Starting phenix.real_space_refine on Mon Apr 6 02:45:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y8z_72683/04_2026/9y8z_72683.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y8z_72683/04_2026/9y8z_72683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y8z_72683/04_2026/9y8z_72683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y8z_72683/04_2026/9y8z_72683.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y8z_72683/04_2026/9y8z_72683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y8z_72683/04_2026/9y8z_72683.map" } resolution = 2.5 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 9795 2.51 5 N 2305 2.21 5 O 2670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14860 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2828 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 333} Chain breaks: 1 Chain: "E" Number of atoms: 2828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2828 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 333} Chain breaks: 1 Chain: "A" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 144 Unusual residues: {'CLR': 1, 'NAG': 2, 'PX4': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PX4:plan-1': 4, 'PX4:plan-2': 2} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 144 Unusual residues: {'CLR': 1, 'NAG': 2, 'PX4': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PX4:plan-1': 4, 'PX4:plan-2': 2} Unresolved non-hydrogen planarities: 24 Restraints were copied for chains: B, C, D Time building chain proxies: 2.70, per 1000 atoms: 0.18 Number of scatterers: 14860 At special positions: 0 Unit cell: (93.24, 90.72, 131.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2670 8.00 N 2305 7.00 C 9795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 243 " distance=2.07 Simple disulfide: pdb=" SG CYS B 75 " - pdb=" SG CYS B 75 " distance=0.00 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 172 " distance=0.00 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 186 " distance=0.00 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 243 " distance=2.07 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 232 " distance=0.00 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 243 " distance=2.07 Simple disulfide: pdb=" SG CYS B 243 " - pdb=" SG CYS B 232 " distance=2.07 Simple disulfide: pdb=" SG CYS B 243 " - pdb=" SG CYS B 243 " distance=0.00 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 324 " distance=0.00 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 243 " distance=2.07 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 243 " distance=2.07 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 243 " distance=2.07 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=5, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 72 " " NAG A 502 " - " ASN A 103 " " NAG B 501 " - " ASN B 72 " " NAG B 502 " - " ASN B 103 " " NAG C 501 " - " ASN C 72 " " NAG C 502 " - " ASN C 103 " " NAG D 501 " - " ASN D 72 " " NAG D 502 " - " ASN D 103 " " NAG E 505 " - " ASN E 72 " " NAG E 506 " - " ASN E 103 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 651.7 milliseconds 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3350 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 25 sheets defined 40.1% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 105 through 108 Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.783A pdb=" N LEU A 124 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASP A 125 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 261 through 273 removed outlier: 3.543A pdb=" N TRP A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 282 through 306 removed outlier: 4.111A pdb=" N ALA A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 347 removed outlier: 3.508A pdb=" N TYR A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 443 removed outlier: 3.709A pdb=" N ALA A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'B' and resid 43 through 53 Processing helix chain 'B' and resid 105 through 108 Processing helix chain 'B' and resid 120 through 127 removed outlier: 3.783A pdb=" N LEU B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASP B 125 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 Processing helix chain 'B' and resid 261 through 273 removed outlier: 3.543A pdb=" N TRP B 273 " --> pdb=" O VAL B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 282 through 306 removed outlier: 4.111A pdb=" N ALA B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 347 removed outlier: 3.509A pdb=" N TYR B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 443 removed outlier: 3.709A pdb=" N ALA B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'C' and resid 43 through 53 Processing helix chain 'C' and resid 105 through 108 Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.784A pdb=" N LEU C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASP C 125 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 261 Processing helix chain 'C' and resid 261 through 273 removed outlier: 3.543A pdb=" N TRP C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 278 Processing helix chain 'C' and resid 282 through 306 removed outlier: 4.111A pdb=" N ALA C 306 " --> pdb=" O SER C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 347 removed outlier: 3.508A pdb=" N TYR C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 443 removed outlier: 3.710A pdb=" N ALA C 424 " --> pdb=" O THR C 420 " (cutoff:3.500A) Proline residue: C 427 - end of helix Processing helix chain 'D' and resid 43 through 53 Processing helix chain 'D' and resid 105 through 108 Processing helix chain 'D' and resid 120 through 127 removed outlier: 3.783A pdb=" N LEU D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASP D 125 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 261 Processing helix chain 'D' and resid 261 through 273 removed outlier: 3.544A pdb=" N TRP D 273 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 Processing helix chain 'D' and resid 282 through 306 removed outlier: 4.111A pdb=" N ALA D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 347 removed outlier: 3.508A pdb=" N TYR D 335 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS D 345 " --> pdb=" O VAL D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 443 removed outlier: 3.708A pdb=" N ALA D 424 " --> pdb=" O THR D 420 " (cutoff:3.500A) Proline residue: D 427 - end of helix Processing helix chain 'E' and resid 43 through 53 Processing helix chain 'E' and resid 105 through 108 Processing helix chain 'E' and resid 120 through 127 removed outlier: 3.783A pdb=" N LEU E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASP E 125 " --> pdb=" O SER E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 261 Processing helix chain 'E' and resid 261 through 273 removed outlier: 3.543A pdb=" N TRP E 273 " --> pdb=" O VAL E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 278 Processing helix chain 'E' and resid 282 through 306 removed outlier: 4.111A pdb=" N ALA E 306 " --> pdb=" O SER E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 347 removed outlier: 3.508A pdb=" N TYR E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS E 345 " --> pdb=" O VAL E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 443 removed outlier: 3.709A pdb=" N ALA E 424 " --> pdb=" O THR E 420 " (cutoff:3.500A) Proline residue: E 427 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 119 removed outlier: 4.674A pdb=" N LEU A 152 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 141 removed outlier: 6.674A pdb=" N THR A 169 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA A 140 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A 167 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA5, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 119 removed outlier: 4.674A pdb=" N LEU B 152 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 137 through 141 removed outlier: 6.673A pdb=" N THR B 169 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA B 140 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR B 167 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 132 through 134 Processing sheet with id=AA9, first strand: chain 'B' and resid 132 through 134 Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AB2, first strand: chain 'C' and resid 116 through 119 removed outlier: 4.675A pdb=" N LEU C 152 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 137 through 141 removed outlier: 6.675A pdb=" N THR C 169 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA C 140 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR C 167 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 132 through 134 Processing sheet with id=AB5, first strand: chain 'C' and resid 132 through 134 Processing sheet with id=AB6, first strand: chain 'C' and resid 234 through 235 Processing sheet with id=AB7, first strand: chain 'D' and resid 116 through 119 removed outlier: 4.674A pdb=" N LEU D 152 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 137 through 141 removed outlier: 6.674A pdb=" N THR D 169 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA D 140 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR D 167 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 132 through 134 Processing sheet with id=AC1, first strand: chain 'D' and resid 132 through 134 Processing sheet with id=AC2, first strand: chain 'D' and resid 234 through 235 Processing sheet with id=AC3, first strand: chain 'E' and resid 116 through 119 removed outlier: 4.674A pdb=" N LEU E 152 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS E 159 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 137 through 141 removed outlier: 6.674A pdb=" N THR E 169 " --> pdb=" O LYS E 138 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA E 140 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR E 167 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 132 through 134 Processing sheet with id=AC6, first strand: chain 'E' and resid 132 through 134 Processing sheet with id=AC7, first strand: chain 'E' and resid 234 through 235 890 hydrogen bonds defined for protein. 2550 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2275 1.31 - 1.44: 4156 1.44 - 1.57: 8545 1.57 - 1.70: 74 1.70 - 1.83: 150 Bond restraints: 15200 Sorted by residual: bond pdb=" C23 PX4 E 507 " pdb=" O7 PX4 E 507 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C23 PX4 C 503 " pdb=" O7 PX4 C 503 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C23 PX4 A 503 " pdb=" O7 PX4 A 503 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C23 PX4 C 504 " pdb=" O7 PX4 C 504 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C23 PX4 D 503 " pdb=" O7 PX4 D 503 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.93e+01 ... (remaining 15195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 19297 1.74 - 3.48: 913 3.48 - 5.22: 254 5.22 - 6.96: 31 6.96 - 8.70: 15 Bond angle restraints: 20510 Sorted by residual: angle pdb=" CA ASP C 144 " pdb=" CB ASP C 144 " pdb=" CG ASP C 144 " ideal model delta sigma weight residual 112.60 116.07 -3.47 1.00e+00 1.00e+00 1.21e+01 angle pdb=" CA ASP A 144 " pdb=" CB ASP A 144 " pdb=" CG ASP A 144 " ideal model delta sigma weight residual 112.60 116.05 -3.45 1.00e+00 1.00e+00 1.19e+01 angle pdb=" CA ASP B 144 " pdb=" CB ASP B 144 " pdb=" CG ASP B 144 " ideal model delta sigma weight residual 112.60 116.04 -3.44 1.00e+00 1.00e+00 1.18e+01 angle pdb=" CA ASP D 144 " pdb=" CB ASP D 144 " pdb=" CG ASP D 144 " ideal model delta sigma weight residual 112.60 116.03 -3.43 1.00e+00 1.00e+00 1.18e+01 angle pdb=" CA ASP E 144 " pdb=" CB ASP E 144 " pdb=" CG ASP E 144 " ideal model delta sigma weight residual 112.60 116.02 -3.42 1.00e+00 1.00e+00 1.17e+01 ... (remaining 20505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.43: 7963 12.43 - 24.85: 1026 24.85 - 37.28: 272 37.28 - 49.71: 165 49.71 - 62.14: 75 Dihedral angle restraints: 9501 sinusoidal: 4341 harmonic: 5160 Sorted by residual: dihedral pdb=" CB CYS B 172 " pdb=" SG CYS B 172 " pdb=" SG CYS B 172 " pdb=" CB CYS B 172 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS B 186 " pdb=" SG CYS B 186 " pdb=" SG CYS B 186 " pdb=" CB CYS B 186 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CA ARG B 252 " pdb=" CB ARG B 252 " pdb=" CG ARG B 252 " pdb=" CD ARG B 252 " ideal model delta sinusoidal sigma weight residual 60.00 117.80 -57.80 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 9498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1591 0.043 - 0.085: 438 0.085 - 0.128: 207 0.128 - 0.171: 44 0.171 - 0.213: 30 Chirality restraints: 2310 Sorted by residual: chirality pdb=" CA ILE C 201 " pdb=" N ILE C 201 " pdb=" C ILE C 201 " pdb=" CB ILE C 201 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ILE B 201 " pdb=" N ILE B 201 " pdb=" C ILE B 201 " pdb=" CB ILE B 201 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE E 201 " pdb=" N ILE E 201 " pdb=" C ILE E 201 " pdb=" CB ILE E 201 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 2307 not shown) Planarity restraints: 2505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 72 " -0.084 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN C 72 " 0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN C 72 " -0.177 2.00e-02 2.50e+03 pdb=" ND2 ASN C 72 " 0.519 2.00e-02 2.50e+03 pdb=" C1 NAG C 501 " -0.342 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 72 " -0.084 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN A 72 " 0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN A 72 " -0.177 2.00e-02 2.50e+03 pdb=" ND2 ASN A 72 " 0.519 2.00e-02 2.50e+03 pdb=" C1 NAG A 501 " -0.342 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 72 " -0.084 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN B 72 " 0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN B 72 " -0.177 2.00e-02 2.50e+03 pdb=" ND2 ASN B 72 " 0.519 2.00e-02 2.50e+03 pdb=" C1 NAG B 501 " -0.342 2.00e-02 2.50e+03 ... (remaining 2502 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 108 2.61 - 3.18: 11718 3.18 - 3.75: 21949 3.75 - 4.33: 32499 4.33 - 4.90: 54142 Nonbonded interactions: 120416 Sorted by model distance: nonbonded pdb=" SG CYS E 172 " pdb=" SG CYS E 186 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS E 232 " pdb=" SG CYS E 243 " model vdw 2.067 3.760 nonbonded pdb=" ND2 ASN C 279 " pdb=" OD1 ASP C 281 " model vdw 2.268 3.120 nonbonded pdb=" O LEU D 42 " pdb=" OH TYR D 112 " model vdw 2.268 3.040 nonbonded pdb=" ND2 ASN D 279 " pdb=" OD1 ASP D 281 " model vdw 2.268 3.120 ... (remaining 120411 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 449 or resid 503 or resid 508)) selection = (chain 'B' and (resid 41 through 449 or resid 503 or resid 508)) selection = (chain 'C' and (resid 41 through 449 or resid 503 or resid 508)) selection = (chain 'D' and (resid 41 through 449 or resid 503 or resid 508)) selection = (chain 'E' and (resid 41 through 449 or resid 503 or resid 508)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.950 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 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 : 0.011 0.396 15223 Z= 0.840 Angle : 0.914 8.698 20562 Z= 0.532 Chirality : 0.053 0.213 2310 Planarity : 0.011 0.175 2495 Dihedral : 14.057 62.137 6115 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: -0.41 (0.19), residues: 1725 helix: 0.13 (0.19), residues: 580 sheet: -0.26 (0.27), residues: 375 loop : -0.44 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 414 TYR 0.012 0.001 TYR B 335 PHE 0.008 0.001 PHE C 133 TRP 0.011 0.001 TRP B 102 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00821 (15200) covalent geometry : angle 0.90269 (20510) SS BOND : bond 0.02570 ( 8) SS BOND : angle 3.09567 ( 22) hydrogen bonds : bond 0.22943 ( 745) hydrogen bonds : angle 7.98685 ( 2550) Misc. bond : bond 0.37795 ( 5) link_NAG-ASN : bond 0.00743 ( 10) link_NAG-ASN : angle 2.91814 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 321 MET cc_start: 0.8595 (mmt) cc_final: 0.8371 (mmt) REVERT: D 118 ASP cc_start: 0.8492 (m-30) cc_final: 0.7876 (m-30) REVERT: D 153 ARG cc_start: 0.7359 (mtt90) cc_final: 0.7140 (mtt-85) REVERT: D 414 ARG cc_start: 0.7719 (ttm110) cc_final: 0.7458 (ttp-110) REVERT: E 118 ASP cc_start: 0.8509 (m-30) cc_final: 0.7590 (m-30) REVERT: E 414 ARG cc_start: 0.7749 (ttm110) cc_final: 0.7534 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.7961 time to fit residues: 139.4257 Evaluate side-chains 123 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 260 GLN A 345 HIS B 345 HIS C 260 GLN C 345 HIS D 345 HIS E 101 GLN E 345 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.070585 restraints weight = 22445.707| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.71 r_work: 0.2626 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15223 Z= 0.150 Angle : 0.673 18.096 20562 Z= 0.326 Chirality : 0.045 0.248 2310 Planarity : 0.004 0.064 2495 Dihedral : 9.183 58.916 2745 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.46 % Allowed : 10.16 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 0.81 (0.20), residues: 1725 helix: 1.95 (0.20), residues: 580 sheet: 0.12 (0.27), residues: 375 loop : -0.28 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 153 TYR 0.018 0.001 TYR A 335 PHE 0.012 0.001 PHE D 47 TRP 0.008 0.001 TRP E 102 HIS 0.002 0.000 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00329 (15200) covalent geometry : angle 0.57934 (20510) SS BOND : bond 0.00357 ( 8) SS BOND : angle 1.49994 ( 22) hydrogen bonds : bond 0.05712 ( 745) hydrogen bonds : angle 4.98741 ( 2550) Misc. bond : bond 0.00009 ( 5) link_NAG-ASN : bond 0.00497 ( 10) link_NAG-ASN : angle 8.89238 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8353 (mtm) cc_final: 0.8099 (ptp) REVERT: B 254 MET cc_start: 0.8893 (ttp) cc_final: 0.8642 (ttp) REVERT: B 414 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7437 (ttm110) REVERT: C 279 ASN cc_start: 0.8465 (t0) cc_final: 0.8226 (t0) REVERT: D 279 ASN cc_start: 0.8525 (t0) cc_final: 0.8167 (t0) REVERT: E 226 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7559 (pp20) REVERT: E 344 GLN cc_start: 0.8307 (pp30) cc_final: 0.7677 (pp30) outliers start: 23 outliers final: 6 residues processed: 150 average time/residue: 0.6992 time to fit residues: 113.8676 Evaluate side-chains 136 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain E residue 226 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 125 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN C 260 GLN E 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.097880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.069092 restraints weight = 22858.176| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.71 r_work: 0.2598 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15223 Z= 0.185 Angle : 0.595 10.239 20562 Z= 0.300 Chirality : 0.045 0.244 2310 Planarity : 0.004 0.033 2495 Dihedral : 8.954 56.138 2745 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.10 % Allowed : 10.98 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.21 (0.20), residues: 1725 helix: 2.15 (0.20), residues: 585 sheet: 0.65 (0.28), residues: 355 loop : -0.11 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 414 TYR 0.022 0.001 TYR A 335 PHE 0.012 0.002 PHE C 133 TRP 0.011 0.001 TRP E 102 HIS 0.002 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00431 (15200) covalent geometry : angle 0.56247 (20510) SS BOND : bond 0.00422 ( 8) SS BOND : angle 1.34805 ( 22) hydrogen bonds : bond 0.05019 ( 745) hydrogen bonds : angle 4.60307 ( 2550) Misc. bond : bond 0.00040 ( 5) link_NAG-ASN : bond 0.00385 ( 10) link_NAG-ASN : angle 4.97057 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8282 (mtm) cc_final: 0.8038 (ptp) REVERT: B 254 MET cc_start: 0.8875 (ttp) cc_final: 0.8571 (ttp) REVERT: C 153 ARG cc_start: 0.8109 (mtt-85) cc_final: 0.7754 (mtt-85) REVERT: C 279 ASN cc_start: 0.8410 (t0) cc_final: 0.8158 (t0) REVERT: C 344 GLN cc_start: 0.8334 (pp30) cc_final: 0.7651 (pp30) REVERT: D 279 ASN cc_start: 0.8581 (t0) cc_final: 0.8187 (t0) REVERT: D 344 GLN cc_start: 0.8345 (pp30) cc_final: 0.7659 (pp30) REVERT: E 47 PHE cc_start: 0.8084 (t80) cc_final: 0.7828 (t80) REVERT: E 226 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7490 (pp20) REVERT: E 344 GLN cc_start: 0.8406 (pp30) cc_final: 0.7685 (pp30) outliers start: 33 outliers final: 9 residues processed: 163 average time/residue: 0.6446 time to fit residues: 114.6926 Evaluate side-chains 149 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 416 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.0050 chunk 91 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN C 101 GLN C 260 GLN D 260 GLN E 260 GLN E 279 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.099435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.070264 restraints weight = 22608.311| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.74 r_work: 0.2626 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15223 Z= 0.126 Angle : 0.548 9.448 20562 Z= 0.276 Chirality : 0.043 0.242 2310 Planarity : 0.003 0.027 2495 Dihedral : 8.629 59.647 2745 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.40 % Allowed : 12.51 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.32 (0.20), residues: 1725 helix: 2.33 (0.21), residues: 585 sheet: 0.79 (0.28), residues: 355 loop : -0.17 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 414 TYR 0.020 0.001 TYR A 335 PHE 0.011 0.001 PHE A 329 TRP 0.010 0.001 TRP A 102 HIS 0.001 0.000 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00282 (15200) covalent geometry : angle 0.51900 (20510) SS BOND : bond 0.00385 ( 8) SS BOND : angle 1.01855 ( 22) hydrogen bonds : bond 0.04380 ( 745) hydrogen bonds : angle 4.30580 ( 2550) Misc. bond : bond 0.00026 ( 5) link_NAG-ASN : bond 0.00284 ( 10) link_NAG-ASN : angle 4.61361 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8260 (mtm) cc_final: 0.8041 (ptp) REVERT: A 153 ARG cc_start: 0.8025 (mtt-85) cc_final: 0.7605 (mtt-85) REVERT: A 207 ASP cc_start: 0.8012 (p0) cc_final: 0.7701 (p0) REVERT: B 254 MET cc_start: 0.8881 (ttm) cc_final: 0.8559 (ttp) REVERT: C 153 ARG cc_start: 0.8083 (mtt-85) cc_final: 0.7874 (mtt-85) REVERT: C 279 ASN cc_start: 0.8399 (t0) cc_final: 0.8139 (t0) REVERT: C 344 GLN cc_start: 0.8269 (pp30) cc_final: 0.7577 (pp30) REVERT: D 153 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7618 (mtt-85) REVERT: D 279 ASN cc_start: 0.8551 (t0) cc_final: 0.8136 (t0) REVERT: D 344 GLN cc_start: 0.8353 (pp30) cc_final: 0.7657 (pp30) REVERT: E 47 PHE cc_start: 0.8147 (t80) cc_final: 0.7818 (t80) REVERT: E 226 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7420 (pp20) REVERT: E 344 GLN cc_start: 0.8413 (pp30) cc_final: 0.7706 (pp30) outliers start: 22 outliers final: 8 residues processed: 152 average time/residue: 0.7046 time to fit residues: 116.2504 Evaluate side-chains 150 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 226 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 19 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN C 260 GLN E 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.098628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.069483 restraints weight = 22532.107| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.71 r_work: 0.2613 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15223 Z= 0.154 Angle : 0.554 9.534 20562 Z= 0.279 Chirality : 0.044 0.248 2310 Planarity : 0.003 0.028 2495 Dihedral : 8.515 58.126 2745 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.21 % Allowed : 13.59 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.34 (0.20), residues: 1725 helix: 2.36 (0.21), residues: 585 sheet: 0.86 (0.28), residues: 355 loop : -0.19 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.021 0.001 TYR A 335 PHE 0.012 0.001 PHE D 133 TRP 0.010 0.001 TRP D 102 HIS 0.001 0.000 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00358 (15200) covalent geometry : angle 0.52844 (20510) SS BOND : bond 0.00441 ( 8) SS BOND : angle 1.06048 ( 22) hydrogen bonds : bond 0.04468 ( 745) hydrogen bonds : angle 4.27571 ( 2550) Misc. bond : bond 0.00033 ( 5) link_NAG-ASN : bond 0.00365 ( 10) link_NAG-ASN : angle 4.27271 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ARG cc_start: 0.8038 (mtt-85) cc_final: 0.7729 (mtt-85) REVERT: A 207 ASP cc_start: 0.8132 (p0) cc_final: 0.7826 (p0) REVERT: B 153 ARG cc_start: 0.8060 (mtt-85) cc_final: 0.7646 (mtt-85) REVERT: B 254 MET cc_start: 0.8871 (ttm) cc_final: 0.8531 (ttp) REVERT: B 344 GLN cc_start: 0.8417 (pp30) cc_final: 0.7690 (pp30) REVERT: C 153 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.7584 (mtt-85) REVERT: C 279 ASN cc_start: 0.8383 (t0) cc_final: 0.8116 (t0) REVERT: C 344 GLN cc_start: 0.8290 (pp30) cc_final: 0.7567 (pp30) REVERT: D 153 ARG cc_start: 0.8099 (mtt90) cc_final: 0.7663 (mtt-85) REVERT: D 225 GLU cc_start: 0.8066 (mp0) cc_final: 0.7857 (mp0) REVERT: D 279 ASN cc_start: 0.8534 (t0) cc_final: 0.8070 (t0) REVERT: D 344 GLN cc_start: 0.8370 (pp30) cc_final: 0.7659 (pp30) REVERT: E 225 GLU cc_start: 0.8264 (mp0) cc_final: 0.8055 (pm20) REVERT: E 344 GLN cc_start: 0.8422 (pp30) cc_final: 0.7688 (pp30) outliers start: 19 outliers final: 10 residues processed: 155 average time/residue: 0.7008 time to fit residues: 117.6992 Evaluate side-chains 151 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 166 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 157 optimal weight: 0.5980 chunk 89 optimal weight: 0.0020 chunk 11 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN C 260 GLN D 260 GLN E 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.100706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.071997 restraints weight = 22621.871| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.71 r_work: 0.2672 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15223 Z= 0.098 Angle : 0.517 9.483 20562 Z= 0.259 Chirality : 0.042 0.240 2310 Planarity : 0.003 0.026 2495 Dihedral : 8.059 59.189 2745 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.21 % Allowed : 13.84 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.49 (0.20), residues: 1725 helix: 2.54 (0.20), residues: 585 sheet: 0.95 (0.28), residues: 355 loop : -0.17 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.019 0.001 TYR A 335 PHE 0.012 0.001 PHE A 329 TRP 0.010 0.001 TRP E 102 HIS 0.001 0.000 HIS E 446 Details of bonding type rmsd covalent geometry : bond 0.00203 (15200) covalent geometry : angle 0.49442 (20510) SS BOND : bond 0.00344 ( 8) SS BOND : angle 0.87928 ( 22) hydrogen bonds : bond 0.03862 ( 745) hydrogen bonds : angle 3.97525 ( 2550) Misc. bond : bond 0.00009 ( 5) link_NAG-ASN : bond 0.00517 ( 10) link_NAG-ASN : angle 3.90768 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ARG cc_start: 0.7855 (mtt-85) cc_final: 0.7431 (mtt-85) REVERT: A 207 ASP cc_start: 0.8116 (p0) cc_final: 0.7808 (p0) REVERT: A 304 SER cc_start: 0.9092 (p) cc_final: 0.8873 (m) REVERT: B 153 ARG cc_start: 0.7815 (mtt-85) cc_final: 0.7435 (mtt-85) REVERT: B 344 GLN cc_start: 0.8533 (pp30) cc_final: 0.7741 (pp30) REVERT: C 153 ARG cc_start: 0.7829 (mtt-85) cc_final: 0.7442 (mtt-85) REVERT: C 279 ASN cc_start: 0.8376 (t0) cc_final: 0.8149 (t0) REVERT: C 344 GLN cc_start: 0.8399 (pp30) cc_final: 0.7608 (pp30) REVERT: D 153 ARG cc_start: 0.7871 (mtt90) cc_final: 0.7467 (mtt-85) REVERT: D 279 ASN cc_start: 0.8513 (t0) cc_final: 0.8073 (t0) REVERT: D 304 SER cc_start: 0.9044 (p) cc_final: 0.8728 (m) REVERT: D 344 GLN cc_start: 0.8505 (pp30) cc_final: 0.7747 (pp30) REVERT: E 344 GLN cc_start: 0.8499 (pp30) cc_final: 0.7724 (pp30) outliers start: 19 outliers final: 7 residues processed: 157 average time/residue: 0.6614 time to fit residues: 112.7843 Evaluate side-chains 148 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 15 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN C 260 GLN D 260 GLN E 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.098923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.070094 restraints weight = 22615.624| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.69 r_work: 0.2634 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15223 Z= 0.147 Angle : 0.541 9.565 20562 Z= 0.273 Chirality : 0.043 0.248 2310 Planarity : 0.003 0.027 2495 Dihedral : 8.052 59.988 2745 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.46 % Allowed : 13.78 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.54 (0.20), residues: 1725 helix: 2.53 (0.21), residues: 585 sheet: 1.00 (0.29), residues: 355 loop : -0.11 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 414 TYR 0.020 0.001 TYR A 335 PHE 0.012 0.001 PHE D 133 TRP 0.010 0.001 TRP D 102 HIS 0.001 0.000 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00340 (15200) covalent geometry : angle 0.51967 (20510) SS BOND : bond 0.00425 ( 8) SS BOND : angle 1.01601 ( 22) hydrogen bonds : bond 0.04231 ( 745) hydrogen bonds : angle 4.10680 ( 2550) Misc. bond : bond 0.00037 ( 5) link_NAG-ASN : bond 0.00383 ( 10) link_NAG-ASN : angle 3.91295 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.7798 (mtt-85) REVERT: A 174 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8103 (mmm) REVERT: A 207 ASP cc_start: 0.8193 (p0) cc_final: 0.7877 (p0) REVERT: A 304 SER cc_start: 0.9079 (p) cc_final: 0.8859 (m) REVERT: A 344 GLN cc_start: 0.8413 (pp30) cc_final: 0.7695 (pp30) REVERT: B 153 ARG cc_start: 0.8079 (mtt-85) cc_final: 0.7599 (mtt-85) REVERT: B 344 GLN cc_start: 0.8497 (pp30) cc_final: 0.7712 (pp30) REVERT: C 153 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7875 (mtt-85) REVERT: C 279 ASN cc_start: 0.8435 (t0) cc_final: 0.8203 (t0) REVERT: C 344 GLN cc_start: 0.8300 (pp30) cc_final: 0.7534 (pp30) REVERT: D 153 ARG cc_start: 0.8154 (mtt90) cc_final: 0.7706 (mtt-85) REVERT: D 174 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.9147 (mtt) REVERT: D 225 GLU cc_start: 0.8085 (mp0) cc_final: 0.7824 (mp0) REVERT: D 279 ASN cc_start: 0.8576 (t0) cc_final: 0.8070 (t0) REVERT: D 304 SER cc_start: 0.9004 (p) cc_final: 0.8699 (m) REVERT: D 344 GLN cc_start: 0.8363 (pp30) cc_final: 0.7617 (pp30) REVERT: E 344 GLN cc_start: 0.8376 (pp30) cc_final: 0.7607 (pp30) outliers start: 23 outliers final: 15 residues processed: 155 average time/residue: 0.6935 time to fit residues: 116.7763 Evaluate side-chains 158 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 80 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN C 260 GLN D 101 GLN D 260 GLN E 260 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.100155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.071379 restraints weight = 22691.140| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.70 r_work: 0.2660 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15223 Z= 0.110 Angle : 0.523 9.522 20562 Z= 0.262 Chirality : 0.042 0.243 2310 Planarity : 0.003 0.026 2495 Dihedral : 7.748 55.372 2745 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.65 % Allowed : 14.03 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.63 (0.20), residues: 1725 helix: 2.62 (0.21), residues: 585 sheet: 1.14 (0.29), residues: 350 loop : -0.10 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 153 TYR 0.019 0.001 TYR A 335 PHE 0.011 0.001 PHE A 329 TRP 0.010 0.001 TRP E 102 HIS 0.001 0.000 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00243 (15200) covalent geometry : angle 0.50206 (20510) SS BOND : bond 0.00361 ( 8) SS BOND : angle 0.89485 ( 22) hydrogen bonds : bond 0.03897 ( 745) hydrogen bonds : angle 3.96477 ( 2550) Misc. bond : bond 0.00019 ( 5) link_NAG-ASN : bond 0.00477 ( 10) link_NAG-ASN : angle 3.78727 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ARG cc_start: 0.8109 (mtt-85) cc_final: 0.7790 (mtt-85) REVERT: A 207 ASP cc_start: 0.8145 (p0) cc_final: 0.7839 (p0) REVERT: A 344 GLN cc_start: 0.8399 (pp30) cc_final: 0.7655 (pp30) REVERT: B 153 ARG cc_start: 0.8062 (mtt-85) cc_final: 0.7658 (mtt-85) REVERT: B 344 GLN cc_start: 0.8494 (pp30) cc_final: 0.7712 (pp30) REVERT: C 153 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.7595 (mtt-85) REVERT: C 279 ASN cc_start: 0.8415 (t0) cc_final: 0.8171 (t0) REVERT: C 344 GLN cc_start: 0.8311 (pp30) cc_final: 0.7553 (pp30) REVERT: D 52 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8132 (ptm) REVERT: D 153 ARG cc_start: 0.8155 (mtt90) cc_final: 0.7709 (mtt-85) REVERT: D 174 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.9137 (mtt) REVERT: D 279 ASN cc_start: 0.8559 (t0) cc_final: 0.8078 (t0) REVERT: D 304 SER cc_start: 0.8990 (p) cc_final: 0.8690 (m) REVERT: D 344 GLN cc_start: 0.8359 (pp30) cc_final: 0.7602 (pp30) REVERT: E 344 GLN cc_start: 0.8358 (pp30) cc_final: 0.7575 (pp30) outliers start: 26 outliers final: 18 residues processed: 156 average time/residue: 0.7014 time to fit residues: 118.7473 Evaluate side-chains 163 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN C 260 GLN D 260 GLN E 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.099677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.070807 restraints weight = 22710.755| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.71 r_work: 0.2650 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15223 Z= 0.123 Angle : 0.529 9.557 20562 Z= 0.266 Chirality : 0.043 0.244 2310 Planarity : 0.003 0.027 2495 Dihedral : 7.634 55.033 2745 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.40 % Allowed : 14.48 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.63 (0.20), residues: 1725 helix: 2.60 (0.21), residues: 585 sheet: 1.16 (0.29), residues: 350 loop : -0.10 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 343 TYR 0.020 0.001 TYR C 335 PHE 0.011 0.001 PHE D 133 TRP 0.010 0.001 TRP D 102 HIS 0.001 0.000 HIS B 345 Details of bonding type rmsd covalent geometry : bond 0.00279 (15200) covalent geometry : angle 0.50860 (20510) SS BOND : bond 0.00393 ( 8) SS BOND : angle 0.95171 ( 22) hydrogen bonds : bond 0.03993 ( 745) hydrogen bonds : angle 3.99609 ( 2550) Misc. bond : bond 0.00027 ( 5) link_NAG-ASN : bond 0.00428 ( 10) link_NAG-ASN : angle 3.74085 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ARG cc_start: 0.8118 (mtt-85) cc_final: 0.7805 (mtt-85) REVERT: A 207 ASP cc_start: 0.8155 (p0) cc_final: 0.7847 (p0) REVERT: A 344 GLN cc_start: 0.8396 (pp30) cc_final: 0.7658 (pp30) REVERT: B 153 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7647 (mtt-85) REVERT: B 225 GLU cc_start: 0.8287 (mp0) cc_final: 0.8035 (mp0) REVERT: B 344 GLN cc_start: 0.8471 (pp30) cc_final: 0.7685 (pp30) REVERT: C 153 ARG cc_start: 0.8090 (mtt-85) cc_final: 0.7864 (mtt-85) REVERT: C 279 ASN cc_start: 0.8439 (t0) cc_final: 0.8196 (t0) REVERT: C 344 GLN cc_start: 0.8310 (pp30) cc_final: 0.7552 (pp30) REVERT: D 52 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8097 (ptm) REVERT: D 153 ARG cc_start: 0.8166 (mtt90) cc_final: 0.7711 (mtt-85) REVERT: D 225 GLU cc_start: 0.8094 (mp0) cc_final: 0.7863 (mp0) REVERT: D 279 ASN cc_start: 0.8567 (t0) cc_final: 0.8058 (t0) REVERT: D 304 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8695 (m) REVERT: D 344 GLN cc_start: 0.8376 (pp30) cc_final: 0.7625 (pp30) REVERT: E 344 GLN cc_start: 0.8351 (pp30) cc_final: 0.7561 (pp30) outliers start: 22 outliers final: 18 residues processed: 153 average time/residue: 0.6678 time to fit residues: 111.2167 Evaluate side-chains 162 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 304 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 45 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 16 optimal weight: 0.0980 chunk 115 optimal weight: 0.0040 chunk 34 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN C 260 GLN D 260 GLN E 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.100932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.072335 restraints weight = 22651.222| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.70 r_work: 0.2677 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15223 Z= 0.098 Angle : 0.513 9.523 20562 Z= 0.257 Chirality : 0.042 0.239 2310 Planarity : 0.003 0.026 2495 Dihedral : 7.332 55.383 2745 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.14 % Allowed : 14.86 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.69 (0.20), residues: 1725 helix: 2.67 (0.21), residues: 585 sheet: 1.20 (0.29), residues: 350 loop : -0.08 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 153 TYR 0.018 0.001 TYR C 335 PHE 0.012 0.001 PHE A 329 TRP 0.010 0.001 TRP E 102 HIS 0.003 0.000 HIS C 446 Details of bonding type rmsd covalent geometry : bond 0.00211 (15200) covalent geometry : angle 0.49407 (20510) SS BOND : bond 0.00319 ( 8) SS BOND : angle 0.86766 ( 22) hydrogen bonds : bond 0.03694 ( 745) hydrogen bonds : angle 3.86678 ( 2550) Misc. bond : bond 0.00014 ( 5) link_NAG-ASN : bond 0.00518 ( 10) link_NAG-ASN : angle 3.57834 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3450 Ramachandran restraints generated. 1725 Oldfield, 0 Emsley, 1725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7753 (mtt-85) REVERT: A 207 ASP cc_start: 0.8098 (p0) cc_final: 0.7809 (p0) REVERT: A 344 GLN cc_start: 0.8372 (pp30) cc_final: 0.7653 (pp30) REVERT: B 153 ARG cc_start: 0.8033 (mtt-85) cc_final: 0.7630 (mtt-85) REVERT: B 344 GLN cc_start: 0.8468 (pp30) cc_final: 0.7694 (pp30) REVERT: C 153 ARG cc_start: 0.8063 (mtt-85) cc_final: 0.7564 (mtt-85) REVERT: C 279 ASN cc_start: 0.8427 (t0) cc_final: 0.8175 (t0) REVERT: C 344 GLN cc_start: 0.8320 (pp30) cc_final: 0.7557 (pp30) REVERT: D 153 ARG cc_start: 0.8130 (mtt90) cc_final: 0.7677 (mtt-85) REVERT: D 225 GLU cc_start: 0.8070 (mp0) cc_final: 0.7834 (mp0) REVERT: D 279 ASN cc_start: 0.8562 (t0) cc_final: 0.8056 (t0) REVERT: D 304 SER cc_start: 0.8923 (p) cc_final: 0.8659 (m) REVERT: D 344 GLN cc_start: 0.8387 (pp30) cc_final: 0.7642 (pp30) REVERT: E 344 GLN cc_start: 0.8354 (pp30) cc_final: 0.7572 (pp30) outliers start: 18 outliers final: 13 residues processed: 154 average time/residue: 0.6941 time to fit residues: 116.2029 Evaluate side-chains 154 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 112 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 81 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN C 260 GLN E 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.072460 restraints weight = 22624.132| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.69 r_work: 0.2680 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15223 Z= 0.103 Angle : 0.514 9.557 20562 Z= 0.257 Chirality : 0.042 0.241 2310 Planarity : 0.003 0.027 2495 Dihedral : 7.196 55.182 2745 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.95 % Allowed : 15.17 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 are not related in a simple way. whole: 1.74 (0.20), residues: 1725 helix: 2.72 (0.21), residues: 590 sheet: 1.21 (0.29), residues: 350 loop : -0.08 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 343 TYR 0.019 0.001 TYR C 335 PHE 0.011 0.001 PHE A 329 TRP 0.010 0.001 TRP E 102 HIS 0.001 0.000 HIS B 345 Details of bonding type rmsd covalent geometry : bond 0.00225 (15200) covalent geometry : angle 0.49585 (20510) SS BOND : bond 0.00346 ( 8) SS BOND : angle 0.89709 ( 22) hydrogen bonds : bond 0.03713 ( 745) hydrogen bonds : angle 3.86540 ( 2550) Misc. bond : bond 0.00018 ( 5) link_NAG-ASN : bond 0.00477 ( 10) link_NAG-ASN : angle 3.50368 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4704.71 seconds wall clock time: 80 minutes 48.95 seconds (4848.95 seconds total)