3772 (OUTLIER) cc_final: 0.3520 (p) REVERT: R 134 LYS cc_start: 0.6282 (ttpt) cc_final: 0.5975 (mmtt) REVERT: R 182 PHE cc_start: 0.7607 (t80) cc_final: 0.7080 (t80) REVERT: R 202 GLN cc_start: 0.6587 (tp40) cc_final: 0.5900 (mm-40) REVERT: R 213 LYS cc_start: 0.7160 (mtmt) cc_final: 0.6658 (mttt) REVERT: R 215 SER cc_start: 0.6463 (OUTLIER) cc_final: 0.5928 (p) REVERT: R 253 MET cc_start: 0.7924 (ttt) cc_final: 0.7716 (ttt) REVERT: R 370 HIS cc_start: 0.6542 (m-70) cc_final: 0.6230 (m90) REVERT: R 373 MET cc_start: 0.7226 (ttp) cc_final: 0.6872 (ttp) REVERT: R 381 SER cc_start: 0.8078 (t) cc_final: 0.7683 (m) outliers start: 25 outliers final: 17 residues processed: 154 average time/residue: 1.2013 time to fit residues: 197.5988 Evaluate side-chains 153 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 66 optimal weight: 0.0050 chunk 43 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 85 optimal weight: 50.0000 chunk 68 optimal weight: 0.6980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN R 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.180640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138379 restraints weight = 10356.712| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.03 r_work: 0.3288 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9163 Z= 0.107 Angle : 0.506 7.108 12457 Z= 0.268 Chirality : 0.041 0.151 1438 Planarity : 0.003 0.030 1597 Dihedral : 4.344 53.358 1290 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.95 % Allowed : 19.55 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.52 (0.25), residues: 1176 helix: 2.13 (0.25), residues: 458 sheet: -0.62 (0.32), residues: 211 loop : -0.88 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE R 228 TYR 0.017 0.001 TYR P 31 ARG 0.004 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03004 ( 453) hydrogen bonds : angle 4.08199 ( 1287) SS BOND : bond 0.00150 ( 9) SS BOND : angle 0.72959 ( 18) covalent geometry : bond 0.00239 ( 9154) covalent geometry : angle 0.50609 (12439) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7737.03 seconds wall clock time: 133 minutes 29.23 seconds (8009.23 seconds total)