Starting phenix.real_space_refine on Fri Feb 14 11:25:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ki1_22883/02_2025/7ki1_22883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ki1_22883/02_2025/7ki1_22883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ki1_22883/02_2025/7ki1_22883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ki1_22883/02_2025/7ki1_22883.map" model { file = "/net/cci-nas-00/data/ceres_data/7ki1_22883/02_2025/7ki1_22883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ki1_22883/02_2025/7ki1_22883.cif" } resolution = 2.5 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 6497 2.51 5 N 1755 2.21 5 O 1954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10265 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2772 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} 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: "R" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3186 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 370} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 236 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.50, per 1000 atoms: 0.54 Number of scatterers: 10265 At special positions: 0 Unit cell: (92.939, 184.671, 102.595, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1954 8.00 N 1755 7.00 C 6497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.04 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.3 seconds 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 45.0% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.509A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.518A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 109 removed outlier: 3.633A pdb=" N THR A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 124 through 135 Processing helix chain 'A' and resid 143 through 155 removed outlier: 3.663A pdb=" N GLU A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.603A pdb=" N CYS A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 181 removed outlier: 3.623A pdb=" N LYS A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 Processing helix chain 'A' and resid 193 through 200 removed outlier: 3.586A pdb=" N CYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.513A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.564A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.513A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 22 removed outlier: 3.627A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.634A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.597A pdb=" N SER R 49 " --> pdb=" O GLN R 45 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 93 removed outlier: 4.482A pdb=" N SER R 93 " --> pdb=" O PRO R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 141 Processing helix chain 'R' and resid 142 through 169 removed outlier: 3.561A pdb=" N GLY R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 173 Processing helix chain 'R' and resid 174 through 198 Processing helix chain 'R' and resid 200 through 205 Processing helix chain 'R' and resid 215 through 223 Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.774A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 274 removed outlier: 3.645A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 291 Proline residue: R 283 - end of helix removed outlier: 3.504A pdb=" N VAL R 287 " --> pdb=" O PRO R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 298 Processing helix chain 'R' and resid 306 through 338 Proline residue: R 312 - end of helix removed outlier: 3.794A pdb=" N ALA R 337 " --> pdb=" O SER R 333 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN R 338 " --> pdb=" O LYS R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 366 removed outlier: 3.748A pdb=" N ILE R 366 " --> pdb=" O HIS R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 380 Processing helix chain 'R' and resid 381 through 403 removed outlier: 3.977A pdb=" N PHE R 390 " --> pdb=" O THR R 386 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR R 391 " --> pdb=" O GLU R 387 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 419 Processing helix chain 'P' and resid 8 through 36 removed outlier: 3.729A pdb=" N GLU P 27 " --> pdb=" O GLN P 23 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG P 36 " --> pdb=" O LEU P 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.456A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.760A 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: 6.541A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.574A 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: 6.938A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.907A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.696A 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: 3.557A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.781A 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: 6.754A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.264A 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: 6.514A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.942A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.669A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AB3, first strand: chain 'R' and resid 79 through 84 removed outlier: 3.773A pdb=" N SER R 79 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR R 101 " --> pdb=" O ASP R 122 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1392 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: 2.99 Time building geometry restraints manager: 3.15 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: 3270 1.34 - 1.46: 2055 1.46 - 1.58: 5018 1.58 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 10422 Sorted by residual: bond pdb=" C LEU R 118 " pdb=" N PRO R 119 " ideal model delta sigma weight residual 1.332 1.384 -0.052 1.34e-02 5.57e+03 1.50e+01 bond pdb=" C ASP R 293 " pdb=" N GLU R 294 " ideal model delta sigma weight residual 1.331 1.281 0.050 1.33e-02 5.65e+03 1.44e+01 bond pdb=" C ARG R 421 " pdb=" N LEU R 422 " ideal model delta sigma weight residual 1.334 1.288 0.047 1.27e-02 6.20e+03 1.36e+01 bond pdb=" C ASP B 38 " pdb=" N PRO B 39 " ideal model delta sigma weight residual 1.332 1.380 -0.048 1.34e-02 5.57e+03 1.30e+01 bond pdb=" C LEU R 422 " pdb=" N GLU R 423 " ideal model delta sigma weight residual 1.329 1.377 -0.048 1.40e-02 5.10e+03 1.20e+01 ... (remaining 10417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 13139 1.77 - 3.53: 889 3.53 - 5.30: 93 5.30 - 7.06: 19 7.06 - 8.83: 2 Bond angle restraints: 14142 Sorted by residual: angle pdb=" N PHE R 381 " pdb=" CA PHE R 381 " pdb=" C PHE R 381 " ideal model delta sigma weight residual 111.96 103.13 8.83 1.41e+00 5.03e-01 3.92e+01 angle pdb=" N PHE R 143 " pdb=" CA PHE R 143 " pdb=" C PHE R 143 " ideal model delta sigma weight residual 111.28 104.99 6.29 1.09e+00 8.42e-01 3.33e+01 angle pdb=" N TYR R 305 " pdb=" CA TYR R 305 " pdb=" C TYR R 305 " ideal model delta sigma weight residual 113.50 106.68 6.82 1.23e+00 6.61e-01 3.07e+01 angle pdb=" N ARG R 380 " pdb=" CA ARG R 380 " pdb=" C ARG R 380 " ideal model delta sigma weight residual 113.17 106.33 6.84 1.26e+00 6.30e-01 2.94e+01 angle pdb=" C ASP B 38 " pdb=" N PRO B 39 " pdb=" CA PRO B 39 " ideal model delta sigma weight residual 119.78 124.91 -5.13 1.03e+00 9.43e-01 2.48e+01 ... (remaining 14137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5509 17.82 - 35.63: 495 35.63 - 53.45: 137 53.45 - 71.27: 28 71.27 - 89.08: 12 Dihedral angle restraints: 6181 sinusoidal: 2426 harmonic: 3755 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 171.19 -78.19 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual -86.00 -148.30 62.30 1 1.00e+01 1.00e-02 5.14e+01 dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -150.91 -29.09 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 6178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1247 0.068 - 0.137: 260 0.137 - 0.205: 47 0.205 - 0.273: 6 0.273 - 0.341: 4 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CA GLU R 128 " pdb=" N GLU R 128 " pdb=" C GLU R 128 " pdb=" CB GLU R 128 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA ARG R 376 " pdb=" N ARG R 376 " pdb=" C ARG R 376 " pdb=" CB ARG R 376 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA VAL R 370 " pdb=" N VAL R 370 " pdb=" C VAL R 370 " pdb=" CB VAL R 370 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1561 not shown) Planarity restraints: 1805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO B 236 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR P 19 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C TYR P 19 " 0.036 2.00e-02 2.50e+03 pdb=" O TYR P 19 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU P 20 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 141 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C LEU R 141 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU R 141 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU R 142 " 0.012 2.00e-02 2.50e+03 ... (remaining 1802 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2429 2.79 - 3.31: 9798 3.31 - 3.84: 17356 3.84 - 4.37: 22184 4.37 - 4.90: 35911 Nonbonded interactions: 87678 Sorted by model distance: nonbonded pdb=" O SER A 51 " pdb=" ND2 ASN A 292 " model vdw 2.257 3.120 nonbonded pdb=" N ARG R 64 " pdb=" OD1 ASP R 74 " model vdw 2.284 3.120 nonbonded pdb=" O THR A 325 " pdb=" OG1 THR A 325 " model vdw 2.296 3.040 nonbonded pdb=" O ASN R 115 " pdb=" OG SER R 116 " model vdw 2.321 3.040 nonbonded pdb=" O HOH R 506 " pdb=" O HOH R 507 " model vdw 2.322 3.040 ... (remaining 87673 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.560 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:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 : 0.008 0.068 10422 Z= 0.523 Angle : 0.931 8.830 14142 Z= 0.633 Chirality : 0.061 0.341 1564 Planarity : 0.005 0.056 1805 Dihedral : 15.536 89.084 3733 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.28 % Allowed : 12.56 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.22), residues: 1261 helix: -1.58 (0.20), residues: 532 sheet: -0.20 (0.31), residues: 228 loop : -0.69 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 47 HIS 0.008 0.002 HIS R 99 PHE 0.022 0.002 PHE B 151 TYR 0.024 0.003 TYR R 69 ARG 0.014 0.001 ARG R 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 1.778 Fit side-chains REVERT: B 23 LYS cc_start: 0.8124 (tttp) cc_final: 0.7912 (tttm) REVERT: B 217 MET cc_start: 0.7777 (ppp) cc_final: 0.7420 (pmm) outliers start: 3 outliers final: 1 residues processed: 153 average time/residue: 1.6343 time to fit residues: 264.7707 Evaluate side-chains 131 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 13 GLN R 177 ASN R 182 ASN R 263 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.198499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109973 restraints weight = 9928.518| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.80 r_work: 0.2968 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10422 Z= 0.257 Angle : 0.619 5.900 14142 Z= 0.339 Chirality : 0.044 0.158 1564 Planarity : 0.005 0.058 1805 Dihedral : 5.536 51.190 1405 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.49 % Allowed : 13.39 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.22), residues: 1261 helix: 0.12 (0.22), residues: 535 sheet: -0.03 (0.32), residues: 227 loop : -0.53 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 39 HIS 0.004 0.001 HIS A 362 PHE 0.016 0.002 PHE A 212 TYR 0.021 0.002 TYR R 148 ARG 0.005 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7947 (pptt) cc_final: 0.7296 (ptmm) REVERT: A 20 ARG cc_start: 0.7725 (ptp90) cc_final: 0.7477 (ptp90) REVERT: B 23 LYS cc_start: 0.8214 (tttp) cc_final: 0.7678 (tmtm) REVERT: B 44 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7897 (mt0) REVERT: B 146 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8713 (tp) REVERT: B 197 ARG cc_start: 0.8863 (mtp180) cc_final: 0.8625 (mtm110) REVERT: B 217 MET cc_start: 0.8752 (ppp) cc_final: 0.8425 (pmm) REVERT: G 36 ASP cc_start: 0.8510 (m-30) cc_final: 0.8292 (m-30) REVERT: G 37 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8408 (mp) REVERT: R 41 GLU cc_start: 0.5984 (mm-30) cc_final: 0.5471 (tt0) REVERT: R 232 LEU cc_start: 0.7322 (tp) cc_final: 0.6738 (mm) REVERT: R 262 GLU cc_start: 0.6081 (OUTLIER) cc_final: 0.5845 (tp30) REVERT: R 303 MET cc_start: 0.7567 (mmt) cc_final: 0.7292 (tpt) REVERT: P 9 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6385 (mp0) outliers start: 27 outliers final: 7 residues processed: 158 average time/residue: 1.4723 time to fit residues: 247.8158 Evaluate side-chains 136 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 79 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 155 ASN R 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.199051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.110335 restraints weight = 10121.145| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.05 r_work: 0.2962 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10422 Z= 0.213 Angle : 0.551 5.363 14142 Z= 0.300 Chirality : 0.042 0.156 1564 Planarity : 0.004 0.062 1805 Dihedral : 5.051 30.261 1403 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.42 % Allowed : 14.04 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1261 helix: 0.87 (0.23), residues: 536 sheet: 0.17 (0.32), residues: 228 loop : -0.39 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.014 0.002 PHE A 212 TYR 0.021 0.001 TYR R 148 ARG 0.003 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7857 (pptt) cc_final: 0.7189 (ptmm) REVERT: A 20 ARG cc_start: 0.7581 (ptp90) cc_final: 0.7329 (ptp90) REVERT: A 203 LEU cc_start: 0.4481 (OUTLIER) cc_final: 0.4003 (tt) REVERT: A 392 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8607 (mt-10) REVERT: B 23 LYS cc_start: 0.8188 (tttp) cc_final: 0.7648 (tmtm) REVERT: B 42 ARG cc_start: 0.7642 (tpt170) cc_final: 0.7284 (tpt170) REVERT: B 44 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: B 59 TYR cc_start: 0.9243 (OUTLIER) cc_final: 0.8160 (t80) REVERT: B 146 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8683 (tp) REVERT: B 197 ARG cc_start: 0.8851 (mtp180) cc_final: 0.8619 (mtm110) REVERT: B 217 MET cc_start: 0.8795 (ppp) cc_final: 0.8416 (pmm) REVERT: B 340 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8263 (m-40) REVERT: G 36 ASP cc_start: 0.8564 (m-30) cc_final: 0.8290 (m-30) REVERT: G 37 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8291 (mt) REVERT: G 47 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7368 (pt0) REVERT: R 41 GLU cc_start: 0.6176 (mm-30) cc_final: 0.5743 (tt0) REVERT: R 232 LEU cc_start: 0.7348 (tp) cc_final: 0.6667 (mm) REVERT: R 262 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.6069 (tp30) REVERT: R 292 GLU cc_start: 0.6932 (tt0) cc_final: 0.6657 (tp30) REVERT: R 407 ASN cc_start: 0.8052 (OUTLIER) cc_final: 0.7738 (m-40) REVERT: P 9 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6431 (mp0) outliers start: 37 outliers final: 15 residues processed: 158 average time/residue: 1.5243 time to fit residues: 256.4327 Evaluate side-chains 150 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 407 ASN Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 55 optimal weight: 0.0270 chunk 35 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 93 optimal weight: 40.0000 chunk 120 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.200880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.113085 restraints weight = 10047.367| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.82 r_work: 0.3021 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10422 Z= 0.152 Angle : 0.492 4.950 14142 Z= 0.268 Chirality : 0.040 0.152 1564 Planarity : 0.004 0.063 1805 Dihedral : 4.695 30.667 1403 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.86 % Allowed : 16.07 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.23), residues: 1261 helix: 1.29 (0.23), residues: 542 sheet: 0.26 (0.32), residues: 228 loop : -0.30 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.014 0.001 PHE A 212 TYR 0.018 0.001 TYR R 148 ARG 0.002 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6906 (pt0) cc_final: 0.6215 (pp20) REVERT: A 17 LYS cc_start: 0.7873 (pptt) cc_final: 0.7189 (ptmm) REVERT: A 203 LEU cc_start: 0.4410 (OUTLIER) cc_final: 0.3959 (tt) REVERT: A 392 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8506 (mt-10) REVERT: B 15 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7095 (ttmm) REVERT: B 23 LYS cc_start: 0.8164 (tttp) cc_final: 0.7632 (tmtm) REVERT: B 42 ARG cc_start: 0.7671 (tpt170) cc_final: 0.7397 (tpt170) REVERT: B 44 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7890 (mt0) REVERT: B 46 ARG cc_start: 0.8576 (mmt-90) cc_final: 0.8228 (mmp80) REVERT: B 59 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.8062 (t80) REVERT: B 134 ARG cc_start: 0.7879 (ptp-110) cc_final: 0.7056 (ppt170) REVERT: B 146 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8642 (tp) REVERT: B 155 ASN cc_start: 0.8916 (t0) cc_final: 0.8708 (t0) REVERT: B 197 ARG cc_start: 0.8869 (mtp180) cc_final: 0.8657 (mtp85) REVERT: B 217 MET cc_start: 0.8812 (ppp) cc_final: 0.8446 (pmm) REVERT: B 340 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8306 (m110) REVERT: G 36 ASP cc_start: 0.8485 (m-30) cc_final: 0.8126 (m-30) REVERT: R 41 GLU cc_start: 0.6186 (mm-30) cc_final: 0.5765 (tt0) REVERT: R 123 LEU cc_start: 0.2545 (OUTLIER) cc_final: 0.2074 (pp) REVERT: R 232 LEU cc_start: 0.7293 (tp) cc_final: 0.6621 (mm) REVERT: R 376 ARG cc_start: 0.5507 (mmp80) cc_final: 0.5128 (mmp80) REVERT: R 407 ASN cc_start: 0.8038 (OUTLIER) cc_final: 0.7699 (m-40) REVERT: R 418 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6421 (pt0) REVERT: P 9 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6379 (mp0) outliers start: 31 outliers final: 9 residues processed: 164 average time/residue: 1.4456 time to fit residues: 252.7544 Evaluate side-chains 147 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 407 ASN Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain R residue 420 TRP Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 32 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.199438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.111269 restraints weight = 10015.209| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.00 r_work: 0.2967 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10422 Z= 0.217 Angle : 0.530 5.604 14142 Z= 0.287 Chirality : 0.042 0.155 1564 Planarity : 0.004 0.064 1805 Dihedral : 4.782 32.672 1403 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.23 % Allowed : 16.34 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.24), residues: 1261 helix: 1.36 (0.23), residues: 541 sheet: 0.21 (0.32), residues: 228 loop : -0.26 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 362 PHE 0.014 0.002 PHE A 212 TYR 0.020 0.001 TYR R 148 ARG 0.006 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6909 (pt0) cc_final: 0.6240 (pp20) REVERT: A 17 LYS cc_start: 0.7880 (pptt) cc_final: 0.7222 (ptmm) REVERT: A 203 LEU cc_start: 0.4411 (OUTLIER) cc_final: 0.3962 (tt) REVERT: A 392 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8567 (mt-10) REVERT: B 15 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7125 (ttmm) REVERT: B 23 LYS cc_start: 0.8166 (tttp) cc_final: 0.7609 (tmtm) REVERT: B 42 ARG cc_start: 0.7662 (tpt170) cc_final: 0.7405 (tpt170) REVERT: B 44 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: B 46 ARG cc_start: 0.8604 (mmt-90) cc_final: 0.8239 (mmp80) REVERT: B 59 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.8175 (t80) REVERT: B 134 ARG cc_start: 0.7892 (ptp-110) cc_final: 0.7225 (ppp80) REVERT: B 146 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8703 (tp) REVERT: B 155 ASN cc_start: 0.8952 (t0) cc_final: 0.8746 (t0) REVERT: B 197 ARG cc_start: 0.8849 (mtp180) cc_final: 0.8619 (mtp85) REVERT: B 217 MET cc_start: 0.8829 (ppp) cc_final: 0.8453 (pmm) REVERT: G 36 ASP cc_start: 0.8586 (m-30) cc_final: 0.8270 (m-30) REVERT: R 41 GLU cc_start: 0.6181 (mm-30) cc_final: 0.5768 (tt0) REVERT: R 376 ARG cc_start: 0.5669 (mmp80) cc_final: 0.5276 (mmp80) REVERT: R 407 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7764 (m-40) REVERT: P 9 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6332 (mp0) outliers start: 35 outliers final: 16 residues processed: 156 average time/residue: 1.4488 time to fit residues: 240.9220 Evaluate side-chains 156 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 303 MET Chi-restraints excluded: chain R residue 351 LYS Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 407 ASN Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain R residue 420 TRP Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 79 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 91 optimal weight: 40.0000 chunk 66 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.200380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.112483 restraints weight = 10094.883| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.03 r_work: 0.2985 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10422 Z= 0.171 Angle : 0.497 5.015 14142 Z= 0.269 Chirality : 0.041 0.152 1564 Planarity : 0.004 0.063 1805 Dihedral : 4.615 32.649 1403 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.68 % Allowed : 17.54 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.24), residues: 1261 helix: 1.56 (0.23), residues: 540 sheet: 0.21 (0.32), residues: 229 loop : -0.23 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.013 0.001 PHE A 212 TYR 0.020 0.001 TYR R 148 ARG 0.006 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6837 (pt0) cc_final: 0.6186 (pp20) REVERT: A 17 LYS cc_start: 0.7720 (pptt) cc_final: 0.7060 (ptpt) REVERT: A 203 LEU cc_start: 0.4411 (OUTLIER) cc_final: 0.3969 (tt) REVERT: A 392 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8538 (mt-10) REVERT: B 15 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7131 (ttmm) REVERT: B 23 LYS cc_start: 0.8165 (tttp) cc_final: 0.7618 (tmtm) REVERT: B 42 ARG cc_start: 0.7643 (tpt170) cc_final: 0.7240 (tpt170) REVERT: B 44 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7892 (mt0) REVERT: B 59 TYR cc_start: 0.9237 (OUTLIER) cc_final: 0.8084 (t80) REVERT: B 134 ARG cc_start: 0.7862 (ptp-110) cc_final: 0.7207 (ppp80) REVERT: B 146 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8680 (tp) REVERT: B 217 MET cc_start: 0.8819 (ppp) cc_final: 0.8430 (pmm) REVERT: B 298 ASP cc_start: 0.9123 (t0) cc_final: 0.8874 (t0) REVERT: G 36 ASP cc_start: 0.8567 (m-30) cc_final: 0.8169 (m-30) REVERT: R 41 GLU cc_start: 0.5978 (mm-30) cc_final: 0.5558 (tt0) REVERT: R 376 ARG cc_start: 0.5754 (mmp80) cc_final: 0.5351 (mmp80) REVERT: R 407 ASN cc_start: 0.8113 (OUTLIER) cc_final: 0.7769 (m-40) REVERT: R 418 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6518 (pt0) REVERT: P 9 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6416 (mp0) outliers start: 29 outliers final: 13 residues processed: 147 average time/residue: 1.5875 time to fit residues: 247.4788 Evaluate side-chains 142 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 303 MET Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 407 ASN Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain R residue 420 TRP Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 95 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.200663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.112997 restraints weight = 10209.995| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.99 r_work: 0.2986 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10422 Z= 0.169 Angle : 0.489 5.015 14142 Z= 0.265 Chirality : 0.041 0.154 1564 Planarity : 0.004 0.063 1805 Dihedral : 4.540 33.635 1403 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.68 % Allowed : 17.54 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.24), residues: 1261 helix: 1.77 (0.23), residues: 534 sheet: 0.23 (0.32), residues: 231 loop : -0.21 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.013 0.001 PHE A 212 TYR 0.020 0.001 TYR R 148 ARG 0.007 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6733 (pt0) cc_final: 0.6093 (pp20) REVERT: A 17 LYS cc_start: 0.7768 (pptt) cc_final: 0.7079 (ptpt) REVERT: A 203 LEU cc_start: 0.4407 (OUTLIER) cc_final: 0.3969 (tt) REVERT: A 392 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8551 (mt-10) REVERT: B 15 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7094 (ttmm) REVERT: B 23 LYS cc_start: 0.8163 (tttp) cc_final: 0.7618 (tmtm) REVERT: B 42 ARG cc_start: 0.7745 (tpt170) cc_final: 0.7357 (tpt170) REVERT: B 44 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7902 (mt0) REVERT: B 59 TYR cc_start: 0.9240 (OUTLIER) cc_final: 0.8131 (t80) REVERT: B 134 ARG cc_start: 0.7859 (ptp-110) cc_final: 0.7232 (ppp80) REVERT: B 146 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8678 (tp) REVERT: B 197 ARG cc_start: 0.8833 (mtp180) cc_final: 0.8596 (mtp85) REVERT: B 217 MET cc_start: 0.8806 (ppp) cc_final: 0.8411 (pmm) REVERT: G 36 ASP cc_start: 0.8567 (m-30) cc_final: 0.8186 (m-30) REVERT: R 41 GLU cc_start: 0.5733 (mm-30) cc_final: 0.5320 (tt0) REVERT: R 293 ASP cc_start: 0.7321 (t0) cc_final: 0.6902 (t70) REVERT: R 354 LEU cc_start: 0.8653 (mp) cc_final: 0.8360 (mt) REVERT: R 376 ARG cc_start: 0.5723 (mmp80) cc_final: 0.5297 (mmp80) REVERT: R 414 ARG cc_start: 0.6320 (mmp-170) cc_final: 0.5093 (mmt90) REVERT: P 9 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6405 (mp0) outliers start: 29 outliers final: 15 residues processed: 146 average time/residue: 1.5179 time to fit residues: 236.0477 Evaluate side-chains 144 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 351 LYS Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain R residue 420 TRP Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 82 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.0870 chunk 109 optimal weight: 20.0000 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.202032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114567 restraints weight = 10039.109| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.85 r_work: 0.3058 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10422 Z= 0.136 Angle : 0.468 4.951 14142 Z= 0.253 Chirality : 0.040 0.152 1564 Planarity : 0.004 0.063 1805 Dihedral : 4.336 33.285 1403 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.85 % Allowed : 19.02 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.24), residues: 1261 helix: 1.86 (0.23), residues: 541 sheet: 0.28 (0.32), residues: 219 loop : -0.14 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.013 0.001 PHE A 212 TYR 0.019 0.001 TYR R 148 ARG 0.006 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6647 (pt0) cc_final: 0.6104 (pp20) REVERT: A 17 LYS cc_start: 0.7783 (pptt) cc_final: 0.7104 (ptpt) REVERT: A 203 LEU cc_start: 0.4411 (OUTLIER) cc_final: 0.3988 (tt) REVERT: A 392 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8489 (mt-10) REVERT: B 15 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7130 (ttmm) REVERT: B 23 LYS cc_start: 0.8162 (tttp) cc_final: 0.7665 (tmtm) REVERT: B 42 ARG cc_start: 0.7711 (tpt170) cc_final: 0.7350 (tpt170) REVERT: B 44 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7894 (mt0) REVERT: B 46 ARG cc_start: 0.8495 (mmt-90) cc_final: 0.8158 (mmp80) REVERT: B 59 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8008 (t80) REVERT: B 76 ASP cc_start: 0.8618 (p0) cc_final: 0.8354 (p0) REVERT: B 134 ARG cc_start: 0.7863 (ptp-110) cc_final: 0.7224 (ppp80) REVERT: B 146 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8630 (tp) REVERT: B 197 ARG cc_start: 0.8822 (mtp180) cc_final: 0.8588 (mtp85) REVERT: B 217 MET cc_start: 0.8799 (ppp) cc_final: 0.8413 (pmm) REVERT: G 36 ASP cc_start: 0.8562 (m-30) cc_final: 0.8176 (m-30) REVERT: R 41 GLU cc_start: 0.5725 (mm-30) cc_final: 0.5317 (tt0) REVERT: R 293 ASP cc_start: 0.7295 (t0) cc_final: 0.6834 (t70) REVERT: R 354 LEU cc_start: 0.8609 (mp) cc_final: 0.8355 (mt) REVERT: R 407 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7744 (m-40) REVERT: R 414 ARG cc_start: 0.6357 (mmp-170) cc_final: 0.5114 (mmt90) REVERT: R 418 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6545 (pt0) REVERT: P 9 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6330 (mp0) outliers start: 20 outliers final: 10 residues processed: 138 average time/residue: 1.5340 time to fit residues: 225.2856 Evaluate side-chains 134 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 303 MET Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 407 ASN Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain R residue 420 TRP Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 27 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 86 optimal weight: 0.1980 chunk 97 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.200055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.111727 restraints weight = 10118.367| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.00 r_work: 0.2995 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10422 Z= 0.217 Angle : 0.515 5.525 14142 Z= 0.278 Chirality : 0.042 0.153 1564 Planarity : 0.004 0.062 1805 Dihedral : 4.534 34.644 1403 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.94 % Allowed : 18.74 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.24), residues: 1261 helix: 1.87 (0.23), residues: 535 sheet: 0.24 (0.32), residues: 231 loop : -0.18 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.025 0.001 PHE A 212 TYR 0.018 0.001 TYR R 148 ARG 0.007 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6666 (pt0) cc_final: 0.6080 (pp20) REVERT: A 17 LYS cc_start: 0.7770 (pptt) cc_final: 0.7069 (ptpt) REVERT: A 203 LEU cc_start: 0.4422 (OUTLIER) cc_final: 0.3985 (tt) REVERT: B 23 LYS cc_start: 0.8167 (tttp) cc_final: 0.7633 (tmtm) REVERT: B 42 ARG cc_start: 0.7739 (tpt170) cc_final: 0.7343 (tpt170) REVERT: B 44 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: B 46 ARG cc_start: 0.8596 (mmt-90) cc_final: 0.8228 (mmp80) REVERT: B 59 TYR cc_start: 0.9242 (OUTLIER) cc_final: 0.8113 (t80) REVERT: B 134 ARG cc_start: 0.7872 (ptp-110) cc_final: 0.7217 (ppp80) REVERT: B 146 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8709 (tp) REVERT: B 217 MET cc_start: 0.8812 (ppp) cc_final: 0.8416 (pmm) REVERT: G 36 ASP cc_start: 0.8581 (m-30) cc_final: 0.8221 (m-30) REVERT: R 41 GLU cc_start: 0.5730 (mm-30) cc_final: 0.5317 (tt0) REVERT: R 293 ASP cc_start: 0.7287 (t0) cc_final: 0.6872 (t70) REVERT: R 354 LEU cc_start: 0.8623 (mp) cc_final: 0.8357 (mt) REVERT: R 373 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.5861 (pt0) REVERT: R 407 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7767 (m-40) REVERT: R 414 ARG cc_start: 0.6279 (mmp-170) cc_final: 0.5098 (mmt90) REVERT: P 9 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6414 (mp0) outliers start: 21 outliers final: 10 residues processed: 140 average time/residue: 1.4786 time to fit residues: 220.3935 Evaluate side-chains 141 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 351 LYS Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 407 ASN Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 87 optimal weight: 50.0000 chunk 6 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.200766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.117044 restraints weight = 10134.320| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.38 r_work: 0.2913 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10422 Z= 0.151 Angle : 0.481 4.974 14142 Z= 0.260 Chirality : 0.040 0.150 1564 Planarity : 0.004 0.063 1805 Dihedral : 4.385 34.184 1403 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.94 % Allowed : 18.74 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.24), residues: 1261 helix: 2.01 (0.23), residues: 530 sheet: 0.26 (0.32), residues: 232 loop : -0.15 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.018 0.001 TYR R 148 ARG 0.007 0.000 ARG A 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6613 (pt0) cc_final: 0.6049 (pp20) REVERT: A 17 LYS cc_start: 0.7697 (pptt) cc_final: 0.7001 (ptpt) REVERT: A 203 LEU cc_start: 0.4336 (OUTLIER) cc_final: 0.3921 (tt) REVERT: A 392 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8562 (mt-10) REVERT: B 15 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7035 (ttmm) REVERT: B 23 LYS cc_start: 0.8131 (tttp) cc_final: 0.7550 (tmtm) REVERT: B 42 ARG cc_start: 0.7740 (tpt170) cc_final: 0.7317 (tpt170) REVERT: B 44 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7918 (mt0) REVERT: B 46 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.8232 (mmp80) REVERT: B 59 TYR cc_start: 0.9244 (OUTLIER) cc_final: 0.8086 (t80) REVERT: B 134 ARG cc_start: 0.7872 (ptp-110) cc_final: 0.7177 (ppp80) REVERT: B 146 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8716 (tp) REVERT: B 197 ARG cc_start: 0.8870 (mtp180) cc_final: 0.8635 (mtp85) REVERT: B 217 MET cc_start: 0.8839 (ppp) cc_final: 0.8435 (pmm) REVERT: G 36 ASP cc_start: 0.8605 (m-30) cc_final: 0.8224 (m-30) REVERT: N 6 GLU cc_start: 0.8635 (mp0) cc_final: 0.8385 (mp0) REVERT: R 41 GLU cc_start: 0.5712 (mm-30) cc_final: 0.5308 (tt0) REVERT: R 293 ASP cc_start: 0.7251 (t0) cc_final: 0.6797 (t70) REVERT: R 354 LEU cc_start: 0.8570 (mp) cc_final: 0.8279 (mt) REVERT: R 373 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5698 (pt0) REVERT: R 376 ARG cc_start: 0.4862 (mmp80) cc_final: 0.4573 (mmp80) REVERT: R 407 ASN cc_start: 0.8113 (OUTLIER) cc_final: 0.7746 (m-40) REVERT: R 414 ARG cc_start: 0.6254 (mmp-170) cc_final: 0.5028 (mmt90) REVERT: R 418 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6499 (pt0) REVERT: P 9 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6339 (mp0) outliers start: 21 outliers final: 8 residues processed: 140 average time/residue: 1.5834 time to fit residues: 235.6515 Evaluate side-chains 139 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 407 ASN Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 56 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.198827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.110940 restraints weight = 10048.633| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.99 r_work: 0.2962 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10422 Z= 0.249 Angle : 0.541 6.856 14142 Z= 0.292 Chirality : 0.043 0.155 1564 Planarity : 0.004 0.061 1805 Dihedral : 4.681 35.943 1403 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.22 % Allowed : 18.65 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.04 (0.24), residues: 1261 helix: 1.84 (0.23), residues: 530 sheet: 0.29 (0.31), residues: 237 loop : -0.31 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.004 0.001 HIS G 44 PHE 0.013 0.002 PHE A 212 TYR 0.018 0.002 TYR R 242 ARG 0.008 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11449.78 seconds wall clock time: 201 minutes 33.50 seconds (12093.50 seconds total)