Starting phenix.real_space_refine on Fri Mar 14 02:25:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jr2_61746/03_2025/9jr2_61746.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jr2_61746/03_2025/9jr2_61746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jr2_61746/03_2025/9jr2_61746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jr2_61746/03_2025/9jr2_61746.map" model { file = "/net/cci-nas-00/data/ceres_data/9jr2_61746/03_2025/9jr2_61746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jr2_61746/03_2025/9jr2_61746.cif" } resolution = 2.8 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 1.650 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 60 5.16 5 C 6036 2.51 5 N 1614 2.21 5 O 1708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9418 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1722 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2473 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 88 Chain: "G" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "S" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1727 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 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: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "P" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 288 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} 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: "R" Number of atoms: 2856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2856 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 342} Chain breaks: 5 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.52, per 1000 atoms: 0.69 Number of scatterers: 9418 At special positions: 0 Unit cell: (89.544, 123.492, 157.44, 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 60 16.00 O 1708 8.00 N 1614 7.00 C 6036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " 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: 2.54 Conformation dependent library (CDL) restraints added in 1.1 seconds 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2298 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 15 sheets defined 40.4% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 49 removed outlier: 4.019A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.653A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.910A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 183 through 202 Processing helix chain 'A' and resid 223 through 243 Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.643A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.575A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.952A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.006A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.018A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 34 Processing helix chain 'R' and resid 33 through 54 Processing helix chain 'R' and resid 168 through 172 Processing helix chain 'R' and resid 178 through 212 removed outlier: 3.596A pdb=" N VAL R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 removed outlier: 3.555A pdb=" N HIS R 216 " --> pdb=" O ARG R 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 213 through 216' Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 279 through 312 removed outlier: 4.178A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL R 285 " --> pdb=" O CYS R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 347 removed outlier: 3.830A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY R 323 " --> pdb=" O LYS R 319 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.718A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 413 removed outlier: 4.076A pdb=" N LYS R 405 " --> pdb=" O GLN R 401 " (cutoff:3.500A) Processing helix chain 'R' and resid 413 through 418 removed outlier: 3.674A pdb=" N PHE R 417 " --> pdb=" O LEU R 413 " (cutoff:3.500A) Processing helix chain 'R' and resid 419 through 423 Processing helix chain 'R' and resid 434 through 448 removed outlier: 3.784A pdb=" N LEU R 446 " --> pdb=" O HIS R 442 " (cutoff:3.500A) Processing helix chain 'R' and resid 450 through 459 Processing helix chain 'R' and resid 463 through 482 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 76 removed outlier: 7.158A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL A 139 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N HIS A 214 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU A 141 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 43 through 44 removed outlier: 3.862A pdb=" N VAL B 307 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.231A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.719A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.332A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.645A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.962A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.506A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.574A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.598A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.882A pdb=" N ARG S 148 " --> pdb=" O THR S 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.793A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 143 through 146 Processing sheet with id=AB5, first strand: chain 'R' and resid 111 through 112 removed outlier: 3.785A pdb=" N GLU R 111 " --> pdb=" O TRP R 118 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 127 through 130 removed outlier: 4.598A pdb=" N ARG R 147 " --> pdb=" O TRP R 164 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP R 164 " --> pdb=" O ARG R 147 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU R 155 " --> pdb=" O TRP R 164 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1368 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: 2.97 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3021 1.34 - 1.46: 2464 1.46 - 1.58: 4063 1.58 - 1.70: 0 1.70 - 1.81: 86 Bond restraints: 9634 Sorted by residual: bond pdb=" N LEU B 4 " pdb=" CA LEU B 4 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 bond pdb=" N GLN G 11 " pdb=" CA GLN G 11 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N MET R 32 " pdb=" CA MET R 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N VAL S 2 " pdb=" CA VAL S 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 bond pdb=" N PHE P 34 " pdb=" CA PHE P 34 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 ... (remaining 9629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 12667 1.22 - 2.44: 354 2.44 - 3.66: 55 3.66 - 4.88: 14 4.88 - 6.10: 1 Bond angle restraints: 13091 Sorted by residual: angle pdb=" N VAL A 219 " pdb=" CA VAL A 219 " pdb=" C VAL A 219 " ideal model delta sigma weight residual 113.53 108.93 4.60 9.80e-01 1.04e+00 2.21e+01 angle pdb=" N ILE R 310 " pdb=" CA ILE R 310 " pdb=" C ILE R 310 " ideal model delta sigma weight residual 113.53 110.06 3.47 9.80e-01 1.04e+00 1.25e+01 angle pdb=" CA TRP A 96 " pdb=" CB TRP A 96 " pdb=" CG TRP A 96 " ideal model delta sigma weight residual 113.60 119.70 -6.10 1.90e+00 2.77e-01 1.03e+01 angle pdb=" N HIS R 114 " pdb=" CA HIS R 114 " pdb=" CB HIS R 114 " ideal model delta sigma weight residual 114.17 110.74 3.43 1.14e+00 7.69e-01 9.07e+00 angle pdb=" N MET S 180 " pdb=" CA MET S 180 " pdb=" CB MET S 180 " ideal model delta sigma weight residual 113.65 109.71 3.94 1.47e+00 4.63e-01 7.17e+00 ... (remaining 13086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 4943 15.24 - 30.48: 505 30.48 - 45.72: 135 45.72 - 60.96: 33 60.96 - 76.20: 8 Dihedral angle restraints: 5624 sinusoidal: 2066 harmonic: 3558 Sorted by residual: dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 55.76 37.24 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CA ASP A 199 " pdb=" C ASP A 199 " pdb=" N ILE A 200 " pdb=" CA ILE A 200 " ideal model delta harmonic sigma weight residual 180.00 161.00 19.00 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 163.09 16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 929 0.028 - 0.057: 367 0.057 - 0.085: 105 0.085 - 0.113: 60 0.113 - 0.142: 20 Chirality restraints: 1481 Sorted by residual: chirality pdb=" CA ILE S 177 " pdb=" N ILE S 177 " pdb=" C ILE S 177 " pdb=" CB ILE S 177 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA VAL B 133 " pdb=" N VAL B 133 " pdb=" C VAL B 133 " pdb=" CB VAL B 133 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 1478 not shown) Planarity restraints: 1651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO G 49 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 96 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C TRP A 96 " 0.028 2.00e-02 2.50e+03 pdb=" O TRP A 96 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE A 97 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER S 172 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO S 173 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO S 173 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO S 173 " 0.021 5.00e-02 4.00e+02 ... (remaining 1648 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 217 2.69 - 3.25: 9193 3.25 - 3.80: 14917 3.80 - 4.35: 20426 4.35 - 4.90: 33671 Nonbonded interactions: 78424 Sorted by model distance: nonbonded pdb=" O GLU R 302 " pdb=" O HOH R 601 " model vdw 2.142 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.151 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.222 3.040 nonbonded pdb=" O TYR R 245 " pdb=" OG SER R 246 " model vdw 2.282 3.040 nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.314 3.040 ... (remaining 78419 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: 7.430 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: 0.640 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.940 Find NCS groups from input model: 0.120 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 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 : 0.003 0.038 9634 Z= 0.175 Angle : 0.512 6.102 13091 Z= 0.306 Chirality : 0.038 0.142 1481 Planarity : 0.003 0.041 1651 Dihedral : 14.039 76.198 3308 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.31 % Allowed : 12.56 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.25), residues: 1197 helix: 1.73 (0.26), residues: 429 sheet: -0.19 (0.31), residues: 269 loop : -0.47 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.005 0.001 HIS R 420 PHE 0.009 0.001 PHE B 151 TYR 0.011 0.001 TYR R 191 ARG 0.003 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 179 time to evaluate : 0.966 Fit side-chains REVERT: A 10 LYS cc_start: 0.5062 (mtpp) cc_final: 0.4531 (mttt) REVERT: A 20 ASP cc_start: 0.5550 (m-30) cc_final: 0.5069 (m-30) REVERT: A 22 ASN cc_start: 0.5722 (m-40) cc_final: 0.5347 (m110) REVERT: A 85 ASP cc_start: 0.7274 (t0) cc_final: 0.6900 (t0) REVERT: A 126 LYS cc_start: 0.5284 (ttmt) cc_final: 0.5039 (mttt) REVERT: A 208 ARG cc_start: 0.5996 (mtt180) cc_final: 0.5538 (mtp180) REVERT: B 48 ARG cc_start: 0.5231 (mmt90) cc_final: 0.4933 (mmt90) REVERT: B 98 SER cc_start: 0.7910 (p) cc_final: 0.7640 (p) REVERT: B 101 MET cc_start: 0.6965 (mtp) cc_final: 0.6695 (mtp) REVERT: B 118 ASP cc_start: 0.6513 (t0) cc_final: 0.5622 (p0) REVERT: B 192 LEU cc_start: 0.7065 (mt) cc_final: 0.6849 (mp) REVERT: B 251 ARG cc_start: 0.5567 (mtm-85) cc_final: 0.4785 (ttm-80) REVERT: B 283 ARG cc_start: 0.6104 (tpt-90) cc_final: 0.5557 (mtp180) REVERT: S 116 THR cc_start: 0.5860 (t) cc_final: 0.5615 (m) REVERT: S 221 LEU cc_start: 0.5781 (tp) cc_final: 0.5472 (tp) REVERT: R 312 MET cc_start: 0.4552 (mmm) cc_final: 0.4172 (mtp) REVERT: R 348 ASN cc_start: 0.6925 (t0) cc_final: 0.5977 (p0) REVERT: R 380 ASN cc_start: 0.6869 (m-40) cc_final: 0.6541 (m-40) REVERT: R 383 ARG cc_start: 0.5385 (ttm-80) cc_final: 0.5062 (ptm160) REVERT: R 425 MET cc_start: 0.6180 (ptm) cc_final: 0.5979 (ptt) REVERT: R 431 GLU cc_start: 0.6390 (tt0) cc_final: 0.6004 (tt0) outliers start: 3 outliers final: 0 residues processed: 182 average time/residue: 1.3571 time to fit residues: 267.5891 Evaluate side-chains 152 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.8980 chunk 91 optimal weight: 30.0000 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 35 ASN B 88 ASN B 259 GLN B 295 ASN R 442 HIS R 463 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.213357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.176179 restraints weight = 10048.299| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.58 r_work: 0.3728 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9634 Z= 0.183 Angle : 0.530 6.087 13091 Z= 0.287 Chirality : 0.042 0.142 1481 Planarity : 0.004 0.041 1651 Dihedral : 4.036 23.553 1321 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.08 % Allowed : 15.58 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.25), residues: 1197 helix: 2.44 (0.25), residues: 428 sheet: -0.03 (0.31), residues: 273 loop : -0.42 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 298 HIS 0.007 0.001 HIS S 155 PHE 0.017 0.001 PHE R 227 TYR 0.020 0.001 TYR R 191 ARG 0.005 0.000 ARG P 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.082 Fit side-chains REVERT: A 10 LYS cc_start: 0.7038 (mtpp) cc_final: 0.6522 (mttt) REVERT: A 20 ASP cc_start: 0.7369 (m-30) cc_final: 0.6972 (m-30) REVERT: A 22 ASN cc_start: 0.6827 (m-40) cc_final: 0.6500 (m110) REVERT: A 85 ASP cc_start: 0.7708 (t0) cc_final: 0.7474 (t0) REVERT: A 209 HIS cc_start: 0.8097 (p-80) cc_final: 0.7778 (p90) REVERT: B 118 ASP cc_start: 0.7659 (t0) cc_final: 0.7282 (p0) REVERT: B 241 PHE cc_start: 0.6848 (p90) cc_final: 0.5914 (p90) REVERT: B 283 ARG cc_start: 0.6647 (tpt-90) cc_final: 0.6027 (mtp180) REVERT: S 116 THR cc_start: 0.6034 (t) cc_final: 0.5740 (m) REVERT: S 175 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8100 (tp) REVERT: S 221 LEU cc_start: 0.6673 (tp) cc_final: 0.6136 (tp) REVERT: R 214 ARG cc_start: 0.6395 (OUTLIER) cc_final: 0.6193 (mtp180) outliers start: 20 outliers final: 11 residues processed: 159 average time/residue: 1.3021 time to fit residues: 223.6239 Evaluate side-chains 151 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 214 ARG Chi-restraints excluded: chain R residue 387 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 43 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 131 ASN B 54 HIS S 155 HIS R 225 HIS R 463 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.211869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.176656 restraints weight = 10503.200| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.89 r_work: 0.3650 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9634 Z= 0.263 Angle : 0.572 7.751 13091 Z= 0.306 Chirality : 0.043 0.193 1481 Planarity : 0.004 0.043 1651 Dihedral : 4.409 27.305 1321 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.32 % Allowed : 17.03 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.95 (0.25), residues: 1197 helix: 2.27 (0.25), residues: 432 sheet: -0.09 (0.30), residues: 283 loop : -0.39 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 298 HIS 0.010 0.002 HIS S 155 PHE 0.014 0.002 PHE R 227 TYR 0.016 0.002 TYR R 459 ARG 0.005 0.000 ARG P 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7130 (mtpp) cc_final: 0.6585 (mttt) REVERT: A 20 ASP cc_start: 0.7414 (m-30) cc_final: 0.7034 (m-30) REVERT: A 22 ASN cc_start: 0.6854 (m-40) cc_final: 0.6472 (m110) REVERT: B 118 ASP cc_start: 0.7932 (t0) cc_final: 0.7379 (p0) REVERT: B 262 MET cc_start: 0.5160 (OUTLIER) cc_final: 0.4914 (tpt) REVERT: B 283 ARG cc_start: 0.6806 (tpt-90) cc_final: 0.6055 (mtp180) REVERT: S 83 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.5526 (mmt) REVERT: S 116 THR cc_start: 0.6016 (t) cc_final: 0.5707 (m) REVERT: S 175 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8151 (tp) REVERT: S 218 MET cc_start: 0.6098 (OUTLIER) cc_final: 0.5368 (mtp) REVERT: S 221 LEU cc_start: 0.6744 (tp) cc_final: 0.6212 (tp) REVERT: R 214 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.6247 (mtp180) outliers start: 32 outliers final: 16 residues processed: 157 average time/residue: 1.2510 time to fit residues: 210.2569 Evaluate side-chains 155 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 214 ARG Chi-restraints excluded: chain R residue 373 LEU Chi-restraints excluded: chain R residue 387 THR Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 61 optimal weight: 0.0970 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 209 HIS B 54 HIS R 463 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.215292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.179868 restraints weight = 10437.975| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 1.64 r_work: 0.3910 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9634 Z= 0.163 Angle : 0.496 6.754 13091 Z= 0.268 Chirality : 0.041 0.140 1481 Planarity : 0.004 0.041 1651 Dihedral : 4.115 27.519 1321 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.70 % Allowed : 17.96 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.26 (0.25), residues: 1197 helix: 2.65 (0.25), residues: 432 sheet: 0.06 (0.31), residues: 281 loop : -0.34 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 298 HIS 0.007 0.001 HIS S 155 PHE 0.016 0.001 PHE R 227 TYR 0.018 0.001 TYR R 191 ARG 0.004 0.000 ARG P 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7136 (mtpp) cc_final: 0.6646 (mttt) REVERT: A 20 ASP cc_start: 0.7481 (m-30) cc_final: 0.7135 (m-30) REVERT: A 22 ASN cc_start: 0.6786 (m-40) cc_final: 0.6531 (m110) REVERT: B 118 ASP cc_start: 0.7819 (t0) cc_final: 0.7495 (p0) REVERT: B 283 ARG cc_start: 0.6655 (tpt-90) cc_final: 0.5985 (mtp180) REVERT: S 30 SER cc_start: 0.8000 (OUTLIER) cc_final: 0.7740 (p) REVERT: S 175 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7996 (tp) REVERT: S 221 LEU cc_start: 0.6746 (tp) cc_final: 0.6199 (tp) outliers start: 26 outliers final: 11 residues processed: 149 average time/residue: 1.2487 time to fit residues: 198.9880 Evaluate side-chains 144 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 0.0270 chunk 44 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN R 448 ASN R 463 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.213014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.177034 restraints weight = 10410.287| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.71 r_work: 0.3686 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9634 Z= 0.217 Angle : 0.530 6.979 13091 Z= 0.284 Chirality : 0.042 0.258 1481 Planarity : 0.004 0.042 1651 Dihedral : 4.234 26.964 1321 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.95 % Allowed : 17.76 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.13 (0.25), residues: 1197 helix: 2.50 (0.25), residues: 432 sheet: -0.08 (0.30), residues: 284 loop : -0.30 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 298 HIS 0.004 0.001 HIS S 155 PHE 0.017 0.002 PHE R 227 TYR 0.017 0.001 TYR R 191 ARG 0.007 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7119 (mtpp) cc_final: 0.6606 (mttt) REVERT: A 20 ASP cc_start: 0.7338 (m-30) cc_final: 0.6950 (m-30) REVERT: A 22 ASN cc_start: 0.6817 (m-40) cc_final: 0.6418 (m110) REVERT: B 118 ASP cc_start: 0.7934 (t0) cc_final: 0.7404 (p0) REVERT: B 134 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7201 (ptt180) REVERT: B 262 MET cc_start: 0.5037 (OUTLIER) cc_final: 0.4760 (tpt) REVERT: B 283 ARG cc_start: 0.6744 (tpt-90) cc_final: 0.5993 (mtp180) REVERT: S 175 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8135 (tp) REVERT: S 221 LEU cc_start: 0.6740 (tp) cc_final: 0.6229 (tp) REVERT: R 214 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.6121 (mtp180) REVERT: R 469 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6984 (mm-30) outliers start: 38 outliers final: 22 residues processed: 158 average time/residue: 1.1319 time to fit residues: 192.6973 Evaluate side-chains 161 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 214 ARG Chi-restraints excluded: chain R residue 387 THR Chi-restraints excluded: chain R residue 425 MET Chi-restraints excluded: chain R residue 469 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 ASN R 463 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.206382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.170814 restraints weight = 10392.250| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.92 r_work: 0.3606 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 9634 Z= 0.502 Angle : 0.739 8.054 13091 Z= 0.395 Chirality : 0.051 0.404 1481 Planarity : 0.005 0.065 1651 Dihedral : 5.206 27.345 1321 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.19 % Allowed : 17.45 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.31 (0.24), residues: 1197 helix: 1.47 (0.24), residues: 433 sheet: -0.38 (0.29), residues: 286 loop : -0.49 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP R 298 HIS 0.010 0.002 HIS R 225 PHE 0.025 0.003 PHE R 227 TYR 0.023 0.003 TYR R 297 ARG 0.007 0.001 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 1.082 Fit side-chains REVERT: A 10 LYS cc_start: 0.7435 (mtpp) cc_final: 0.6957 (mtmt) REVERT: A 20 ASP cc_start: 0.7528 (m-30) cc_final: 0.7194 (m-30) REVERT: A 22 ASN cc_start: 0.7011 (m-40) cc_final: 0.6587 (m110) REVERT: A 35 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6458 (mtp180) REVERT: A 233 ASP cc_start: 0.7866 (t70) cc_final: 0.7612 (m-30) REVERT: B 118 ASP cc_start: 0.8047 (t0) cc_final: 0.7510 (p0) REVERT: B 134 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7199 (ptt180) REVERT: B 283 ARG cc_start: 0.6876 (tpt-90) cc_final: 0.5996 (mtp180) REVERT: S 19 LYS cc_start: 0.7599 (tttp) cc_final: 0.6959 (tptt) REVERT: S 175 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8179 (tp) outliers start: 50 outliers final: 29 residues processed: 166 average time/residue: 1.2905 time to fit residues: 230.5149 Evaluate side-chains 167 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain R residue 351 CYS Chi-restraints excluded: chain R residue 387 THR Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 5 optimal weight: 20.0000 chunk 84 optimal weight: 0.7980 chunk 73 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN R 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.212474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.177051 restraints weight = 10475.369| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.69 r_work: 0.3757 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9634 Z= 0.180 Angle : 0.528 6.487 13091 Z= 0.283 Chirality : 0.042 0.229 1481 Planarity : 0.004 0.050 1651 Dihedral : 4.413 28.424 1321 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.01 % Allowed : 19.94 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.92 (0.25), residues: 1197 helix: 2.32 (0.25), residues: 431 sheet: -0.06 (0.31), residues: 272 loop : -0.50 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 298 HIS 0.004 0.001 HIS R 420 PHE 0.022 0.001 PHE R 227 TYR 0.016 0.001 TYR R 191 ARG 0.005 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.973 Fit side-chains REVERT: A 10 LYS cc_start: 0.7311 (mtpp) cc_final: 0.6739 (mttt) REVERT: A 20 ASP cc_start: 0.7449 (m-30) cc_final: 0.7083 (m-30) REVERT: A 22 ASN cc_start: 0.6860 (m-40) cc_final: 0.6477 (m110) REVERT: A 233 ASP cc_start: 0.7730 (t70) cc_final: 0.7518 (m-30) REVERT: B 118 ASP cc_start: 0.8004 (t0) cc_final: 0.7553 (p0) REVERT: B 262 MET cc_start: 0.5100 (OUTLIER) cc_final: 0.4749 (tpt) REVERT: B 283 ARG cc_start: 0.6699 (tpt-90) cc_final: 0.5968 (mtp180) REVERT: S 19 LYS cc_start: 0.7528 (tttp) cc_final: 0.6911 (tptt) REVERT: S 154 LEU cc_start: 0.7030 (tp) cc_final: 0.6501 (tm) REVERT: S 175 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8012 (tp) outliers start: 29 outliers final: 13 residues processed: 154 average time/residue: 1.2490 time to fit residues: 205.6166 Evaluate side-chains 144 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain P residue 27 LYS Chi-restraints excluded: chain R residue 387 THR Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 110 optimal weight: 3.9990 chunk 45 optimal weight: 0.0010 chunk 25 optimal weight: 0.0980 chunk 73 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 448 ASN R 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.220388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.185691 restraints weight = 10499.414| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.53 r_work: 0.3734 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9634 Z= 0.178 Angle : 0.520 6.599 13091 Z= 0.279 Chirality : 0.041 0.187 1481 Planarity : 0.004 0.045 1651 Dihedral : 4.248 26.804 1321 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.39 % Allowed : 20.98 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.05 (0.25), residues: 1197 helix: 2.44 (0.25), residues: 431 sheet: -0.08 (0.31), residues: 278 loop : -0.39 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 298 HIS 0.003 0.001 HIS R 420 PHE 0.019 0.001 PHE R 227 TYR 0.018 0.001 TYR R 191 ARG 0.007 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.649 Fit side-chains REVERT: A 10 LYS cc_start: 0.7205 (mtpp) cc_final: 0.6645 (mttt) REVERT: A 20 ASP cc_start: 0.7327 (m-30) cc_final: 0.6952 (m-30) REVERT: A 22 ASN cc_start: 0.6821 (m-40) cc_final: 0.6429 (m110) REVERT: A 233 ASP cc_start: 0.7625 (t70) cc_final: 0.7401 (m-30) REVERT: B 118 ASP cc_start: 0.7896 (t0) cc_final: 0.7436 (p0) REVERT: B 262 MET cc_start: 0.4930 (OUTLIER) cc_final: 0.4547 (tpt) REVERT: B 283 ARG cc_start: 0.6697 (tpt-90) cc_final: 0.5986 (mtp180) REVERT: S 19 LYS cc_start: 0.7502 (tttp) cc_final: 0.6842 (tptt) REVERT: S 83 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.5299 (mmm) REVERT: S 154 LEU cc_start: 0.7037 (tp) cc_final: 0.6523 (tm) REVERT: S 175 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8054 (tp) REVERT: R 182 GLU cc_start: 0.7645 (tt0) cc_final: 0.7286 (mt-10) outliers start: 23 outliers final: 14 residues processed: 147 average time/residue: 1.6182 time to fit residues: 256.4439 Evaluate side-chains 146 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain P residue 27 LYS Chi-restraints excluded: chain R residue 387 THR Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 97 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 69 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.220210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.185135 restraints weight = 10354.658| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.49 r_work: 0.3734 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9634 Z= 0.194 Angle : 0.527 6.713 13091 Z= 0.282 Chirality : 0.041 0.177 1481 Planarity : 0.004 0.043 1651 Dihedral : 4.244 26.506 1321 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.12 % Allowed : 20.35 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.06 (0.25), residues: 1197 helix: 2.46 (0.25), residues: 430 sheet: -0.01 (0.31), residues: 273 loop : -0.42 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 298 HIS 0.010 0.001 HIS R 420 PHE 0.021 0.001 PHE R 227 TYR 0.014 0.001 TYR R 191 ARG 0.009 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.048 Fit side-chains REVERT: A 10 LYS cc_start: 0.7227 (mtpp) cc_final: 0.6675 (mttt) REVERT: A 20 ASP cc_start: 0.7326 (m-30) cc_final: 0.6978 (m-30) REVERT: A 22 ASN cc_start: 0.6813 (m-40) cc_final: 0.6429 (m110) REVERT: A 232 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7265 (mtpm) REVERT: A 233 ASP cc_start: 0.7644 (t70) cc_final: 0.7420 (m-30) REVERT: B 118 ASP cc_start: 0.7908 (t0) cc_final: 0.7470 (p0) REVERT: B 262 MET cc_start: 0.4939 (OUTLIER) cc_final: 0.4610 (tpt) REVERT: B 283 ARG cc_start: 0.6692 (tpt-90) cc_final: 0.5994 (mtp180) REVERT: S 19 LYS cc_start: 0.7548 (tttp) cc_final: 0.6879 (tptt) REVERT: S 67 ARG cc_start: 0.7002 (mtm180) cc_final: 0.6582 (ptt90) REVERT: S 154 LEU cc_start: 0.7023 (tp) cc_final: 0.6575 (tm) REVERT: S 175 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8043 (tp) outliers start: 30 outliers final: 19 residues processed: 147 average time/residue: 1.2330 time to fit residues: 195.8180 Evaluate side-chains 147 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain P residue 27 LYS Chi-restraints excluded: chain R residue 387 THR Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 116 optimal weight: 0.0040 chunk 79 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN B 32 GLN ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 463 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.222659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.188479 restraints weight = 10493.609| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.47 r_work: 0.3762 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9634 Z= 0.150 Angle : 0.499 6.006 13091 Z= 0.267 Chirality : 0.041 0.148 1481 Planarity : 0.003 0.040 1651 Dihedral : 4.026 26.636 1321 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.28 % Allowed : 20.98 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.21 (0.25), residues: 1197 helix: 2.60 (0.25), residues: 430 sheet: 0.12 (0.31), residues: 276 loop : -0.38 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP R 298 HIS 0.009 0.001 HIS R 420 PHE 0.017 0.001 PHE R 227 TYR 0.019 0.001 TYR R 191 ARG 0.004 0.000 ARG B 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.937 Fit side-chains REVERT: A 10 LYS cc_start: 0.7137 (mtpp) cc_final: 0.6569 (mttt) REVERT: A 20 ASP cc_start: 0.7243 (m-30) cc_final: 0.6852 (m-30) REVERT: A 22 ASN cc_start: 0.6752 (m-40) cc_final: 0.6337 (m110) REVERT: A 232 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7244 (mtpm) REVERT: B 118 ASP cc_start: 0.7872 (t0) cc_final: 0.7386 (p0) REVERT: B 262 MET cc_start: 0.4779 (OUTLIER) cc_final: 0.4457 (tpt) REVERT: B 283 ARG cc_start: 0.6676 (tpt-90) cc_final: 0.5992 (mtp180) REVERT: S 19 LYS cc_start: 0.7422 (tttp) cc_final: 0.6787 (tptt) REVERT: S 67 ARG cc_start: 0.6948 (mtm180) cc_final: 0.6591 (ptt180) REVERT: S 83 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.5159 (mmm) REVERT: S 154 LEU cc_start: 0.6954 (tp) cc_final: 0.6527 (tm) REVERT: S 175 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8074 (tp) REVERT: S 183 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7822 (tt) REVERT: R 414 MET cc_start: 0.7762 (mtm) cc_final: 0.7559 (mtp) outliers start: 22 outliers final: 17 residues processed: 142 average time/residue: 1.1444 time to fit residues: 174.6870 Evaluate side-chains 148 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain P residue 27 LYS Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.1980 chunk 101 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.221048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.186491 restraints weight = 10488.232| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.53 r_work: 0.3776 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9634 Z= 0.187 Angle : 0.519 6.501 13091 Z= 0.278 Chirality : 0.041 0.156 1481 Planarity : 0.004 0.041 1651 Dihedral : 4.111 26.064 1321 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.70 % Allowed : 20.66 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.19 (0.25), residues: 1197 helix: 2.56 (0.25), residues: 429 sheet: 0.05 (0.31), residues: 278 loop : -0.34 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 298 HIS 0.009 0.001 HIS R 420 PHE 0.018 0.001 PHE R 335 TYR 0.014 0.001 TYR R 191 ARG 0.010 0.000 ARG S 18 =============================================================================== Job complete usr+sys time: 9968.55 seconds wall clock time: 176 minutes 14.89 seconds (10574.89 seconds total)