Starting phenix.real_space_refine on Sun Aug 24 20:16:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ve3_21153/08_2025/6ve3_21153.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ve3_21153/08_2025/6ve3_21153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ve3_21153/08_2025/6ve3_21153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ve3_21153/08_2025/6ve3_21153.map" model { file = "/net/cci-nas-00/data/ceres_data/6ve3_21153/08_2025/6ve3_21153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ve3_21153/08_2025/6ve3_21153.cif" } resolution = 4.3 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.075 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: 3 Type Number sf(0) Gaussians C 13328 2.51 5 N 4578 2.21 5 O 4578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22484 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'ARG:plan': 15, 'GLU:plan': 20, 'GLN:plan1': 13, 'ASN:plan1': 19, 'TYR:plan': 8, 'ASP:plan': 21, 'PHE:plan': 9, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 460 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N Time building chain proxies: 2.26, per 1000 atoms: 0.10 Number of scatterers: 22484 At special positions: 0 Unit cell: (143.55, 143.55, 129.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 4578 8.00 N 4578 7.00 C 13328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 476.8 nanoseconds 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8344 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 57 sheets defined 25.4% alpha, 65.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 12 through 27 Processing helix chain 'A' and resid 44 through 59 Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.687A pdb=" N LEU A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 325 Processing helix chain 'B' and resid 12 through 27 Processing helix chain 'B' and resid 44 through 59 Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.616A pdb=" N ARG B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'C' and resid 12 through 27 Processing helix chain 'C' and resid 44 through 59 Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.816A pdb=" N LYS C 107 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 removed outlier: 4.220A pdb=" N VAL C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 299 removed outlier: 3.616A pdb=" N ARG C 297 " --> pdb=" O PRO C 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 298 " --> pdb=" O TYR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 325 Processing helix chain 'D' and resid 12 through 27 Processing helix chain 'D' and resid 44 through 59 Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS D 107 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL D 136 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 246 Processing helix chain 'D' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG D 297 " --> pdb=" O PRO D 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 298 " --> pdb=" O TYR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 325 Processing helix chain 'E' and resid 12 through 27 Processing helix chain 'E' and resid 44 through 59 Processing helix chain 'E' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS E 107 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 142 removed outlier: 4.219A pdb=" N VAL E 136 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 246 Processing helix chain 'E' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU E 292 " --> pdb=" O PHE E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG E 297 " --> pdb=" O PRO E 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU E 298 " --> pdb=" O TYR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 325 Processing helix chain 'F' and resid 12 through 27 Processing helix chain 'F' and resid 44 through 59 Processing helix chain 'F' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS F 107 " --> pdb=" O ASN F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 142 removed outlier: 4.219A pdb=" N VAL F 136 " --> pdb=" O PRO F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 246 Processing helix chain 'F' and resid 286 through 292 removed outlier: 3.688A pdb=" N LEU F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 299 removed outlier: 3.617A pdb=" N ARG F 297 " --> pdb=" O PRO F 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 298 " --> pdb=" O TYR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 325 Processing helix chain 'G' and resid 12 through 27 Processing helix chain 'G' and resid 44 through 59 Processing helix chain 'G' and resid 103 through 115 removed outlier: 3.816A pdb=" N LYS G 107 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 142 removed outlier: 4.217A pdb=" N VAL G 136 " --> pdb=" O PRO G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 246 Processing helix chain 'G' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU G 292 " --> pdb=" O PHE G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG G 297 " --> pdb=" O PRO G 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU G 298 " --> pdb=" O TYR G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 325 Processing helix chain 'H' and resid 12 through 27 Processing helix chain 'H' and resid 44 through 59 Processing helix chain 'H' and resid 103 through 115 removed outlier: 3.817A pdb=" N LYS H 107 " --> pdb=" O ASN H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 142 removed outlier: 4.219A pdb=" N VAL H 136 " --> pdb=" O PRO H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 246 Processing helix chain 'H' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU H 292 " --> pdb=" O PHE H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 299 removed outlier: 3.616A pdb=" N ARG H 297 " --> pdb=" O PRO H 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU H 298 " --> pdb=" O TYR H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 325 Processing helix chain 'I' and resid 12 through 27 Processing helix chain 'I' and resid 44 through 59 Processing helix chain 'I' and resid 103 through 115 removed outlier: 3.816A pdb=" N LYS I 107 " --> pdb=" O ASN I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL I 136 " --> pdb=" O PRO I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 246 Processing helix chain 'I' and resid 286 through 292 removed outlier: 3.687A pdb=" N LEU I 292 " --> pdb=" O PHE I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 292 through 299 removed outlier: 3.617A pdb=" N ARG I 297 " --> pdb=" O PRO I 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU I 298 " --> pdb=" O TYR I 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 320 through 325 Processing helix chain 'J' and resid 12 through 27 Processing helix chain 'J' and resid 44 through 59 Processing helix chain 'J' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS J 107 " --> pdb=" O ASN J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL J 136 " --> pdb=" O PRO J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 246 Processing helix chain 'J' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU J 292 " --> pdb=" O PHE J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG J 297 " --> pdb=" O PRO J 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU J 298 " --> pdb=" O TYR J 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 through 325 Processing helix chain 'K' and resid 12 through 27 Processing helix chain 'K' and resid 44 through 59 Processing helix chain 'K' and resid 103 through 115 removed outlier: 3.816A pdb=" N LYS K 107 " --> pdb=" O ASN K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL K 136 " --> pdb=" O PRO K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 246 Processing helix chain 'K' and resid 286 through 292 removed outlier: 3.687A pdb=" N LEU K 292 " --> pdb=" O PHE K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 299 removed outlier: 3.617A pdb=" N ARG K 297 " --> pdb=" O PRO K 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU K 298 " --> pdb=" O TYR K 294 " (cutoff:3.500A) Processing helix chain 'K' and resid 320 through 325 Processing helix chain 'L' and resid 12 through 27 Processing helix chain 'L' and resid 44 through 59 Processing helix chain 'L' and resid 103 through 115 removed outlier: 3.814A pdb=" N LYS L 107 " --> pdb=" O ASN L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL L 136 " --> pdb=" O PRO L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 286 through 292 removed outlier: 3.688A pdb=" N LEU L 292 " --> pdb=" O PHE L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 299 removed outlier: 3.614A pdb=" N ARG L 297 " --> pdb=" O PRO L 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU L 298 " --> pdb=" O TYR L 294 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 325 Processing helix chain 'M' and resid 12 through 27 Processing helix chain 'M' and resid 44 through 59 Processing helix chain 'M' and resid 103 through 115 removed outlier: 3.816A pdb=" N LYS M 107 " --> pdb=" O ASN M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 142 removed outlier: 4.220A pdb=" N VAL M 136 " --> pdb=" O PRO M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 241 through 246 Processing helix chain 'M' and resid 286 through 292 removed outlier: 3.687A pdb=" N LEU M 292 " --> pdb=" O PHE M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG M 297 " --> pdb=" O PRO M 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 325 Processing helix chain 'N' and resid 12 through 27 Processing helix chain 'N' and resid 44 through 59 Processing helix chain 'N' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS N 107 " --> pdb=" O ASN N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 142 removed outlier: 4.219A pdb=" N VAL N 136 " --> pdb=" O PRO N 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 241 through 246 Processing helix chain 'N' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU N 292 " --> pdb=" O PHE N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 299 removed outlier: 3.616A pdb=" N ARG N 297 " --> pdb=" O PRO N 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU N 298 " --> pdb=" O TYR N 294 " (cutoff:3.500A) Processing helix chain 'N' and resid 320 through 325 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 152 Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 95 removed outlier: 3.582A pdb=" N ASP A 302 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL A 84 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG A 300 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 272 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU A 315 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL A 270 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 271 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 152 Processing sheet with id=AA5, first strand: chain 'B' and resid 93 through 95 removed outlier: 3.582A pdb=" N ASP B 302 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL B 84 " --> pdb=" O ARG B 300 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG B 300 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY B 272 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU B 315 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL B 270 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE B 271 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 148 through 152 Processing sheet with id=AA7, first strand: chain 'C' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP C 302 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL C 84 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG C 300 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY C 272 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU C 315 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL C 270 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE C 271 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 166 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 148 through 152 Processing sheet with id=AA9, first strand: chain 'D' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP D 302 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL D 84 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG D 300 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY D 272 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU D 315 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL D 270 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE D 271 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU E 166 " --> pdb=" O LYS D 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 148 through 152 Processing sheet with id=AB2, first strand: chain 'E' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP E 302 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL E 84 " --> pdb=" O ARG E 300 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG E 300 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY E 272 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU E 315 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL E 270 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE E 271 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU F 166 " --> pdb=" O LYS E 285 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 148 through 152 Processing sheet with id=AB4, first strand: chain 'F' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP F 302 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL F 84 " --> pdb=" O ARG F 300 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG F 300 " --> pdb=" O VAL F 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY F 272 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU F 315 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL F 270 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE F 271 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 148 through 152 Processing sheet with id=AB6, first strand: chain 'G' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP G 302 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL G 84 " --> pdb=" O ARG G 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG G 300 " --> pdb=" O VAL G 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY G 272 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU G 315 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL G 270 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE G 271 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU H 166 " --> pdb=" O LYS G 285 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 148 through 152 Processing sheet with id=AB8, first strand: chain 'H' and resid 93 through 95 removed outlier: 3.581A pdb=" N ASP H 302 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL H 84 " --> pdb=" O ARG H 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG H 300 " --> pdb=" O VAL H 84 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY H 272 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU H 315 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL H 270 " --> pdb=" O LEU H 315 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE H 271 " --> pdb=" O VAL I 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 148 through 152 Processing sheet with id=AC1, first strand: chain 'I' and resid 93 through 95 removed outlier: 3.582A pdb=" N ASP I 302 " --> pdb=" O LEU I 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL I 84 " --> pdb=" O ARG I 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG I 300 " --> pdb=" O VAL I 84 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY I 272 " --> pdb=" O VAL I 313 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU I 315 " --> pdb=" O VAL I 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL I 270 " --> pdb=" O LEU I 315 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE I 271 " --> pdb=" O VAL J 180 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 148 through 152 Processing sheet with id=AC3, first strand: chain 'J' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP J 302 " --> pdb=" O LEU J 82 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL J 84 " --> pdb=" O ARG J 300 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG J 300 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY J 272 " --> pdb=" O VAL J 313 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU J 315 " --> pdb=" O VAL J 270 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL J 270 " --> pdb=" O LEU J 315 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE J 271 " --> pdb=" O VAL K 180 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU K 166 " --> pdb=" O LYS J 285 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 148 through 152 Processing sheet with id=AC5, first strand: chain 'K' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP K 302 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL K 84 " --> pdb=" O ARG K 300 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG K 300 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY K 272 " --> pdb=" O VAL K 313 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU K 315 " --> pdb=" O VAL K 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL K 270 " --> pdb=" O LEU K 315 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE K 271 " --> pdb=" O VAL L 180 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU L 166 " --> pdb=" O LYS K 285 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 148 through 152 Processing sheet with id=AC7, first strand: chain 'L' and resid 93 through 95 removed outlier: 3.582A pdb=" N ASP L 302 " --> pdb=" O LEU L 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL L 84 " --> pdb=" O ARG L 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG L 300 " --> pdb=" O VAL L 84 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY L 272 " --> pdb=" O VAL L 313 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU L 315 " --> pdb=" O VAL L 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL L 270 " --> pdb=" O LEU L 315 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE L 271 " --> pdb=" O VAL M 180 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU M 166 " --> pdb=" O LYS L 285 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 148 through 152 Processing sheet with id=AC9, first strand: chain 'M' and resid 93 through 95 removed outlier: 3.584A pdb=" N ASP M 302 " --> pdb=" O LEU M 82 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL M 84 " --> pdb=" O ARG M 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG M 300 " --> pdb=" O VAL M 84 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY M 272 " --> pdb=" O VAL M 313 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU M 315 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL M 270 " --> pdb=" O LEU M 315 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE M 271 " --> pdb=" O VAL N 180 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 148 through 152 Processing sheet with id=AD2, first strand: chain 'N' and resid 93 through 95 removed outlier: 3.581A pdb=" N ASP N 302 " --> pdb=" O LEU N 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL N 84 " --> pdb=" O ARG N 300 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG N 300 " --> pdb=" O VAL N 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY N 272 " --> pdb=" O VAL N 313 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU N 315 " --> pdb=" O VAL N 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL N 270 " --> pdb=" O LEU N 315 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE N 271 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 166 " --> pdb=" O LYS N 285 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 117 through 119 Processing sheet with id=AD4, first strand: chain 'A' and resid 187 through 201 removed outlier: 3.869A pdb=" N ARG A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG C 228 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG D 228 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG E 228 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG F 228 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG G 228 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG H 228 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG I 228 " --> pdb=" O THR I 224 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG J 228 " --> pdb=" O THR J 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG K 228 " --> pdb=" O THR K 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG L 228 " --> pdb=" O THR L 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG M 228 " --> pdb=" O THR M 224 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG N 228 " --> pdb=" O THR N 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 2 through 7 Processing sheet with id=AD6, first strand: chain 'B' and resid 117 through 119 Processing sheet with id=AD7, first strand: chain 'C' and resid 2 through 7 Processing sheet with id=AD8, first strand: chain 'C' and resid 117 through 119 Processing sheet with id=AD9, first strand: chain 'D' and resid 2 through 7 Processing sheet with id=AE1, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AE2, first strand: chain 'E' and resid 2 through 7 Processing sheet with id=AE3, first strand: chain 'E' and resid 117 through 119 Processing sheet with id=AE4, first strand: chain 'F' and resid 2 through 7 Processing sheet with id=AE5, first strand: chain 'F' and resid 117 through 119 Processing sheet with id=AE6, first strand: chain 'G' and resid 2 through 7 Processing sheet with id=AE7, first strand: chain 'G' and resid 117 through 119 Processing sheet with id=AE8, first strand: chain 'H' and resid 2 through 7 Processing sheet with id=AE9, first strand: chain 'H' and resid 117 through 119 Processing sheet with id=AF1, first strand: chain 'I' and resid 2 through 7 Processing sheet with id=AF2, first strand: chain 'I' and resid 117 through 119 Processing sheet with id=AF3, first strand: chain 'J' and resid 2 through 7 Processing sheet with id=AF4, first strand: chain 'J' and resid 117 through 119 Processing sheet with id=AF5, first strand: chain 'K' and resid 2 through 7 Processing sheet with id=AF6, first strand: chain 'K' and resid 117 through 119 Processing sheet with id=AF7, first strand: chain 'L' and resid 2 through 7 Processing sheet with id=AF8, first strand: chain 'L' and resid 117 through 119 Processing sheet with id=AF9, first strand: chain 'M' and resid 2 through 7 Processing sheet with id=AG1, first strand: chain 'M' and resid 117 through 119 Processing sheet with id=AG2, first strand: chain 'N' and resid 2 through 7 Processing sheet with id=AG3, first strand: chain 'N' and resid 117 through 119 2750 hydrogen bonds defined for protein. 7620 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: 6.53 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 4578 1.29 - 1.35: 4550 1.35 - 1.42: 0 1.42 - 1.49: 4578 1.49 - 1.56: 8750 Bond restraints: 22456 Sorted by residual: bond pdb=" CA SER J 203 " pdb=" CB SER J 203 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.33e-02 5.65e+03 3.68e+00 bond pdb=" CA SER G 203 " pdb=" CB SER G 203 " ideal model delta sigma weight residual 1.524 1.498 0.025 1.33e-02 5.65e+03 3.57e+00 bond pdb=" CA SER C 203 " pdb=" CB SER C 203 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.33e-02 5.65e+03 3.56e+00 bond pdb=" CA SER K 203 " pdb=" CB SER K 203 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.33e-02 5.65e+03 3.52e+00 bond pdb=" C SER G 209 " pdb=" N PHE G 210 " ideal model delta sigma weight residual 1.331 1.307 0.024 1.30e-02 5.92e+03 3.42e+00 ... (remaining 22451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 28881 1.97 - 3.94: 1810 3.94 - 5.92: 355 5.92 - 7.89: 76 7.89 - 9.86: 28 Bond angle restraints: 31150 Sorted by residual: angle pdb=" N SER D 203 " pdb=" CA SER D 203 " pdb=" C SER D 203 " ideal model delta sigma weight residual 108.56 118.41 -9.85 1.74e+00 3.30e-01 3.21e+01 angle pdb=" N SER F 203 " pdb=" CA SER F 203 " pdb=" C SER F 203 " ideal model delta sigma weight residual 108.56 118.40 -9.84 1.74e+00 3.30e-01 3.20e+01 angle pdb=" N SER L 203 " pdb=" CA SER L 203 " pdb=" C SER L 203 " ideal model delta sigma weight residual 108.56 118.39 -9.83 1.74e+00 3.30e-01 3.19e+01 angle pdb=" N SER H 203 " pdb=" CA SER H 203 " pdb=" C SER H 203 " ideal model delta sigma weight residual 108.56 118.39 -9.83 1.74e+00 3.30e-01 3.19e+01 angle pdb=" N SER A 203 " pdb=" CA SER A 203 " pdb=" C SER A 203 " ideal model delta sigma weight residual 108.56 118.35 -9.79 1.74e+00 3.30e-01 3.17e+01 ... (remaining 31145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.74: 9907 3.74 - 7.48: 2160 7.48 - 11.22: 589 11.22 - 14.96: 210 14.96 - 18.70: 28 Dihedral angle restraints: 12894 sinusoidal: 0 harmonic: 12894 Sorted by residual: dihedral pdb=" C SER D 203 " pdb=" N SER D 203 " pdb=" CA SER D 203 " pdb=" CB SER D 203 " ideal model delta harmonic sigma weight residual -122.60 -133.37 10.77 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" C SER H 203 " pdb=" N SER H 203 " pdb=" CA SER H 203 " pdb=" CB SER H 203 " ideal model delta harmonic sigma weight residual -122.60 -133.34 10.74 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" C SER J 203 " pdb=" N SER J 203 " pdb=" CA SER J 203 " pdb=" CB SER J 203 " ideal model delta harmonic sigma weight residual -122.60 -133.27 10.67 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 12891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 3696 0.106 - 0.212: 448 0.212 - 0.318: 14 0.318 - 0.424: 0 0.424 - 0.530: 14 Chirality restraints: 4172 Sorted by residual: chirality pdb=" CA SER D 203 " pdb=" N SER D 203 " pdb=" C SER D 203 " pdb=" CB SER D 203 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.02e+00 chirality pdb=" CA SER H 203 " pdb=" N SER H 203 " pdb=" C SER H 203 " pdb=" CB SER H 203 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CA SER F 203 " pdb=" N SER F 203 " pdb=" C SER F 203 " pdb=" CB SER F 203 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.53 2.00e-01 2.50e+01 6.90e+00 ... (remaining 4169 not shown) Planarity restraints: 4550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 201 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C SER A 201 " -0.077 2.00e-02 2.50e+03 pdb=" O SER A 201 " 0.029 2.00e-02 2.50e+03 pdb=" N SER A 202 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 201 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C SER C 201 " -0.077 2.00e-02 2.50e+03 pdb=" O SER C 201 " 0.029 2.00e-02 2.50e+03 pdb=" N SER C 202 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE L 135 " -0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C PHE L 135 " 0.077 2.00e-02 2.50e+03 pdb=" O PHE L 135 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL L 136 " -0.026 2.00e-02 2.50e+03 ... (remaining 4547 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3707 2.77 - 3.30: 20769 3.30 - 3.83: 34554 3.83 - 4.37: 36610 4.37 - 4.90: 61221 Nonbonded interactions: 156861 Sorted by model distance: nonbonded pdb=" O SER E 203 " pdb=" N GLY F 204 " model vdw 2.233 3.120 nonbonded pdb=" O SER L 203 " pdb=" N GLY M 204 " model vdw 2.234 3.120 nonbonded pdb=" N GLY A 204 " pdb=" O SER N 203 " model vdw 2.239 3.120 nonbonded pdb=" O SER G 203 " pdb=" N GLY H 204 " model vdw 2.242 3.120 nonbonded pdb=" O SER I 203 " pdb=" N GLY J 204 " model vdw 2.264 3.120 ... (remaining 156856 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.640 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 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 : 0.005 0.036 22456 Z= 0.376 Angle : 1.167 9.861 31150 Z= 0.742 Chirality : 0.071 0.530 4172 Planarity : 0.007 0.045 4550 Dihedral : 5.955 18.704 4550 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.41 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.12), residues: 4522 helix: 0.88 (0.17), residues: 854 sheet: 1.02 (0.11), residues: 1946 loop : -2.32 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 10 PHE 0.000 0.000 PHE A 20 TRP 0.000 0.000 TRP A 86 Details of bonding type rmsd covalent geometry : bond 0.00515 (22456) covalent geometry : angle 1.16655 (31150) hydrogen bonds : bond 0.18058 ( 2610) hydrogen bonds : angle 10.03608 ( 7620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.859 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1012 time to fit residues: 14.4885 Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 432 optimal weight: 50.0000 chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 50.0000 chunk 424 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.063198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.046850 restraints weight = 193960.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.047981 restraints weight = 159915.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.047986 restraints weight = 132393.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.048144 restraints weight = 128375.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.048210 restraints weight = 126165.443| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22456 Z= 0.325 Angle : 0.780 7.011 31150 Z= 0.484 Chirality : 0.055 0.246 4172 Planarity : 0.005 0.028 4550 Dihedral : 7.575 30.632 4550 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.44 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.10 (0.12), residues: 4522 helix: 1.15 (0.18), residues: 826 sheet: 1.04 (0.10), residues: 2184 loop : -2.12 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 10 PHE 0.000 0.000 PHE A 20 TRP 0.000 0.000 TRP A 86 Details of bonding type rmsd covalent geometry : bond 0.00445 (22456) covalent geometry : angle 0.78007 (31150) hydrogen bonds : bond 0.05664 ( 2610) hydrogen bonds : angle 8.01792 ( 7620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.930 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1016 time to fit residues: 14.5372 Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 424 optimal weight: 50.0000 chunk 211 optimal weight: 30.0000 chunk 23 optimal weight: 50.0000 chunk 204 optimal weight: 30.0000 chunk 30 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 chunk 210 optimal weight: 9.9990 chunk 335 optimal weight: 30.0000 chunk 305 optimal weight: 50.0000 chunk 388 optimal weight: 6.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.055644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.044374 restraints weight = 213289.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.044862 restraints weight = 180977.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.045227 restraints weight = 161773.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.045449 restraints weight = 149099.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.045648 restraints weight = 141382.635| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 22456 Z= 0.274 Angle : 0.663 6.456 31150 Z= 0.415 Chirality : 0.053 0.136 4172 Planarity : 0.004 0.022 4550 Dihedral : 7.143 26.078 4550 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.12), residues: 4522 helix: 1.62 (0.19), residues: 742 sheet: 0.66 (0.10), residues: 2240 loop : -2.27 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 10 PHE 0.000 0.000 PHE A 20 TRP 0.000 0.000 TRP A 86 Details of bonding type rmsd covalent geometry : bond 0.00379 (22456) covalent geometry : angle 0.66271 (31150) hydrogen bonds : bond 0.04569 ( 2610) hydrogen bonds : angle 7.37652 ( 7620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.688 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0976 time to fit residues: 14.0003 Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 144 optimal weight: 50.0000 chunk 313 optimal weight: 30.0000 chunk 141 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 71 optimal weight: 50.0000 chunk 315 optimal weight: 50.0000 chunk 215 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 260 optimal weight: 10.0000 chunk 407 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.054780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.043520 restraints weight = 212295.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.044021 restraints weight = 179033.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.044317 restraints weight = 159380.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.044590 restraints weight = 147935.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.044695 restraints weight = 139784.424| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.7882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 22456 Z= 0.259 Angle : 0.627 7.310 31150 Z= 0.394 Chirality : 0.053 0.143 4172 Planarity : 0.004 0.020 4550 Dihedral : 7.159 27.733 4550 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.12 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.12), residues: 4522 helix: 0.67 (0.19), residues: 924 sheet: 0.96 (0.11), residues: 1904 loop : -3.21 (0.11), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 10 PHE 0.000 0.000 PHE A 20 TRP 0.000 0.000 TRP A 86 Details of bonding type rmsd covalent geometry : bond 0.00358 (22456) covalent geometry : angle 0.62748 (31150) hydrogen bonds : bond 0.04168 ( 2610) hydrogen bonds : angle 7.22705 ( 7620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.842 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1007 time to fit residues: 14.3389 Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 446 optimal weight: 30.0000 chunk 403 optimal weight: 40.0000 chunk 100 optimal weight: 6.9990 chunk 128 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 353 optimal weight: 8.9990 chunk 376 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 117 optimal weight: 40.0000 chunk 279 optimal weight: 9.9990 chunk 379 optimal weight: 50.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.053935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.042941 restraints weight = 211353.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.043446 restraints weight = 178536.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.043797 restraints weight = 158190.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.043958 restraints weight = 145880.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.044190 restraints weight = 139210.322| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.8484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22456 Z= 0.272 Angle : 0.634 7.408 31150 Z= 0.396 Chirality : 0.053 0.139 4172 Planarity : 0.004 0.018 4550 Dihedral : 7.205 27.820 4550 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.13), residues: 4522 helix: 0.94 (0.19), residues: 840 sheet: 0.58 (0.11), residues: 2044 loop : -3.02 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 10 PHE 0.000 0.000 PHE A 20 TRP 0.000 0.000 TRP A 86 Details of bonding type rmsd covalent geometry : bond 0.00381 (22456) covalent geometry : angle 0.63413 (31150) hydrogen bonds : bond 0.04122 ( 2610) hydrogen bonds : angle 7.15675 ( 7620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.861 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1020 time to fit residues: 14.5417 Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 6 optimal weight: 20.0000 chunk 325 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 158 optimal weight: 50.0000 chunk 149 optimal weight: 40.0000 chunk 352 optimal weight: 30.0000 chunk 123 optimal weight: 50.0000 chunk 212 optimal weight: 5.9990 chunk 447 optimal weight: 0.9990 chunk 308 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.052918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.042093 restraints weight = 213521.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.042626 restraints weight = 177694.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.042980 restraints weight = 156941.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.043128 restraints weight = 144220.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.043319 restraints weight = 136488.551| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.9084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22456 Z= 0.274 Angle : 0.643 7.294 31150 Z= 0.400 Chirality : 0.053 0.136 4172 Planarity : 0.004 0.018 4550 Dihedral : 7.298 29.856 4550 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.09 % Favored : 90.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.12), residues: 4522 helix: 0.39 (0.18), residues: 924 sheet: 0.57 (0.12), residues: 1862 loop : -3.33 (0.12), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 10 PHE 0.000 0.000 PHE A 20 TRP 0.000 0.000 TRP A 86 Details of bonding type rmsd covalent geometry : bond 0.00383 (22456) covalent geometry : angle 0.64327 (31150) hydrogen bonds : bond 0.04079 ( 2610) hydrogen bonds : angle 7.19978 ( 7620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.859 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0987 time to fit residues: 14.0250 Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 445 optimal weight: 3.9990 chunk 431 optimal weight: 30.0000 chunk 338 optimal weight: 30.0000 chunk 123 optimal weight: 50.0000 chunk 439 optimal weight: 30.0000 chunk 281 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 250 optimal weight: 40.0000 chunk 196 optimal weight: 40.0000 chunk 365 optimal weight: 20.0000 chunk 237 optimal weight: 6.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.051941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.041512 restraints weight = 217710.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.042054 restraints weight = 181574.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.042390 restraints weight = 157951.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.042655 restraints weight = 144385.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.042802 restraints weight = 135602.966| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.9411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 22456 Z= 0.281 Angle : 0.650 7.458 31150 Z= 0.403 Chirality : 0.053 0.139 4172 Planarity : 0.004 0.018 4550 Dihedral : 7.271 31.257 4550 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -1.53 (0.12), residues: 4522 helix: 0.86 (0.19), residues: 826 sheet: 0.48 (0.12), residues: 1778 loop : -3.55 (0.12), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 10 PHE 0.000 0.000 PHE A 20 TRP 0.000 0.000 TRP A 86 Details of bonding type rmsd covalent geometry : bond 0.00393 (22456) covalent geometry : angle 0.64971 (31150) hydrogen bonds : bond 0.04101 ( 2610) hydrogen bonds : angle 7.17389 ( 7620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.849 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0990 time to fit residues: 14.0896 Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 361 optimal weight: 0.9990 chunk 111 optimal weight: 30.0000 chunk 246 optimal weight: 2.9990 chunk 341 optimal weight: 40.0000 chunk 294 optimal weight: 9.9990 chunk 309 optimal weight: 7.9990 chunk 330 optimal weight: 50.0000 chunk 43 optimal weight: 50.0000 chunk 156 optimal weight: 30.0000 chunk 136 optimal weight: 40.0000 chunk 302 optimal weight: 50.0000 overall best weight: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.051134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.040966 restraints weight = 218878.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.041416 restraints weight = 181095.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.041817 restraints weight = 160409.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.042018 restraints weight = 145396.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.042217 restraints weight = 136748.134| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.9901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 22456 Z= 0.324 Angle : 0.711 7.872 31150 Z= 0.444 Chirality : 0.053 0.138 4172 Planarity : 0.004 0.018 4550 Dihedral : 7.786 34.863 4550 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.86 % Favored : 88.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.09 % 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: -1.76 (0.12), residues: 4522 helix: 0.20 (0.18), residues: 910 sheet: 0.37 (0.12), residues: 1778 loop : -3.64 (0.12), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 10 PHE 0.000 0.000 PHE A 20 TRP 0.000 0.000 TRP A 86 Details of bonding type rmsd covalent geometry : bond 0.00452 (22456) covalent geometry : angle 0.71075 (31150) hydrogen bonds : bond 0.04592 ( 2610) hydrogen bonds : angle 7.56264 ( 7620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.775 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0974 time to fit residues: 13.9777 Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 61 optimal weight: 8.9990 chunk 412 optimal weight: 30.0000 chunk 321 optimal weight: 9.9990 chunk 206 optimal weight: 50.0000 chunk 306 optimal weight: 0.8980 chunk 60 optimal weight: 30.0000 chunk 443 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 415 optimal weight: 0.8980 chunk 32 optimal weight: 30.0000 chunk 417 optimal weight: 6.9990 overall best weight: 5.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.052092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.041546 restraints weight = 217723.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.042153 restraints weight = 175047.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.042593 restraints weight = 149184.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.042855 restraints weight = 133378.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.043095 restraints weight = 124006.793| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.9791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22456 Z= 0.211 Angle : 0.581 6.838 31150 Z= 0.359 Chirality : 0.052 0.142 4172 Planarity : 0.003 0.017 4550 Dihedral : 6.795 30.386 4550 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.05 % 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: -1.38 (0.13), residues: 4522 helix: 2.06 (0.21), residues: 742 sheet: 0.35 (0.13), residues: 1778 loop : -3.50 (0.12), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 10 PHE 0.000 0.000 PHE A 20 TRP 0.000 0.000 TRP A 86 Details of bonding type rmsd covalent geometry : bond 0.00294 (22456) covalent geometry : angle 0.58133 (31150) hydrogen bonds : bond 0.03419 ( 2610) hydrogen bonds : angle 6.62810 ( 7620) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.869 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0983 time to fit residues: 14.0917 Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 41 optimal weight: 9.9990 chunk 300 optimal weight: 50.0000 chunk 269 optimal weight: 10.0000 chunk 223 optimal weight: 3.9990 chunk 170 optimal weight: 40.0000 chunk 445 optimal weight: 20.0000 chunk 240 optimal weight: 50.0000 chunk 174 optimal weight: 50.0000 chunk 38 optimal weight: 30.0000 chunk 230 optimal weight: 30.0000 chunk 214 optimal weight: 20.0000 overall best weight: 12.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.050270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.040309 restraints weight = 222223.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.040818 restraints weight = 182281.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.041180 restraints weight = 159331.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.041404 restraints weight = 144845.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.041481 restraints weight = 135951.972| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 1.0325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22456 Z= 0.380 Angle : 0.769 7.700 31150 Z= 0.483 Chirality : 0.053 0.144 4172 Planarity : 0.004 0.019 4550 Dihedral : 8.055 36.668 4550 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.47 % Favored : 86.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.42 % 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: -1.85 (0.13), residues: 4522 helix: 0.54 (0.19), residues: 826 sheet: 0.15 (0.13), residues: 1778 loop : -3.56 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 10 PHE 0.000 0.000 PHE A 20 TRP 0.000 0.000 TRP A 86 Details of bonding type rmsd covalent geometry : bond 0.00531 (22456) covalent geometry : angle 0.76947 (31150) hydrogen bonds : bond 0.05105 ( 2610) hydrogen bonds : angle 7.82482 ( 7620) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.867 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1006 time to fit residues: 14.4752 Evaluate side-chains 70 residues out of total 3878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 418 optimal weight: 7.9990 chunk 335 optimal weight: 6.9990 chunk 289 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 379 optimal weight: 50.0000 chunk 119 optimal weight: 30.0000 chunk 420 optimal weight: 20.0000 chunk 276 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.051611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.041285 restraints weight = 218261.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.041813 restraints weight = 172501.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.042318 restraints weight = 148085.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.042568 restraints weight = 131404.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.042818 restraints weight = 122172.490| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 1.0193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22456 Z= 0.219 Angle : 0.602 6.968 31150 Z= 0.372 Chirality : 0.053 0.139 4172 Planarity : 0.003 0.017 4550 Dihedral : 6.991 31.169 4550 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.09 % 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: -1.68 (0.13), residues: 4522 helix: 1.28 (0.20), residues: 826 sheet: 0.10 (0.13), residues: 1778 loop : -3.58 (0.12), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 10 PHE 0.000 0.000 PHE A 20 TRP 0.000 0.000 TRP A 86 Details of bonding type rmsd covalent geometry : bond 0.00304 (22456) covalent geometry : angle 0.60234 (31150) hydrogen bonds : bond 0.03539 ( 2610) hydrogen bonds : angle 6.79985 ( 7620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2866.16 seconds wall clock time: 49 minutes 59.04 seconds (2999.04 seconds total)