Starting phenix.real_space_refine on Wed Sep 17 15:40:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jr2_61746/09_2025/9jr2_61746.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jr2_61746/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jr2_61746/09_2025/9jr2_61746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jr2_61746/09_2025/9jr2_61746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jr2_61746/09_2025/9jr2_61746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jr2_61746/09_2025/9jr2_61746.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} 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: {'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'GLU:plan': 4, 'ASN:plan1': 1} 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, 'ARG:plan': 1, 'GLU:plan': 2, '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, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 2} 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: 2.11, per 1000 atoms: 0.22 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: 0.79 Conformation dependent library (CDL) restraints added in 340.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.34 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: 1.76 Time building geometry restraints manager: 1.04 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: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.650 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:8.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.750 ------------------------------------------------------------------------------- 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 0.106 9641 Z= 0.172 Angle : 0.512 6.102 13103 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 : 3.15 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG B 150 TYR 0.011 0.001 TYR R 191 PHE 0.009 0.001 PHE B 151 TRP 0.008 0.001 TRP B 82 HIS 0.005 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9634) covalent geometry : angle 0.51227 (13091) SS BOND : bond 0.00331 ( 6) SS BOND : angle 0.47622 ( 12) hydrogen bonds : bond 0.18087 ( 492) hydrogen bonds : angle 6.68142 ( 1368) Misc. bond : bond 0.10575 ( 1) *********************** 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 : 0.363 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: 0.5038 (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: 0.5020 time to fit residues: 97.8886 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 : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.0470 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 119 GLN B 32 GLN B 35 ASN B 54 HIS B 88 ASN B 259 GLN B 295 ASN P 16 ASN R 225 HIS R 442 HIS R 463 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.210753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.173684 restraints weight = 10076.736| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.73 r_work: 0.3678 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9641 Z= 0.161 Angle : 0.566 5.973 13103 Z= 0.305 Chirality : 0.043 0.151 1481 Planarity : 0.004 0.042 1651 Dihedral : 4.221 22.071 1321 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.49 % Allowed : 15.47 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.25), residues: 1197 helix: 2.20 (0.25), residues: 430 sheet: -0.19 (0.31), residues: 279 loop : -0.39 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 20 TYR 0.018 0.002 TYR R 191 PHE 0.018 0.002 PHE R 227 TRP 0.015 0.002 TRP R 298 HIS 0.007 0.002 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9634) covalent geometry : angle 0.56551 (13091) SS BOND : bond 0.00250 ( 6) SS BOND : angle 0.89392 ( 12) hydrogen bonds : bond 0.05072 ( 492) hydrogen bonds : angle 4.61770 ( 1368) Misc. bond : bond 0.00018 ( 1) *********************** 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 172 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.287 Fit side-chains REVERT: A 10 LYS cc_start: 0.7079 (mtpp) cc_final: 0.6594 (mttt) REVERT: A 20 ASP cc_start: 0.7407 (m-30) cc_final: 0.7031 (m-30) REVERT: A 22 ASN cc_start: 0.6827 (m-40) cc_final: 0.6478 (m110) REVERT: A 85 ASP cc_start: 0.7795 (t0) cc_final: 0.7571 (t0) REVERT: A 208 ARG cc_start: 0.6927 (mtt180) cc_final: 0.6719 (mmm160) REVERT: B 118 ASP cc_start: 0.7744 (t0) cc_final: 0.7299 (p0) REVERT: B 262 MET cc_start: 0.5075 (OUTLIER) cc_final: 0.4773 (tpt) REVERT: B 283 ARG cc_start: 0.6687 (tpt-90) cc_final: 0.6017 (mtp180) REVERT: S 18 ARG cc_start: 0.6582 (ttm110) cc_final: 0.6382 (ttm110) REVERT: S 116 THR cc_start: 0.6087 (t) cc_final: 0.5791 (m) REVERT: S 175 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8142 (tp) REVERT: S 180 MET cc_start: 0.5627 (tpt) cc_final: 0.5426 (tpt) REVERT: S 221 LEU cc_start: 0.6700 (tp) cc_final: 0.6190 (tp) REVERT: R 214 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.6249 (mtp180) REVERT: R 383 ARG cc_start: 0.7318 (ttm-80) cc_final: 0.7109 (ptm160) outliers start: 24 outliers final: 14 residues processed: 160 average time/residue: 0.5177 time to fit residues: 88.6872 Evaluate side-chains 153 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN 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 252 LEU Chi-restraints excluded: chain B residue 262 MET 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 373 LEU 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 59 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 0.0570 chunk 111 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 119 GLN A 131 ASN A 209 HIS B 54 HIS ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 463 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.212794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.177548 restraints weight = 10447.541| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.86 r_work: 0.3790 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9641 Z= 0.140 Angle : 0.529 7.651 13103 Z= 0.284 Chirality : 0.042 0.145 1481 Planarity : 0.004 0.041 1651 Dihedral : 4.222 26.464 1321 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.74 % Allowed : 15.89 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.25), residues: 1197 helix: 2.37 (0.25), residues: 432 sheet: -0.09 (0.30), residues: 283 loop : -0.38 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 20 TYR 0.013 0.001 TYR R 459 PHE 0.013 0.001 PHE R 453 TRP 0.015 0.001 TRP R 298 HIS 0.009 0.001 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9634) covalent geometry : angle 0.52882 (13091) SS BOND : bond 0.00283 ( 6) SS BOND : angle 0.84530 ( 12) hydrogen bonds : bond 0.04435 ( 492) hydrogen bonds : angle 4.36581 ( 1368) Misc. bond : bond 0.00002 ( 1) *********************** 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 177 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.329 Fit side-chains REVERT: A 10 LYS cc_start: 0.7196 (mtpp) cc_final: 0.6674 (mttt) REVERT: A 20 ASP cc_start: 0.7474 (m-30) cc_final: 0.7118 (m-30) REVERT: A 22 ASN cc_start: 0.6888 (m-40) cc_final: 0.6551 (m110) REVERT: A 238 MET cc_start: 0.7042 (mtm) cc_final: 0.6727 (ptt) REVERT: B 118 ASP cc_start: 0.7861 (t0) cc_final: 0.7460 (p0) REVERT: B 134 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7233 (ptt180) REVERT: B 262 MET cc_start: 0.5116 (OUTLIER) cc_final: 0.4837 (tpt) REVERT: B 283 ARG cc_start: 0.6754 (tpt-90) cc_final: 0.6049 (mtp180) REVERT: S 116 THR cc_start: 0.5996 (t) cc_final: 0.5704 (m) REVERT: S 175 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8032 (tp) REVERT: S 180 MET cc_start: 0.5680 (tpt) cc_final: 0.5415 (tpt) REVERT: S 221 LEU cc_start: 0.6750 (tp) cc_final: 0.6195 (tp) REVERT: R 214 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.6328 (mtp180) outliers start: 36 outliers final: 15 residues processed: 159 average time/residue: 0.5477 time to fit residues: 92.9877 Evaluate side-chains 156 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 134 ARG 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 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 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 7 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 R 463 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.213964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.178834 restraints weight = 10578.374| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.86 r_work: 0.3695 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9641 Z= 0.114 Angle : 0.494 7.102 13103 Z= 0.267 Chirality : 0.041 0.140 1481 Planarity : 0.004 0.040 1651 Dihedral : 4.054 27.364 1321 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.01 % Allowed : 17.86 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.25), residues: 1197 helix: 2.65 (0.25), residues: 432 sheet: 0.03 (0.30), residues: 281 loop : -0.35 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 18 TYR 0.015 0.001 TYR R 191 PHE 0.014 0.001 PHE R 335 TRP 0.018 0.001 TRP R 298 HIS 0.010 0.001 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9634) covalent geometry : angle 0.49373 (13091) SS BOND : bond 0.00187 ( 6) SS BOND : angle 0.81154 ( 12) hydrogen bonds : bond 0.03903 ( 492) hydrogen bonds : angle 4.14860 ( 1368) Misc. bond : bond 0.00002 ( 1) *********************** 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 173 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.413 Fit side-chains REVERT: A 10 LYS cc_start: 0.7063 (mtpp) cc_final: 0.6509 (mttt) REVERT: A 20 ASP cc_start: 0.7339 (m-30) cc_final: 0.6914 (m-30) REVERT: A 22 ASN cc_start: 0.6815 (m-40) cc_final: 0.6433 (m110) REVERT: A 119 GLN cc_start: 0.7356 (mm-40) cc_final: 0.7037 (mm-40) REVERT: A 232 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7618 (mtpm) REVERT: A 238 MET cc_start: 0.6962 (mtm) cc_final: 0.6555 (ptt) REVERT: B 118 ASP cc_start: 0.7912 (t0) cc_final: 0.7376 (p0) REVERT: B 283 ARG cc_start: 0.6710 (tpt-90) cc_final: 0.5988 (mtp180) REVERT: S 30 SER cc_start: 0.8076 (OUTLIER) cc_final: 0.7745 (p) REVERT: S 46 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6547 (mp0) REVERT: S 83 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.5483 (mmt) REVERT: S 175 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8104 (tp) REVERT: S 221 LEU cc_start: 0.6699 (tp) cc_final: 0.6114 (tp) REVERT: R 373 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7547 (tt) outliers start: 29 outliers final: 13 residues processed: 159 average time/residue: 0.5601 time to fit residues: 95.3361 Evaluate side-chains 153 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLN 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 251 ARG 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 83 MET 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 373 LEU 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 92 optimal weight: 50.0000 chunk 53 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 79 optimal weight: 0.5980 chunk 93 optimal weight: 30.0000 chunk 24 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.4296 r_free = 0.4296 target = 0.213945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.178396 restraints weight = 10489.317| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.74 r_work: 0.3691 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9641 Z= 0.136 Angle : 0.523 7.089 13103 Z= 0.279 Chirality : 0.041 0.186 1481 Planarity : 0.004 0.041 1651 Dihedral : 4.197 26.812 1321 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.22 % Allowed : 18.59 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.25), residues: 1197 helix: 2.58 (0.25), residues: 432 sheet: -0.05 (0.30), residues: 283 loop : -0.32 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 18 TYR 0.018 0.001 TYR R 191 PHE 0.016 0.001 PHE R 227 TRP 0.021 0.001 TRP R 298 HIS 0.007 0.001 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9634) covalent geometry : angle 0.52106 (13091) SS BOND : bond 0.00252 ( 6) SS BOND : angle 1.40159 ( 12) hydrogen bonds : bond 0.04083 ( 492) hydrogen bonds : angle 4.21060 ( 1368) Misc. bond : bond 0.00000 ( 1) *********************** 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 169 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.340 Fit side-chains REVERT: A 10 LYS cc_start: 0.7075 (mtpp) cc_final: 0.6516 (mttt) REVERT: A 20 ASP cc_start: 0.7332 (m-30) cc_final: 0.6946 (m-30) REVERT: A 22 ASN cc_start: 0.6822 (m-40) cc_final: 0.6435 (m110) REVERT: A 232 LYS cc_start: 0.7868 (ttpp) cc_final: 0.7620 (mtpm) REVERT: A 238 MET cc_start: 0.6999 (mtm) cc_final: 0.6661 (ptm) REVERT: B 118 ASP cc_start: 0.7898 (t0) cc_final: 0.7367 (p0) REVERT: B 262 MET cc_start: 0.5074 (OUTLIER) cc_final: 0.4819 (tpt) REVERT: B 283 ARG cc_start: 0.6743 (tpt-90) cc_final: 0.5989 (mtp180) REVERT: S 30 SER cc_start: 0.8086 (OUTLIER) cc_final: 0.7753 (p) REVERT: S 46 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6524 (mp0) REVERT: S 83 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.5474 (mmt) REVERT: S 175 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8128 (tp) REVERT: S 221 LEU cc_start: 0.6714 (tp) cc_final: 0.6164 (tp) REVERT: R 214 ARG cc_start: 0.6415 (OUTLIER) cc_final: 0.6101 (mtp180) REVERT: R 469 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6930 (mm-30) outliers start: 31 outliers final: 17 residues processed: 154 average time/residue: 0.5094 time to fit residues: 84.4200 Evaluate side-chains 157 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 83 MET 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 28 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 9 HIS ** 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 = 0.4266 r_free = 0.4266 target = 0.210555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.175062 restraints weight = 10520.818| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.93 r_work: 0.3627 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9641 Z= 0.194 Angle : 0.592 7.855 13103 Z= 0.317 Chirality : 0.044 0.200 1481 Planarity : 0.004 0.051 1651 Dihedral : 4.607 26.566 1321 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.26 % Allowed : 18.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.25), residues: 1197 helix: 2.23 (0.24), residues: 432 sheet: -0.18 (0.30), residues: 283 loop : -0.38 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 18 TYR 0.017 0.002 TYR R 297 PHE 0.018 0.002 PHE R 227 TRP 0.025 0.002 TRP R 298 HIS 0.013 0.002 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 9634) covalent geometry : angle 0.59033 (13091) SS BOND : bond 0.00343 ( 6) SS BOND : angle 1.61613 ( 12) hydrogen bonds : bond 0.04784 ( 492) hydrogen bonds : angle 4.51671 ( 1368) Misc. bond : bond 0.00003 ( 1) *********************** 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 180 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.331 Fit side-chains REVERT: A 10 LYS cc_start: 0.7224 (mtpp) cc_final: 0.6674 (mttt) REVERT: A 20 ASP cc_start: 0.7318 (m-30) cc_final: 0.6948 (m-30) REVERT: A 22 ASN cc_start: 0.6869 (m-40) cc_final: 0.6460 (m110) REVERT: A 232 LYS cc_start: 0.7861 (ttpp) cc_final: 0.7614 (mtpm) REVERT: A 233 ASP cc_start: 0.7750 (t70) cc_final: 0.7507 (m-30) REVERT: A 238 MET cc_start: 0.7102 (mtm) cc_final: 0.6727 (ptm) REVERT: B 118 ASP cc_start: 0.7983 (t0) cc_final: 0.7426 (p0) REVERT: B 134 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7257 (ptt180) REVERT: B 283 ARG cc_start: 0.6793 (tpt-90) cc_final: 0.5968 (mtp180) REVERT: S 19 LYS cc_start: 0.7512 (tttp) cc_final: 0.6754 (tptt) REVERT: S 175 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8133 (tp) REVERT: S 221 LEU cc_start: 0.6750 (tp) cc_final: 0.6361 (tp) REVERT: R 389 LEU cc_start: 0.5679 (OUTLIER) cc_final: 0.5157 (mp) REVERT: R 469 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7021 (mm-30) outliers start: 41 outliers final: 24 residues processed: 162 average time/residue: 0.5130 time to fit residues: 89.1878 Evaluate side-chains 163 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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 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 S residue 198 THR Chi-restraints excluded: chain P residue 27 LYS 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 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 66 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4292 r_free = 0.4292 target = 0.214004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.178534 restraints weight = 10510.959| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.72 r_work: 0.3714 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9641 Z= 0.108 Angle : 0.497 6.542 13103 Z= 0.266 Chirality : 0.040 0.152 1481 Planarity : 0.004 0.042 1651 Dihedral : 4.181 27.047 1321 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.12 % Allowed : 19.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.25), residues: 1197 helix: 2.70 (0.25), residues: 430 sheet: -0.08 (0.30), residues: 283 loop : -0.34 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 18 TYR 0.017 0.001 TYR R 191 PHE 0.017 0.001 PHE R 227 TRP 0.023 0.001 TRP R 298 HIS 0.012 0.001 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9634) covalent geometry : angle 0.49522 (13091) SS BOND : bond 0.00191 ( 6) SS BOND : angle 1.28009 ( 12) hydrogen bonds : bond 0.03741 ( 492) hydrogen bonds : angle 4.12498 ( 1368) Misc. bond : bond 0.00002 ( 1) *********************** 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 166 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7093 (mtpp) cc_final: 0.6555 (mttt) REVERT: A 20 ASP cc_start: 0.7302 (m-30) cc_final: 0.6899 (m-30) REVERT: A 22 ASN cc_start: 0.6806 (m-40) cc_final: 0.6411 (m110) REVERT: A 35 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6292 (mtp180) REVERT: A 232 LYS cc_start: 0.7814 (ttpp) cc_final: 0.7567 (mtpm) REVERT: A 238 MET cc_start: 0.7001 (mtm) cc_final: 0.6643 (ptm) REVERT: B 118 ASP cc_start: 0.7908 (t0) cc_final: 0.7410 (p0) REVERT: B 283 ARG cc_start: 0.6649 (tpt-90) cc_final: 0.5939 (mtp180) REVERT: S 19 LYS cc_start: 0.7502 (tttp) cc_final: 0.6848 (tptt) REVERT: S 154 LEU cc_start: 0.6827 (tp) cc_final: 0.6287 (tm) REVERT: S 175 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8045 (tp) REVERT: S 180 MET cc_start: 0.5393 (tpt) cc_final: 0.5155 (tpp) REVERT: S 221 LEU cc_start: 0.6719 (tp) cc_final: 0.6249 (tp) REVERT: R 389 LEU cc_start: 0.5668 (OUTLIER) cc_final: 0.5169 (mp) outliers start: 30 outliers final: 13 residues processed: 156 average time/residue: 0.5434 time to fit residues: 91.0263 Evaluate side-chains 144 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 172 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 135 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 P residue 27 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 113 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 86 optimal weight: 0.0570 chunk 72 optimal weight: 0.0470 chunk 49 optimal weight: 0.8980 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.216185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.180946 restraints weight = 10450.534| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.67 r_work: 0.3727 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9641 Z= 0.104 Angle : 0.495 6.739 13103 Z= 0.263 Chirality : 0.040 0.151 1481 Planarity : 0.003 0.040 1651 Dihedral : 4.044 26.675 1321 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.70 % Allowed : 20.15 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.25), residues: 1197 helix: 2.82 (0.25), residues: 431 sheet: 0.01 (0.31), residues: 278 loop : -0.32 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 18 TYR 0.016 0.001 TYR S 178 PHE 0.016 0.001 PHE R 335 TRP 0.026 0.001 TRP R 298 HIS 0.010 0.001 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9634) covalent geometry : angle 0.49350 (13091) SS BOND : bond 0.00190 ( 6) SS BOND : angle 1.21245 ( 12) hydrogen bonds : bond 0.03593 ( 492) hydrogen bonds : angle 3.99010 ( 1368) Misc. bond : bond 0.00002 ( 1) *********************** 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 162 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.368 Fit side-chains REVERT: A 10 LYS cc_start: 0.7121 (mtpp) cc_final: 0.6563 (mttt) REVERT: A 20 ASP cc_start: 0.7271 (m-30) cc_final: 0.6879 (m-30) REVERT: A 22 ASN cc_start: 0.6828 (m-40) cc_final: 0.6445 (m110) REVERT: A 35 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.6264 (mtp180) REVERT: A 232 LYS cc_start: 0.7815 (ttpp) cc_final: 0.7563 (mtpm) REVERT: A 238 MET cc_start: 0.6996 (mtm) cc_final: 0.6655 (ptm) REVERT: B 118 ASP cc_start: 0.7932 (t0) cc_final: 0.7424 (p0) REVERT: B 283 ARG cc_start: 0.6673 (tpt-90) cc_final: 0.5976 (mtp180) REVERT: S 19 LYS cc_start: 0.7507 (tttp) cc_final: 0.6822 (tptt) REVERT: S 83 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.5213 (mmm) REVERT: S 154 LEU cc_start: 0.6832 (tp) cc_final: 0.6314 (tm) REVERT: S 175 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8067 (tp) REVERT: S 180 MET cc_start: 0.5431 (tpt) cc_final: 0.5106 (tpp) REVERT: S 221 LEU cc_start: 0.6712 (tp) cc_final: 0.6248 (tp) outliers start: 26 outliers final: 14 residues processed: 154 average time/residue: 0.5372 time to fit residues: 88.7414 Evaluate side-chains 145 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 31 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 P residue 27 LYS Chi-restraints excluded: chain R residue 224 MET 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 102 optimal weight: 2.9990 chunk 25 optimal weight: 0.0370 chunk 53 optimal weight: 6.9990 chunk 101 optimal weight: 0.2980 chunk 110 optimal weight: 0.9980 chunk 91 optimal weight: 30.0000 chunk 28 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN S 155 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 = 0.4376 r_free = 0.4376 target = 0.220696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.185989 restraints weight = 10440.454| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.51 r_work: 0.3736 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9641 Z= 0.125 Angle : 0.516 6.704 13103 Z= 0.275 Chirality : 0.041 0.157 1481 Planarity : 0.004 0.041 1651 Dihedral : 4.132 26.485 1321 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.91 % Allowed : 20.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.25), residues: 1197 helix: 2.67 (0.25), residues: 431 sheet: -0.01 (0.31), residues: 273 loop : -0.35 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 18 TYR 0.016 0.001 TYR R 191 PHE 0.017 0.001 PHE R 335 TRP 0.031 0.002 TRP R 298 HIS 0.010 0.001 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9634) covalent geometry : angle 0.51499 (13091) SS BOND : bond 0.00268 ( 6) SS BOND : angle 1.23294 ( 12) hydrogen bonds : bond 0.03825 ( 492) hydrogen bonds : angle 4.08505 ( 1368) Misc. bond : bond 0.00001 ( 1) *********************** 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 164 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.292 Fit side-chains REVERT: A 10 LYS cc_start: 0.7139 (mtpp) cc_final: 0.6640 (mttt) REVERT: A 20 ASP cc_start: 0.7341 (m-30) cc_final: 0.6971 (m-30) REVERT: A 22 ASN cc_start: 0.6828 (m-40) cc_final: 0.6470 (m110) REVERT: A 35 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6279 (mtp180) REVERT: A 232 LYS cc_start: 0.7844 (ttpp) cc_final: 0.7599 (mtpm) REVERT: A 238 MET cc_start: 0.6948 (mtm) cc_final: 0.6631 (ptm) REVERT: B 118 ASP cc_start: 0.7867 (t0) cc_final: 0.7438 (p0) REVERT: B 283 ARG cc_start: 0.6669 (tpt-90) cc_final: 0.5976 (mtp180) REVERT: S 19 LYS cc_start: 0.7522 (tttp) cc_final: 0.6870 (tptt) REVERT: S 67 ARG cc_start: 0.6982 (mtm180) cc_final: 0.6670 (ptt90) REVERT: S 83 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.5229 (mmm) REVERT: S 154 LEU cc_start: 0.6935 (tp) cc_final: 0.6436 (tm) REVERT: S 175 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8056 (tp) REVERT: S 221 LEU cc_start: 0.6740 (tp) cc_final: 0.6291 (tp) outliers start: 28 outliers final: 18 residues processed: 155 average time/residue: 0.5214 time to fit residues: 86.8979 Evaluate side-chains 152 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 172 THR Chi-restraints excluded: chain A residue 201 SER 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 135 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 31 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 P residue 27 LYS Chi-restraints excluded: chain R residue 224 MET 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 74 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 119 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.219334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.184463 restraints weight = 10353.323| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.55 r_work: 0.3716 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9641 Z= 0.142 Angle : 0.539 7.041 13103 Z= 0.287 Chirality : 0.042 0.167 1481 Planarity : 0.004 0.042 1651 Dihedral : 4.270 26.409 1321 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.70 % Allowed : 20.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.25), residues: 1197 helix: 2.54 (0.25), residues: 431 sheet: -0.05 (0.31), residues: 273 loop : -0.36 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 314 TYR 0.014 0.001 TYR R 297 PHE 0.018 0.002 PHE R 335 TRP 0.036 0.002 TRP R 298 HIS 0.010 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9634) covalent geometry : angle 0.53834 (13091) SS BOND : bond 0.00254 ( 6) SS BOND : angle 1.27510 ( 12) hydrogen bonds : bond 0.04059 ( 492) hydrogen bonds : angle 4.18201 ( 1368) Misc. bond : bond 0.00001 ( 1) ********************** 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 159 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.357 Fit side-chains REVERT: A 10 LYS cc_start: 0.7174 (mtpp) cc_final: 0.6671 (mttt) REVERT: A 20 ASP cc_start: 0.7332 (m-30) cc_final: 0.6988 (m-30) REVERT: A 22 ASN cc_start: 0.6851 (m-40) cc_final: 0.6458 (m110) REVERT: A 35 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.6303 (mtp180) REVERT: A 232 LYS cc_start: 0.7847 (ttpp) cc_final: 0.7590 (mtpm) REVERT: A 233 ASP cc_start: 0.7615 (t70) cc_final: 0.7402 (m-30) REVERT: A 238 MET cc_start: 0.6962 (mtm) cc_final: 0.6644 (ptm) REVERT: B 118 ASP cc_start: 0.7875 (t0) cc_final: 0.7436 (p0) REVERT: B 283 ARG cc_start: 0.6663 (tpt-90) cc_final: 0.5959 (mtp180) REVERT: S 19 LYS cc_start: 0.7470 (tttp) cc_final: 0.6839 (tptt) REVERT: S 67 ARG cc_start: 0.6996 (mtm180) cc_final: 0.6644 (ptt90) REVERT: S 154 LEU cc_start: 0.6939 (tp) cc_final: 0.6468 (tm) REVERT: S 175 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8084 (tp) REVERT: S 221 LEU cc_start: 0.6745 (tp) cc_final: 0.6314 (tp) outliers start: 26 outliers final: 20 residues processed: 151 average time/residue: 0.5611 time to fit residues: 91.0125 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 : 0.373 ------------------------------------------------------------------------------- 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 172 THR Chi-restraints excluded: chain A residue 201 SER 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 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 46 GLU 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 224 MET 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 48 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 80 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.0370 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN S 82 GLN R 463 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.221444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.186881 restraints weight = 10269.548| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.46 r_work: 0.3740 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 9641 Z= 0.110 Angle : 0.506 6.344 13103 Z= 0.270 Chirality : 0.041 0.148 1481 Planarity : 0.004 0.040 1651 Dihedral : 4.099 26.632 1321 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.39 % Allowed : 20.46 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.25), residues: 1197 helix: 2.69 (0.25), residues: 431 sheet: -0.04 (0.31), residues: 280 loop : -0.31 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 314 TYR 0.017 0.001 TYR R 191 PHE 0.017 0.001 PHE R 335 TRP 0.038 0.002 TRP R 298 HIS 0.009 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9634) covalent geometry : angle 0.50536 (13091) SS BOND : bond 0.00193 ( 6) SS BOND : angle 1.16050 ( 12) hydrogen bonds : bond 0.03654 ( 492) hydrogen bonds : angle 4.04742 ( 1368) Misc. bond : bond 0.00001 ( 1) =============================================================================== Job complete usr+sys time: 4791.16 seconds wall clock time: 82 minutes 5.62 seconds (4925.62 seconds total)