Starting phenix.real_space_refine on Fri Feb 14 04:06:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l1v_23119/02_2025/7l1v_23119.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l1v_23119/02_2025/7l1v_23119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l1v_23119/02_2025/7l1v_23119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l1v_23119/02_2025/7l1v_23119.map" model { file = "/net/cci-nas-00/data/ceres_data/7l1v_23119/02_2025/7l1v_23119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l1v_23119/02_2025/7l1v_23119.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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 69 5.16 5 C 6145 2.51 5 N 1649 2.21 5 O 1743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 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: 9606 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1802 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2549 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 429 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1724 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "R" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2251 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "S" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 806 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 107} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'XGD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.36, per 1000 atoms: 0.66 Number of scatterers: 9606 At special positions: 0 Unit cell: (107.52, 107.52, 152.88, 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 69 16.00 O 1743 8.00 N 1649 7.00 C 6145 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 210 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.3 seconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2344 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 16 sheets defined 33.3% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 4.247A pdb=" N ARG A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.829A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.688A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.625A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.697A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.128A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.693A 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 'C' and resid 6 through 24 removed outlier: 3.623A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.508A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 removed outlier: 3.630A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'R' and resid 56 through 82 removed outlier: 3.720A pdb=" N VAL R 66 " --> pdb=" O ILE R 62 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA R 68 " --> pdb=" O VAL R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 86 removed outlier: 3.503A pdb=" N ARG R 86 " --> pdb=" O HIS R 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 83 through 86' Processing helix chain 'R' and resid 90 through 107 Processing helix chain 'R' and resid 107 through 118 Processing helix chain 'R' and resid 122 through 157 removed outlier: 3.939A pdb=" N LEU R 126 " --> pdb=" O PHE R 122 " (cutoff:3.500A) Proline residue: R 131 - end of helix Processing helix chain 'R' and resid 165 through 184 Processing helix chain 'R' and resid 185 through 190 Processing helix chain 'R' and resid 218 through 232 Processing helix chain 'R' and resid 232 through 250 Processing helix chain 'R' and resid 293 through 317 removed outlier: 4.048A pdb=" N LYS R 301 " --> pdb=" O ARG R 297 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR R 302 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA R 303 " --> pdb=" O ARG R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 329 removed outlier: 3.591A pdb=" N SER R 321 " --> pdb=" O TYR R 317 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 341 through 365 removed outlier: 3.709A pdb=" N TRP R 351 " --> pdb=" O THR R 347 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU R 352 " --> pdb=" O PHE R 348 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL R 353 " --> pdb=" O SER R 349 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 368 through 376 Processing helix chain 'S' and resid 86 through 90 removed outlier: 4.311A pdb=" N THR S 90 " --> pdb=" O PRO S 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 213 removed outlier: 6.214A pdb=" N LEU A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N PHE A 222 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.039A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.591A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.904A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.631A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.996A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.616A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.445A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.831A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.871A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 155 through 160 removed outlier: 3.576A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 194 through 195 removed outlier: 5.575A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 191 through 196 removed outlier: 3.684A pdb=" N PHE R 207 " --> pdb=" O VAL R 196 " (cutoff:3.500A) removed outlier: 9.399A pdb=" N PHE S 102 " --> pdb=" O CYS R 210 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLU R 212 " --> pdb=" O PHE S 102 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY S 10 " --> pdb=" O THR S 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 191 through 196 removed outlier: 3.684A pdb=" N PHE R 207 " --> pdb=" O VAL R 196 " (cutoff:3.500A) removed outlier: 9.399A pdb=" N PHE S 102 " --> pdb=" O CYS R 210 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLU R 212 " --> pdb=" O PHE S 102 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG S 37 " --> pdb=" O TRP S 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N TRP S 46 " --> pdb=" O ARG S 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 3 through 7 466 hydrogen bonds defined for protein. 1323 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: 3.33 Time building geometry restraints manager: 3.01 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: 2883 1.34 - 1.46: 2221 1.46 - 1.58: 4616 1.58 - 1.70: 1 1.70 - 1.82: 101 Bond restraints: 9822 Sorted by residual: bond pdb=" C LEU R 108 " pdb=" N PRO R 109 " ideal model delta sigma weight residual 1.336 1.388 -0.052 1.20e-02 6.94e+03 1.87e+01 bond pdb=" CG LEU A 46 " pdb=" CD1 LEU A 46 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.64e+00 bond pdb=" N XGD R 401 " pdb=" S XGD R 401 " ideal model delta sigma weight residual 1.672 1.631 0.041 2.00e-02 2.50e+03 4.10e+00 bond pdb=" CA THR R 204 " pdb=" C THR R 204 " ideal model delta sigma weight residual 1.522 1.548 -0.026 1.51e-02 4.39e+03 3.01e+00 bond pdb=" C ILE R 130 " pdb=" N PRO R 131 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.28e-02 6.10e+03 2.87e+00 ... (remaining 9817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 13190 3.10 - 6.20: 148 6.20 - 9.30: 18 9.30 - 12.39: 2 12.39 - 15.49: 2 Bond angle restraints: 13360 Sorted by residual: angle pdb=" C XGD R 401 " pdb=" N XGD R 401 " pdb=" S XGD R 401 " ideal model delta sigma weight residual 116.72 132.21 -15.49 3.00e+00 1.11e-01 2.67e+01 angle pdb=" C GLN H 183 " pdb=" N SER H 184 " pdb=" CA SER H 184 " ideal model delta sigma weight residual 120.97 131.35 -10.38 2.84e+00 1.24e-01 1.34e+01 angle pdb=" CA LEU B 146 " pdb=" CB LEU B 146 " pdb=" CG LEU B 146 " ideal model delta sigma weight residual 116.30 128.78 -12.48 3.50e+00 8.16e-02 1.27e+01 angle pdb=" C CYS R 107 " pdb=" N LEU R 108 " pdb=" CA LEU R 108 " ideal model delta sigma weight residual 120.26 124.91 -4.65 1.34e+00 5.57e-01 1.20e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 ... (remaining 13355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5285 17.81 - 35.62: 394 35.62 - 53.43: 62 53.43 - 71.24: 11 71.24 - 89.05: 1 Dihedral angle restraints: 5753 sinusoidal: 2114 harmonic: 3639 Sorted by residual: dihedral pdb=" CA PHE R 121 " pdb=" C PHE R 121 " pdb=" N PHE R 122 " pdb=" CA PHE R 122 " ideal model delta harmonic sigma weight residual 180.00 -150.14 -29.86 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 47.16 45.84 1 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 5750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 934 0.044 - 0.088: 432 0.088 - 0.132: 122 0.132 - 0.176: 33 0.176 - 0.220: 8 Chirality restraints: 1529 Sorted by residual: chirality pdb=" CB THR H 116 " pdb=" CA THR H 116 " pdb=" OG1 THR H 116 " pdb=" CG2 THR H 116 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB VAL S 97 " pdb=" CA VAL S 97 " pdb=" CG1 VAL S 97 " pdb=" CG2 VAL S 97 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL B 200 " pdb=" CA VAL B 200 " pdb=" CG1 VAL B 200 " pdb=" CG2 VAL B 200 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 1526 not shown) Planarity restraints: 1681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N XGD R 401 " -0.178 2.00e-02 2.50e+03 1.19e-01 2.85e+02 pdb=" C XGD R 401 " 0.114 2.00e-02 2.50e+03 pdb=" C1 XGD R 401 " 0.196 2.00e-02 2.50e+03 pdb=" C14 XGD R 401 " -0.013 2.00e-02 2.50e+03 pdb=" C15 XGD R 401 " -0.051 2.00e-02 2.50e+03 pdb=" C16 XGD R 401 " -0.001 2.00e-02 2.50e+03 pdb=" C2 XGD R 401 " 0.080 2.00e-02 2.50e+03 pdb=" C3 XGD R 401 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O XGD R 401 " 0.018 2.00e-02 2.50e+03 9.42e-02 1.11e+02 pdb=" C4 XGD R 401 " -0.115 2.00e-02 2.50e+03 pdb=" C5 XGD R 401 " 0.043 2.00e-02 2.50e+03 pdb=" C6 XGD R 401 " -0.090 2.00e-02 2.50e+03 pdb=" N1 XGD R 401 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C19 XGD R 401 " 0.071 2.00e-02 2.50e+03 4.35e-02 3.79e+01 pdb=" C20 XGD R 401 " -0.043 2.00e-02 2.50e+03 pdb=" C21 XGD R 401 " -0.017 2.00e-02 2.50e+03 pdb=" C22 XGD R 401 " 0.017 2.00e-02 2.50e+03 pdb=" C23 XGD R 401 " 0.020 2.00e-02 2.50e+03 pdb=" C24 XGD R 401 " -0.026 2.00e-02 2.50e+03 pdb=" C25 XGD R 401 " 0.045 2.00e-02 2.50e+03 pdb=" C28 XGD R 401 " -0.067 2.00e-02 2.50e+03 ... (remaining 1678 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 3001 2.82 - 3.34: 7886 3.34 - 3.86: 15682 3.86 - 4.38: 18094 4.38 - 4.90: 32904 Nonbonded interactions: 77567 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.306 3.040 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.315 3.040 nonbonded pdb=" OE2 GLU A 15 " pdb=" OH TYR H 175 " model vdw 2.322 3.040 nonbonded pdb=" O SER H 52 " pdb=" NH1 ARG H 72 " model vdw 2.341 3.120 nonbonded pdb=" OG SER H 161 " pdb=" O LYS H 163 " model vdw 2.343 3.040 ... (remaining 77562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.820 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.007 0.071 9822 Z= 0.471 Angle : 0.912 15.494 13360 Z= 0.508 Chirality : 0.056 0.220 1529 Planarity : 0.008 0.119 1681 Dihedral : 12.816 89.055 3397 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.30 % Allowed : 6.36 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -2.91 (0.20), residues: 1235 helix: -1.94 (0.20), residues: 383 sheet: -1.12 (0.26), residues: 341 loop : -2.37 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.006 0.002 HIS H 35 PHE 0.021 0.003 PHE B 241 TYR 0.028 0.003 TYR B 59 ARG 0.005 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 1.078 Fit side-chains REVERT: H 3 GLN cc_start: 0.7596 (pt0) cc_final: 0.7291 (pt0) REVERT: H 69 THR cc_start: 0.7814 (t) cc_final: 0.7593 (m) REVERT: H 202 ARG cc_start: 0.8570 (ptt-90) cc_final: 0.8086 (ptt180) REVERT: R 151 ASP cc_start: 0.8165 (t70) cc_final: 0.7810 (t0) REVERT: R 213 ARG cc_start: 0.7833 (ttt-90) cc_final: 0.7393 (ttt180) REVERT: R 249 LYS cc_start: 0.7883 (tptm) cc_final: 0.7488 (tppt) REVERT: R 327 LYS cc_start: 0.8509 (tttt) cc_final: 0.8300 (tttm) REVERT: S 32 VAL cc_start: 0.8544 (t) cc_final: 0.8321 (p) outliers start: 3 outliers final: 2 residues processed: 169 average time/residue: 1.5627 time to fit residues: 279.2646 Evaluate side-chains 118 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain R residue 87 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 385 GLN B 62 HIS B 88 ASN C 11 GLN H 13 GLN H 171 ASN H 183 GLN R 83 HIS S 38 GLN S 104 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.147912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.119040 restraints weight = 12477.862| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.95 r_work: 0.3382 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9822 Z= 0.225 Angle : 0.561 6.435 13360 Z= 0.301 Chirality : 0.043 0.139 1529 Planarity : 0.004 0.044 1681 Dihedral : 5.826 50.961 1381 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.82 % Allowed : 13.94 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.22), residues: 1235 helix: 0.30 (0.25), residues: 387 sheet: -0.69 (0.27), residues: 340 loop : -1.91 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.005 0.001 HIS A 220 PHE 0.012 0.002 PHE R 122 TYR 0.015 0.001 TYR S 103 ARG 0.007 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.064 Fit side-chains REVERT: B 245 SER cc_start: 0.8488 (m) cc_final: 0.8210 (t) REVERT: C 36 ASP cc_start: 0.8118 (m-30) cc_final: 0.7895 (m-30) REVERT: C 37 LEU cc_start: 0.8007 (tt) cc_final: 0.7755 (mp) REVERT: C 58 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8163 (mp0) REVERT: C 59 ASN cc_start: 0.8343 (t0) cc_final: 0.8143 (t0) REVERT: H 3 GLN cc_start: 0.8175 (pt0) cc_final: 0.7965 (pt0) REVERT: H 202 ARG cc_start: 0.8752 (ptt-90) cc_final: 0.8539 (ptt-90) REVERT: R 86 ARG cc_start: 0.8954 (mtt180) cc_final: 0.8577 (mtt90) REVERT: R 151 ASP cc_start: 0.8531 (t70) cc_final: 0.8151 (t0) REVERT: R 249 LYS cc_start: 0.8098 (tptm) cc_final: 0.7735 (tppt) REVERT: S 82 MET cc_start: 0.6959 (mtt) cc_final: 0.6680 (mpp) outliers start: 18 outliers final: 10 residues processed: 144 average time/residue: 1.4144 time to fit residues: 217.2216 Evaluate side-chains 127 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 38 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN S 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.149096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.120961 restraints weight = 12614.074| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.95 r_work: 0.3427 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9822 Z= 0.178 Angle : 0.517 5.622 13360 Z= 0.276 Chirality : 0.042 0.180 1529 Planarity : 0.004 0.040 1681 Dihedral : 5.253 43.113 1381 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.53 % Allowed : 14.95 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.54 (0.23), residues: 1235 helix: 1.27 (0.26), residues: 387 sheet: -0.44 (0.27), residues: 339 loop : -1.57 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.011 0.001 PHE R 227 TYR 0.015 0.001 TYR S 103 ARG 0.008 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 1.074 Fit side-chains REVERT: B 59 TYR cc_start: 0.8675 (m-80) cc_final: 0.7832 (m-80) REVERT: B 75 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8564 (tp40) REVERT: B 234 PHE cc_start: 0.9272 (OUTLIER) cc_final: 0.8926 (m-80) REVERT: C 36 ASP cc_start: 0.8171 (m-30) cc_final: 0.7877 (m-30) REVERT: C 42 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8149 (tt0) REVERT: C 58 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8153 (mp0) REVERT: R 151 ASP cc_start: 0.8563 (t70) cc_final: 0.8209 (t0) REVERT: R 249 LYS cc_start: 0.8078 (tptm) cc_final: 0.7704 (tppt) outliers start: 25 outliers final: 10 residues processed: 145 average time/residue: 1.2947 time to fit residues: 201.4443 Evaluate side-chains 128 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 111 optimal weight: 5.9990 chunk 48 optimal weight: 0.3980 chunk 80 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN R 83 HIS S 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.142405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113165 restraints weight = 12640.441| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.95 r_work: 0.3298 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 9822 Z= 0.514 Angle : 0.678 10.317 13360 Z= 0.356 Chirality : 0.048 0.179 1529 Planarity : 0.005 0.048 1681 Dihedral : 6.119 56.376 1381 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.23 % Allowed : 16.67 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.64 (0.23), residues: 1235 helix: 1.19 (0.26), residues: 387 sheet: -0.58 (0.27), residues: 333 loop : -1.54 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.008 0.001 HIS A 220 PHE 0.018 0.003 PHE B 234 TYR 0.018 0.002 TYR A 339 ARG 0.009 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.278 Fit side-chains REVERT: B 59 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.8157 (m-80) REVERT: B 75 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8597 (tp40) REVERT: B 234 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8763 (m-80) REVERT: C 42 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8282 (tt0) REVERT: C 58 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8097 (mp0) REVERT: R 100 ASP cc_start: 0.8330 (m-30) cc_final: 0.8071 (m-30) REVERT: R 249 LYS cc_start: 0.8208 (tptm) cc_final: 0.7832 (tppt) REVERT: R 297 ARG cc_start: 0.7800 (ttt-90) cc_final: 0.6988 (mmt180) REVERT: R 305 MET cc_start: 0.7450 (mtm) cc_final: 0.7233 (tpp) REVERT: S 56 MET cc_start: 0.7465 (mtp) cc_final: 0.7011 (mmm) outliers start: 32 outliers final: 19 residues processed: 146 average time/residue: 1.3629 time to fit residues: 212.1160 Evaluate side-chains 136 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 251 TRP Chi-restraints excluded: chain S residue 92 VAL Chi-restraints excluded: chain S residue 103 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 94 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 0.0070 chunk 43 optimal weight: 1.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 83 HIS S 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.149559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.119639 restraints weight = 12476.433| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.28 r_work: 0.3334 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9822 Z= 0.203 Angle : 0.526 6.661 13360 Z= 0.280 Chirality : 0.042 0.147 1529 Planarity : 0.004 0.046 1681 Dihedral : 5.337 44.199 1381 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.33 % Allowed : 18.28 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.24), residues: 1235 helix: 1.64 (0.26), residues: 388 sheet: -0.20 (0.28), residues: 322 loop : -1.44 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.005 0.001 HIS B 225 PHE 0.012 0.001 PHE R 227 TYR 0.014 0.001 TYR S 34 ARG 0.009 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.145 Fit side-chains REVERT: A 221 MET cc_start: 0.8911 (ttm) cc_final: 0.8651 (ttp) REVERT: B 59 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.8124 (m-80) REVERT: B 75 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8505 (tp40) REVERT: B 96 ARG cc_start: 0.8612 (tpp80) cc_final: 0.8239 (ttt-90) REVERT: B 234 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.8880 (m-80) REVERT: C 42 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8291 (tt0) REVERT: C 58 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8207 (mp0) REVERT: R 151 ASP cc_start: 0.8611 (t70) cc_final: 0.8338 (t0) REVERT: R 249 LYS cc_start: 0.8086 (tptm) cc_final: 0.7694 (tppt) REVERT: R 305 MET cc_start: 0.7300 (mtm) cc_final: 0.6993 (mpm) REVERT: S 56 MET cc_start: 0.7404 (mtp) cc_final: 0.6928 (mmm) outliers start: 33 outliers final: 17 residues processed: 144 average time/residue: 1.3188 time to fit residues: 202.8353 Evaluate side-chains 134 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 115 optimal weight: 0.0980 chunk 34 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 392 ASN S 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.145907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.117517 restraints weight = 12559.986| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.94 r_work: 0.3350 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9822 Z= 0.269 Angle : 0.551 6.765 13360 Z= 0.292 Chirality : 0.043 0.147 1529 Planarity : 0.004 0.051 1681 Dihedral : 5.363 44.438 1381 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.64 % Allowed : 18.59 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.12 (0.24), residues: 1235 helix: 1.76 (0.26), residues: 388 sheet: -0.24 (0.28), residues: 316 loop : -1.37 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.005 0.001 HIS R 224 PHE 0.016 0.002 PHE R 122 TYR 0.014 0.001 TYR A 339 ARG 0.011 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 1.107 Fit side-chains REVERT: A 221 MET cc_start: 0.8842 (ttm) cc_final: 0.8506 (ttp) REVERT: B 59 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.8118 (m-80) REVERT: B 75 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8501 (tp40) REVERT: B 96 ARG cc_start: 0.8587 (tpp80) cc_final: 0.8215 (ttt-90) REVERT: B 234 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.8933 (m-80) REVERT: C 42 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8301 (tt0) REVERT: R 151 ASP cc_start: 0.8632 (t70) cc_final: 0.8368 (t0) REVERT: R 249 LYS cc_start: 0.8110 (tptm) cc_final: 0.7727 (tppt) REVERT: R 297 ARG cc_start: 0.7823 (ttt-90) cc_final: 0.7062 (mpt180) REVERT: S 56 MET cc_start: 0.7453 (mtp) cc_final: 0.6943 (mmm) outliers start: 36 outliers final: 24 residues processed: 140 average time/residue: 1.3265 time to fit residues: 198.4595 Evaluate side-chains 142 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 222 MET Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 98 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 116 optimal weight: 0.0470 chunk 68 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN S 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.149940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.119273 restraints weight = 12670.806| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.13 r_work: 0.3343 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9822 Z= 0.199 Angle : 0.515 6.043 13360 Z= 0.274 Chirality : 0.042 0.146 1529 Planarity : 0.004 0.055 1681 Dihedral : 5.061 40.136 1381 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.23 % Allowed : 19.90 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.24), residues: 1235 helix: 1.97 (0.26), residues: 389 sheet: -0.01 (0.28), residues: 321 loop : -1.27 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS R 224 PHE 0.013 0.001 PHE R 122 TYR 0.012 0.001 TYR H 190 ARG 0.012 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.081 Fit side-chains REVERT: A 221 MET cc_start: 0.8845 (ttm) cc_final: 0.8480 (ttp) REVERT: A 330 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6889 (tp30) REVERT: B 59 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: B 75 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8504 (tp40) REVERT: B 217 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7706 (pmm) REVERT: B 234 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8955 (m-80) REVERT: C 42 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8340 (tt0) REVERT: C 58 GLU cc_start: 0.8041 (mp0) cc_final: 0.7548 (pm20) REVERT: R 151 ASP cc_start: 0.8627 (t70) cc_final: 0.8267 (t0) REVERT: R 249 LYS cc_start: 0.8100 (tptm) cc_final: 0.7709 (tppt) REVERT: S 56 MET cc_start: 0.7461 (mtp) cc_final: 0.6953 (mmm) outliers start: 32 outliers final: 24 residues processed: 139 average time/residue: 1.2721 time to fit residues: 189.4444 Evaluate side-chains 145 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 222 MET Chi-restraints excluded: chain S residue 92 VAL Chi-restraints excluded: chain S residue 103 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 109 optimal weight: 0.0980 chunk 60 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 392 ASN H 13 GLN R 83 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.149091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120995 restraints weight = 12638.369| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.94 r_work: 0.3406 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9822 Z= 0.146 Angle : 0.489 5.638 13360 Z= 0.260 Chirality : 0.041 0.145 1529 Planarity : 0.004 0.058 1681 Dihedral : 4.789 38.187 1381 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.03 % Allowed : 20.20 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.37 (0.24), residues: 1235 helix: 2.23 (0.26), residues: 387 sheet: 0.08 (0.29), residues: 316 loop : -1.17 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.005 0.001 HIS B 225 PHE 0.012 0.001 PHE R 122 TYR 0.012 0.001 TYR H 190 ARG 0.013 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 1.020 Fit side-chains REVERT: B 59 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: B 75 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8468 (tp40) REVERT: B 96 ARG cc_start: 0.8596 (tpp80) cc_final: 0.8212 (ttt-90) REVERT: B 217 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7699 (pmm) REVERT: C 42 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8318 (tt0) REVERT: C 58 GLU cc_start: 0.8137 (mp0) cc_final: 0.7595 (pm20) REVERT: R 83 HIS cc_start: 0.8156 (m-70) cc_final: 0.7930 (t-90) REVERT: R 151 ASP cc_start: 0.8580 (t70) cc_final: 0.8259 (t0) REVERT: R 249 LYS cc_start: 0.8078 (tptm) cc_final: 0.7660 (tppt) REVERT: S 45 GLU cc_start: 0.8144 (pt0) cc_final: 0.7840 (pp20) REVERT: S 56 MET cc_start: 0.7448 (mtp) cc_final: 0.6951 (mmm) outliers start: 30 outliers final: 21 residues processed: 136 average time/residue: 1.2993 time to fit residues: 189.1118 Evaluate side-chains 140 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 222 MET Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.0670 chunk 16 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN C 24 ASN H 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.145963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.116864 restraints weight = 12588.098| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.98 r_work: 0.3379 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9822 Z= 0.166 Angle : 0.495 5.662 13360 Z= 0.262 Chirality : 0.041 0.146 1529 Planarity : 0.004 0.062 1681 Dihedral : 4.714 33.658 1381 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.23 % Allowed : 20.40 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.46 (0.24), residues: 1235 helix: 2.29 (0.26), residues: 388 sheet: 0.13 (0.29), residues: 316 loop : -1.11 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS B 225 PHE 0.011 0.001 PHE R 122 TYR 0.011 0.001 TYR H 190 ARG 0.015 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 1.128 Fit side-chains REVERT: B 59 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: B 96 ARG cc_start: 0.8602 (tpp80) cc_final: 0.8219 (ttt-90) REVERT: B 217 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7680 (pmm) REVERT: C 58 GLU cc_start: 0.8166 (mp0) cc_final: 0.7681 (pm20) REVERT: R 83 HIS cc_start: 0.8245 (m-70) cc_final: 0.7935 (t-90) REVERT: R 151 ASP cc_start: 0.8612 (t70) cc_final: 0.8284 (t0) REVERT: R 249 LYS cc_start: 0.8096 (tptm) cc_final: 0.7668 (tppt) REVERT: S 45 GLU cc_start: 0.8120 (pt0) cc_final: 0.7748 (pp20) REVERT: S 56 MET cc_start: 0.7417 (mtp) cc_final: 0.6960 (mmm) outliers start: 32 outliers final: 24 residues processed: 135 average time/residue: 1.2431 time to fit residues: 180.3958 Evaluate side-chains 141 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 222 MET Chi-restraints excluded: chain S residue 92 VAL Chi-restraints excluded: chain S residue 103 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 117 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.0000 chunk 83 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 105 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 30 optimal weight: 0.0000 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.147773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.118813 restraints weight = 12634.172| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.97 r_work: 0.3408 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9822 Z= 0.129 Angle : 0.479 5.596 13360 Z= 0.254 Chirality : 0.041 0.145 1529 Planarity : 0.004 0.066 1681 Dihedral : 4.508 32.434 1381 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.93 % Allowed : 21.41 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.67 (0.25), residues: 1235 helix: 2.53 (0.26), residues: 382 sheet: 0.16 (0.29), residues: 321 loop : -0.95 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.008 0.001 HIS S 104 PHE 0.011 0.001 PHE H 29 TYR 0.024 0.001 TYR S 103 ARG 0.015 0.001 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.153 Fit side-chains REVERT: A 314 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7619 (tp30) REVERT: B 59 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: B 96 ARG cc_start: 0.8619 (tpp80) cc_final: 0.8237 (ttt-90) REVERT: B 217 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7670 (pmm) REVERT: C 58 GLU cc_start: 0.8185 (mp0) cc_final: 0.7629 (pm20) REVERT: R 83 HIS cc_start: 0.8202 (m-70) cc_final: 0.7922 (t-90) REVERT: R 151 ASP cc_start: 0.8595 (t70) cc_final: 0.8269 (t0) REVERT: R 249 LYS cc_start: 0.8068 (tptm) cc_final: 0.7674 (tppt) REVERT: S 45 GLU cc_start: 0.8111 (pt0) cc_final: 0.7770 (pp20) REVERT: S 56 MET cc_start: 0.7394 (mtp) cc_final: 0.6936 (mmm) outliers start: 29 outliers final: 21 residues processed: 135 average time/residue: 1.2841 time to fit residues: 185.4177 Evaluate side-chains 139 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 222 MET Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 93 optimal weight: 0.1980 chunk 121 optimal weight: 2.9990 chunk 105 optimal weight: 0.0970 chunk 81 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.155237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.125524 restraints weight = 12668.089| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.05 r_work: 0.3417 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 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 : 0.002 0.034 9822 Z= 0.156 Angle : 0.493 5.599 13360 Z= 0.261 Chirality : 0.041 0.156 1529 Planarity : 0.004 0.065 1681 Dihedral : 4.479 28.094 1381 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.13 % Allowed : 21.92 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.76 (0.25), residues: 1235 helix: 2.57 (0.26), residues: 383 sheet: 0.20 (0.29), residues: 322 loop : -0.85 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS B 225 PHE 0.011 0.001 PHE R 227 TYR 0.013 0.001 TYR S 34 ARG 0.015 0.001 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7035.07 seconds wall clock time: 124 minutes 44.15 seconds (7484.15 seconds total)