Starting phenix.real_space_refine on Thu Jan 16 12:10:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jr2_61746/01_2025/9jr2_61746.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jr2_61746/01_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_61746/01_2025/9jr2_61746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jr2_61746/01_2025/9jr2_61746.map" model { file = "/net/cci-nas-00/data/ceres_data/9jr2_61746/01_2025/9jr2_61746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jr2_61746/01_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-5571/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: 6.20, per 1000 atoms: 0.66 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: 2.46 Conformation dependent library (CDL) restraints added in 1.2 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: 1.20 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: 2.81 Time building geometry restraints manager: 2.82 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: 2.590 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.110 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:14.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.830 ------------------------------------------------------------------------------- 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 : 0.933 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: 1.1150 time to fit residues: 218.5111 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 : 0.939 ------------------------------------------------------------------------------- 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 = 0.176190 restraints weight = 10048.304| |-----------------------------------------------------------------------------| 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 : 1.038 Fit side-chains REVERT: A 10 LYS cc_start: 0.7043 (mtpp) cc_final: 0.6521 (mttt) REVERT: A 20 ASP cc_start: 0.7373 (m-30) cc_final: 0.6976 (m-30) REVERT: A 22 ASN cc_start: 0.6825 (m-40) cc_final: 0.6499 (m110) REVERT: A 85 ASP cc_start: 0.7708 (t0) cc_final: 0.7473 (t0) REVERT: A 209 HIS cc_start: 0.8097 (p-80) cc_final: 0.7778 (p90) REVERT: B 118 ASP cc_start: 0.7662 (t0) cc_final: 0.7278 (p0) REVERT: B 241 PHE cc_start: 0.6848 (p90) cc_final: 0.5912 (p90) REVERT: B 283 ARG cc_start: 0.6647 (tpt-90) cc_final: 0.6027 (mtp180) REVERT: S 116 THR cc_start: 0.6035 (t) cc_final: 0.5741 (m) REVERT: S 175 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8101 (tp) REVERT: S 221 LEU cc_start: 0.6669 (tp) cc_final: 0.6130 (tp) REVERT: R 214 ARG cc_start: 0.6397 (OUTLIER) cc_final: 0.6195 (mtp180) outliers start: 20 outliers final: 11 residues processed: 159 average time/residue: 1.1798 time to fit residues: 202.0781 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 : 1.016 ------------------------------------------------------------------------------- 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: 0.4980 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 68 optimal weight: 0.0170 chunk 20 optimal weight: 3.9990 overall best weight: 1.7024 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.212959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.177559 restraints weight = 10529.824| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 1.80 r_work: 0.3821 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9634 Z= 0.233 Angle : 0.548 7.634 13091 Z= 0.293 Chirality : 0.043 0.200 1481 Planarity : 0.004 0.041 1651 Dihedral : 4.276 26.869 1321 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.43 % Allowed : 16.93 % 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: 1.05 (0.25), residues: 1197 helix: 2.39 (0.25), residues: 432 sheet: 0.00 (0.30), residues: 281 loop : -0.39 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 298 HIS 0.010 0.001 HIS S 155 PHE 0.014 0.002 PHE R 227 TYR 0.014 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: 33 poor density : 139 time to evaluate : 0.953 Fit side-chains REVERT: A 10 LYS cc_start: 0.7159 (mtpp) cc_final: 0.6656 (mttt) REVERT: A 20 ASP cc_start: 0.7486 (m-30) cc_final: 0.7125 (m-30) REVERT: A 22 ASN cc_start: 0.6849 (m-40) cc_final: 0.6511 (m110) REVERT: A 238 MET cc_start: 0.7018 (mtm) cc_final: 0.6783 (ptm) REVERT: B 118 ASP cc_start: 0.7860 (t0) cc_final: 0.7464 (p0) REVERT: B 262 MET cc_start: 0.5113 (OUTLIER) cc_final: 0.4795 (tpt) REVERT: B 283 ARG cc_start: 0.6753 (tpt-90) cc_final: 0.6073 (mtp180) REVERT: S 116 THR cc_start: 0.5971 (t) cc_final: 0.5678 (m) REVERT: S 175 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8069 (tp) REVERT: S 218 MET cc_start: 0.6140 (OUTLIER) cc_final: 0.5404 (mtp) REVERT: S 221 LEU cc_start: 0.6744 (tp) cc_final: 0.6204 (tp) REVERT: R 214 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.6357 (mtp180) outliers start: 33 outliers final: 14 residues processed: 157 average time/residue: 1.2241 time to fit residues: 206.3405 Evaluate side-chains 152 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 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 214 ARG 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: 4.9990 chunk 116 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 104 optimal weight: 0.0870 chunk 43 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 82 HIS A 209 HIS B 54 HIS R 463 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.212783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.177215 restraints weight = 10409.940| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.69 r_work: 0.3828 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9634 Z= 0.217 Angle : 0.529 7.212 13091 Z= 0.284 Chirality : 0.042 0.171 1481 Planarity : 0.004 0.044 1651 Dihedral : 4.292 27.482 1321 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.43 % Allowed : 17.24 % 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: 1.10 (0.25), residues: 1197 helix: 2.49 (0.25), residues: 432 sheet: -0.03 (0.30), residues: 283 loop : -0.38 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 298 HIS 0.006 0.001 HIS S 155 PHE 0.015 0.002 PHE R 227 TYR 0.014 0.001 TYR R 191 ARG 0.004 0.000 ARG B 314 *********************** 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 174 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.944 Fit side-chains REVERT: A 10 LYS cc_start: 0.7160 (mtpp) cc_final: 0.6678 (mttt) REVERT: A 20 ASP cc_start: 0.7469 (m-30) cc_final: 0.7136 (m-30) REVERT: A 22 ASN cc_start: 0.6831 (m-40) cc_final: 0.6487 (m110) REVERT: A 119 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6429 (mm-40) REVERT: A 238 MET cc_start: 0.7003 (mtm) cc_final: 0.6756 (ptm) REVERT: B 118 ASP cc_start: 0.7916 (t0) cc_final: 0.7468 (p0) REVERT: B 262 MET cc_start: 0.5103 (OUTLIER) cc_final: 0.4805 (tpt) REVERT: B 283 ARG cc_start: 0.6747 (tpt-90) cc_final: 0.6022 (mtp180) REVERT: S 175 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8063 (tp) REVERT: S 221 LEU cc_start: 0.6758 (tp) cc_final: 0.6263 (tp) REVERT: R 214 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.6372 (mtp180) REVERT: R 373 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7521 (tt) outliers start: 33 outliers final: 17 residues processed: 159 average time/residue: 1.2442 time to fit residues: 212.0484 Evaluate side-chains 157 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 119 GLN 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 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 373 LEU Chi-restraints excluded: chain R residue 387 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: 2.9990 chunk 41 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 0.0070 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.219621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.184808 restraints weight = 10362.828| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.61 r_work: 0.3702 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9634 Z= 0.216 Angle : 0.526 7.137 13091 Z= 0.282 Chirality : 0.042 0.171 1481 Planarity : 0.004 0.044 1651 Dihedral : 4.293 27.251 1321 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.74 % Allowed : 17.96 % 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: 1.09 (0.25), residues: 1197 helix: 2.48 (0.25), residues: 432 sheet: -0.06 (0.30), residues: 283 loop : -0.37 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 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 0.004 0.000 ARG B 314 *********************** 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: 36 poor density : 140 time to evaluate : 0.905 Fit side-chains REVERT: A 10 LYS cc_start: 0.7108 (mtpp) cc_final: 0.6582 (mttt) REVERT: A 20 ASP cc_start: 0.7306 (m-30) cc_final: 0.6921 (m-30) REVERT: A 22 ASN cc_start: 0.6794 (m-40) cc_final: 0.6387 (m110) REVERT: A 73 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7034 (mttm) REVERT: A 119 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6663 (mm-40) REVERT: A 233 ASP cc_start: 0.7651 (t70) cc_final: 0.7403 (m-30) REVERT: A 238 MET cc_start: 0.6929 (mtm) cc_final: 0.6621 (ptm) REVERT: B 118 ASP cc_start: 0.7896 (t0) cc_final: 0.7360 (p0) REVERT: B 134 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7201 (ptt180) REVERT: B 262 MET cc_start: 0.4995 (OUTLIER) cc_final: 0.4735 (tpt) REVERT: B 283 ARG cc_start: 0.6705 (tpt-90) cc_final: 0.5965 (mtp180) REVERT: S 83 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.5461 (mmt) REVERT: S 175 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8131 (tp) REVERT: S 221 LEU cc_start: 0.6717 (tp) cc_final: 0.6242 (tp) REVERT: R 373 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7520 (tt) outliers start: 36 outliers final: 17 residues processed: 157 average time/residue: 1.2575 time to fit residues: 211.9449 Evaluate side-chains 155 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS 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 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 336 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 46 GLU 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 P residue 27 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS P 16 ASN ** 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 = 0.4328 r_free = 0.4328 target = 0.215599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.180645 restraints weight = 10348.871| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.59 r_work: 0.3696 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9634 Z= 0.324 Angle : 0.601 7.714 13091 Z= 0.322 Chirality : 0.044 0.196 1481 Planarity : 0.004 0.052 1651 Dihedral : 4.679 27.040 1321 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.15 % Allowed : 18.17 % Favored : 77.67 % 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: 0.83 (0.24), residues: 1197 helix: 2.15 (0.24), residues: 432 sheet: -0.16 (0.30), residues: 283 loop : -0.43 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 332 HIS 0.007 0.001 HIS S 155 PHE 0.023 0.002 PHE R 227 TYR 0.017 0.002 TYR R 297 ARG 0.005 0.001 ARG B 314 *********************** 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 182 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 1.018 Fit side-chains REVERT: A 10 LYS cc_start: 0.7294 (mtpp) cc_final: 0.6793 (mttt) REVERT: A 20 ASP cc_start: 0.7462 (m-30) cc_final: 0.7123 (m-30) REVERT: A 22 ASN cc_start: 0.6933 (m-40) cc_final: 0.6555 (m110) REVERT: A 73 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7052 (mttm) REVERT: A 233 ASP cc_start: 0.7731 (t70) cc_final: 0.7531 (m-30) REVERT: B 118 ASP cc_start: 0.7978 (t0) cc_final: 0.7523 (p0) REVERT: B 134 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7203 (ptt180) REVERT: B 283 ARG cc_start: 0.6761 (tpt-90) cc_final: 0.5953 (mtp180) REVERT: S 19 LYS cc_start: 0.7451 (tttp) cc_final: 0.6825 (tptt) REVERT: S 175 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8093 (tp) REVERT: S 221 LEU cc_start: 0.6796 (tp) cc_final: 0.6521 (tp) REVERT: R 469 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7104 (mm-30) outliers start: 40 outliers final: 24 residues processed: 164 average time/residue: 1.1722 time to fit residues: 206.8825 Evaluate side-chains 165 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 98 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 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 276 VAL 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 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 P residue 27 LYS Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 387 THR Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 425 MET Chi-restraints excluded: chain R residue 469 GLU 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: 0.8980 chunk 5 optimal weight: 20.0000 chunk 84 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 115 optimal weight: 0.0980 chunk 78 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.220230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.185821 restraints weight = 10425.433| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.58 r_work: 0.3721 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9634 Z= 0.156 Angle : 0.505 7.144 13091 Z= 0.272 Chirality : 0.041 0.158 1481 Planarity : 0.004 0.042 1651 Dihedral : 4.280 27.624 1321 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.60 % Allowed : 20.46 % Favored : 76.95 % 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: 1.11 (0.25), residues: 1197 helix: 2.58 (0.25), residues: 430 sheet: -0.10 (0.31), residues: 278 loop : -0.40 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 298 HIS 0.009 0.001 HIS R 420 PHE 0.022 0.001 PHE R 227 TYR 0.026 0.001 TYR R 191 ARG 0.004 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 160 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.119 Fit side-chains REVERT: A 10 LYS cc_start: 0.7124 (mtpp) cc_final: 0.6535 (mttt) REVERT: A 20 ASP cc_start: 0.7264 (m-30) cc_final: 0.6859 (m-30) REVERT: A 22 ASN cc_start: 0.6796 (m-40) cc_final: 0.6379 (m110) REVERT: A 73 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7017 (mttm) REVERT: B 118 ASP cc_start: 0.7877 (t0) cc_final: 0.7379 (p0) REVERT: B 134 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7181 (ptt180) REVERT: B 283 ARG cc_start: 0.6647 (tpt-90) cc_final: 0.5918 (mtp180) REVERT: S 19 LYS cc_start: 0.7354 (tttp) cc_final: 0.6725 (tptt) REVERT: S 83 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.5410 (mmm) REVERT: S 175 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8034 (tp) REVERT: S 221 LEU cc_start: 0.6668 (tp) cc_final: 0.6258 (tp) REVERT: R 389 LEU cc_start: 0.5636 (OUTLIER) cc_final: 0.5122 (mp) outliers start: 25 outliers final: 10 residues processed: 146 average time/residue: 1.2781 time to fit residues: 200.9238 Evaluate side-chains 146 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 232 LYS 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 134 ARG Chi-restraints excluded: chain B residue 181 THR 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 175 LEU Chi-restraints excluded: chain R residue 191 TYR 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: 2.9990 chunk 45 optimal weight: 0.0570 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.2902 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.219587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.184814 restraints weight = 10492.935| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.56 r_work: 0.3785 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9634 Z= 0.193 Angle : 0.518 6.872 13091 Z= 0.278 Chirality : 0.041 0.157 1481 Planarity : 0.004 0.042 1651 Dihedral : 4.285 27.279 1321 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.53 % Allowed : 19.73 % 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: 1.10 (0.25), residues: 1197 helix: 2.57 (0.25), residues: 430 sheet: -0.08 (0.31), residues: 278 loop : -0.40 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 298 HIS 0.008 0.001 HIS R 420 PHE 0.021 0.001 PHE R 227 TYR 0.020 0.001 TYR R 191 ARG 0.006 0.000 ARG B 314 *********************** 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 169 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 1.000 Fit side-chains REVERT: A 10 LYS cc_start: 0.7243 (mtpp) cc_final: 0.6715 (mttt) REVERT: A 20 ASP cc_start: 0.7418 (m-30) cc_final: 0.7063 (m-30) REVERT: A 22 ASN cc_start: 0.6852 (m-40) cc_final: 0.6485 (m110) REVERT: A 73 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7040 (mttm) REVERT: B 118 ASP cc_start: 0.7961 (t0) cc_final: 0.7554 (p0) REVERT: B 134 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7251 (ptt180) REVERT: B 283 ARG cc_start: 0.6651 (tpt-90) cc_final: 0.5938 (mtp180) REVERT: S 19 LYS cc_start: 0.7431 (tttp) cc_final: 0.6843 (tptt) REVERT: S 175 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8011 (tp) REVERT: S 221 LEU cc_start: 0.6761 (tp) cc_final: 0.6395 (tp) REVERT: R 389 LEU cc_start: 0.5728 (OUTLIER) cc_final: 0.5246 (mp) REVERT: R 469 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7070 (mm-30) outliers start: 34 outliers final: 19 residues processed: 152 average time/residue: 1.2156 time to fit residues: 198.5184 Evaluate side-chains 154 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 232 LYS 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 134 ARG Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 31 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 R residue 191 TYR Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 425 MET Chi-restraints excluded: chain R residue 469 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 97 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 209 HIS R 463 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.218612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.183539 restraints weight = 10341.966| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.51 r_work: 0.3776 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2499 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= 0.234 Angle : 0.551 6.974 13091 Z= 0.295 Chirality : 0.042 0.168 1481 Planarity : 0.004 0.044 1651 Dihedral : 4.371 27.069 1321 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.63 % Allowed : 19.83 % 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: 0.98 (0.25), residues: 1197 helix: 2.37 (0.24), residues: 432 sheet: -0.10 (0.31), residues: 274 loop : -0.41 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 298 HIS 0.008 0.001 HIS R 420 PHE 0.023 0.002 PHE R 227 TYR 0.025 0.002 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 170 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.942 Fit side-chains REVERT: A 10 LYS cc_start: 0.7252 (mtpp) cc_final: 0.6731 (mttt) REVERT: A 20 ASP cc_start: 0.7403 (m-30) cc_final: 0.7080 (m-30) REVERT: A 22 ASN cc_start: 0.6873 (m-40) cc_final: 0.6505 (m110) REVERT: A 35 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6339 (mtp180) REVERT: A 73 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7040 (mttm) REVERT: B 118 ASP cc_start: 0.7953 (t0) cc_final: 0.7557 (p0) REVERT: B 134 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7249 (ptt180) REVERT: B 283 ARG cc_start: 0.6656 (tpt-90) cc_final: 0.5943 (mtp180) REVERT: S 19 LYS cc_start: 0.7428 (tttp) cc_final: 0.6881 (tptt) REVERT: S 175 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8023 (tp) REVERT: S 221 LEU cc_start: 0.6772 (tp) cc_final: 0.6424 (tp) REVERT: R 190 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7852 (mp) outliers start: 35 outliers final: 20 residues processed: 154 average time/residue: 1.1970 time to fit residues: 198.9291 Evaluate side-chains 156 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 73 LYS Chi-restraints excluded: chain A residue 98 GLN 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 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 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 31 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 R residue 190 ILE Chi-restraints excluded: chain R residue 224 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4382 r_free = 0.4382 target = 0.221360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.186884 restraints weight = 10469.469| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.48 r_work: 0.3787 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9634 Z= 0.166 Angle : 0.510 6.837 13091 Z= 0.272 Chirality : 0.041 0.144 1481 Planarity : 0.004 0.040 1651 Dihedral : 4.142 27.432 1321 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.39 % Allowed : 20.87 % 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: 1.20 (0.25), residues: 1197 helix: 2.63 (0.25), residues: 430 sheet: 0.02 (0.32), residues: 273 loop : -0.36 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP R 298 HIS 0.007 0.001 HIS R 420 PHE 0.021 0.001 PHE R 227 TYR 0.018 0.001 TYR R 191 ARG 0.012 0.000 ARG S 18 ********************** 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 155 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.826 Fit side-chains REVERT: A 10 LYS cc_start: 0.7187 (mtpp) cc_final: 0.6657 (mttt) REVERT: A 20 ASP cc_start: 0.7374 (m-30) cc_final: 0.7024 (m-30) REVERT: A 22 ASN cc_start: 0.6811 (m-40) cc_final: 0.6450 (m110) REVERT: A 73 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7028 (mttm) REVERT: B 118 ASP cc_start: 0.7911 (t0) cc_final: 0.7522 (p0) REVERT: B 283 ARG cc_start: 0.6659 (tpt-90) cc_final: 0.5984 (mtp180) REVERT: S 19 LYS cc_start: 0.7435 (tttp) cc_final: 0.6808 (tptt) REVERT: S 67 ARG cc_start: 0.7007 (mtm180) cc_final: 0.6573 (ptt180) REVERT: S 175 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8032 (tp) REVERT: S 221 LEU cc_start: 0.6727 (tp) cc_final: 0.6317 (tp) REVERT: R 190 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7872 (mp) REVERT: R 469 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6857 (mm-30) outliers start: 23 outliers final: 16 residues processed: 145 average time/residue: 1.1956 time to fit residues: 187.1966 Evaluate side-chains 148 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 98 GLN 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 317 CYS Chi-restraints excluded: chain B residue 327 VAL 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 143 VAL Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 425 MET Chi-restraints excluded: chain R residue 469 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 9.9990 chunk 101 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.215932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.180822 restraints weight = 10455.449| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.66 r_work: 0.3693 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 9634 Z= 0.364 Angle : 0.634 7.532 13091 Z= 0.337 Chirality : 0.045 0.194 1481 Planarity : 0.005 0.048 1651 Dihedral : 4.704 26.295 1321 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.53 % Allowed : 19.73 % 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: 0.77 (0.24), residues: 1197 helix: 2.06 (0.24), residues: 432 sheet: -0.11 (0.31), residues: 272 loop : -0.46 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP R 298 HIS 0.008 0.002 HIS R 420 PHE 0.021 0.002 PHE R 227 TYR 0.019 0.002 TYR R 297 ARG 0.011 0.001 ARG S 18 =============================================================================== Job complete usr+sys time: 9395.73 seconds wall clock time: 166 minutes 50.40 seconds (10010.40 seconds total)