Starting phenix.real_space_refine on Sun Oct 25 01:21:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y8z_72683/10_2026/9y8z_72683.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y8z_72683/10_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9y8z_72683/10_2026/9y8z_72683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y8z_72683/10_2026/9y8z_72683.map" model { file = "/net/cci-nas-00/data/ceres_data/9y8z_72683/10_2026/9y8z_72683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y8z_72683/10_2026/9y8z_72683.cif" } 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-2.3rc1-6221/lib/python3.11/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: 3.41, per 1000 atoms: 0.23 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=10, 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 172 " - pdb=" SG CYS B 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 172 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 243 " distance=2.07 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 243 " distance=2.07 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 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: 1.31 Conformation dependent library (CDL) restraints added in 596.2 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: 0.32 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: 2.67 Time building geometry restraints manager: 1.82 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: 7965 12.43 - 24.85: 1021 24.85 - 37.28: 269 37.28 - 49.71: 165 49.71 - 62.14: 75 Dihedral angle restraints: 9495 sinusoidal: 4335 harmonic: 5160 Sorted by residual: 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 dihedral pdb=" CA ARG E 252 " pdb=" CB ARG E 252 " pdb=" CG ARG E 252 " pdb=" CD ARG E 252 " ideal model delta sinusoidal sigma weight residual 60.00 117.77 -57.77 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA ARG A 252 " pdb=" CB ARG A 252 " pdb=" CG ARG A 252 " pdb=" CD ARG A 252 " ideal model delta sinusoidal sigma weight residual 60.00 117.77 -57.77 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 9492 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: 2.27 - 2.79: 3507 2.79 - 3.32: 12852 3.32 - 3.85: 23601 3.85 - 4.37: 29577 4.37 - 4.90: 50873 Nonbonded interactions: 120410 Sorted by model distance: 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 nonbonded pdb=" ND2 ASN E 279 " pdb=" OD1 ASP E 281 " model vdw 2.269 3.120 nonbonded pdb=" ND2 ASN A 279 " pdb=" OD1 ASP A 281 " model vdw 2.269 3.120 ... (remaining 120405 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: 0.05 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.550 Find NCS groups from input model: 0.540 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: 0.010 Load rotamer database and sin/cos tables:5.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 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 15225 Z= 0.840 Angle : 0.915 8.698 20560 Z= 0.532 Chirality : 0.053 0.213 2310 Planarity : 0.011 0.175 2495 Dihedral : 14.057 62.137 6115 Min Nonbonded Distance : 2.268 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/Z covalent geometry : bond 0.00821 / 0.48 (15200) covalent geometry : angle 0.90269 / 0.53 (20510) SS BOND : bond 0.02567 / 1.55 ( 10) SS BOND : angle 3.62928 / 2.10 ( 20) hydrogen bonds : bond 0.22943 / 15.05 ( 745) hydrogen bonds : angle 7.98685 / 5.52 ( 2550) Misc. bond : bond 0.37795 / 19.86 ( 5) link_NAG-ASN : bond 0.00743 / 0.44 ( 10) link_NAG-ASN : angle 2.91814 / 1.95 ( 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 : 0.605 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: 0.7121 time to fit residues: 125.3902 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 : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] 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... A 101 GLN A 260 GLN A 345 HIS B 345 HIS C 101 GLN C 260 GLN C 345 HIS D 101 GLN D 345 HIS E 101 GLN E 345 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.070918 restraints weight = 22383.709| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.69 r_work: 0.2631 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15225 Z= 0.155 Angle : 0.659 16.845 20560 Z= 0.321 Chirality : 0.045 0.262 2310 Planarity : 0.004 0.057 2495 Dihedral : 9.148 58.968 2745 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.46 % Allowed : 10.48 % Favored : 88.06 % 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: 0.92 (0.20), residues: 1725 helix: 1.88 (0.20), residues: 580 sheet: 0.42 (0.27), residues: 345 loop : -0.19 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 153 TYR 0.018 0.001 TYR A 335 PHE 0.013 0.001 PHE D 433 TRP 0.009 0.001 TRP E 102 HIS 0.002 0.000 HIS C 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (15200) covalent geometry : angle 0.57394 / 0.30 (20510) SS BOND : bond 0.00660 / 0.44 ( 10) SS BOND : angle 1.88432 / 1.01 ( 20) hydrogen bonds : bond 0.05696 / 3.74 ( 745) hydrogen bonds : angle 4.93790 / 3.41 ( 2550) Misc. bond : bond 0.00055 / 0.03 ( 5) link_NAG-ASN : bond 0.00724 / 0.41 ( 10) link_NAG-ASN : angle 8.36970 / 6.24 ( 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 161 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.645 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: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8372 (mtm) cc_final: 0.8131 (ptp) REVERT: B 254 MET cc_start: 0.8901 (ttp) cc_final: 0.8652 (ttp) REVERT: B 261 MET cc_start: 0.8975 (mtt) cc_final: 0.8744 (mtt) REVERT: B 414 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7440 (ttm110) REVERT: D 279 ASN cc_start: 0.8539 (t0) cc_final: 0.8180 (t0) REVERT: E 226 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7555 (pp20) REVERT: E 344 GLN cc_start: 0.8335 (pp30) cc_final: 0.7708 (pp30) outliers start: 23 outliers final: 7 residues processed: 153 average time/residue: 0.6706 time to fit residues: 112.0696 Evaluate side-chains 139 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 188 MET 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: [125, 59, 15, 10, 168, 101, 23, 147, 158, 126, 129] chunk 125 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 158 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.100263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.071779 restraints weight = 22710.056| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.70 r_work: 0.2649 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15225 Z= 0.119 Angle : 0.557 10.061 20560 Z= 0.278 Chirality : 0.043 0.239 2310 Planarity : 0.003 0.043 2495 Dihedral : 8.582 54.021 2745 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.52 % Allowed : 11.24 % Favored : 87.24 % 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: 1.27 (0.20), residues: 1725 helix: 2.23 (0.21), residues: 585 sheet: 0.67 (0.28), residues: 355 loop : -0.09 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 414 TYR 0.019 0.001 TYR A 335 PHE 0.013 0.001 PHE E 47 TRP 0.009 0.001 TRP E 102 HIS 0.002 0.000 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (15200) covalent geometry : angle 0.52319 / 0.27 (20510) SS BOND : bond 0.00323 / 0.18 ( 10) SS BOND : angle 1.37703 / 0.77 ( 20) hydrogen bonds : bond 0.04622 / 3.02 ( 745) hydrogen bonds : angle 4.41828 / 3.06 ( 2550) Misc. bond : bond 0.00028 / 0.02 ( 5) link_NAG-ASN : bond 0.00381 / 0.21 ( 10) link_NAG-ASN : angle 4.89339 / 3.65 ( 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 168 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.557 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: symmetry clash REVERT: C 279 ASN cc_start: 0.8408 (t0) cc_final: 0.8149 (t0) REVERT: C 344 GLN cc_start: 0.8341 (pp30) cc_final: 0.7709 (pp30) REVERT: D 153 ARG cc_start: 0.8010 (mtt90) cc_final: 0.7612 (mtt-85) REVERT: D 174 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.9216 (mtt) REVERT: D 279 ASN cc_start: 0.8586 (t0) cc_final: 0.8203 (t0) REVERT: D 344 GLN cc_start: 0.8385 (pp30) cc_final: 0.7675 (pp30) REVERT: E 226 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7411 (pp20) REVERT: E 344 GLN cc_start: 0.8404 (pp30) cc_final: 0.7743 (pp30) outliers start: 24 outliers final: 3 residues processed: 157 average time/residue: 0.6678 time to fit residues: 114.6200 Evaluate side-chains 140 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain E residue 226 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [143, 91, 108, 131, 92, 169, 101, 95, 56, 118, 93] chunk 143 optimal weight: 0.0270 chunk 91 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.099394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.069897 restraints weight = 22541.067| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.74 r_work: 0.2624 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15225 Z= 0.146 Angle : 0.555 9.481 20560 Z= 0.279 Chirality : 0.044 0.246 2310 Planarity : 0.004 0.031 2495 Dihedral : 8.514 55.472 2745 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.27 % Allowed : 12.44 % Favored : 86.29 % 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: 2.33 (0.21), residues: 585 sheet: 0.79 (0.28), residues: 355 loop : -0.14 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 414 TYR 0.021 0.001 TYR A 335 PHE 0.012 0.001 PHE D 133 TRP 0.009 0.001 TRP B 102 HIS 0.001 0.000 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (15200) covalent geometry : angle 0.52678 / 0.27 (20510) SS BOND : bond 0.00416 / 0.25 ( 10) SS BOND : angle 1.27881 / 0.74 ( 20) hydrogen bonds : bond 0.04517 / 2.96 ( 745) hydrogen bonds : angle 4.34612 / 3.02 ( 2550) Misc. bond : bond 0.00029 / 0.02 ( 5) link_NAG-ASN : bond 0.00347 / 0.20 ( 10) link_NAG-ASN : angle 4.51695 / 3.37 ( 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 166 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.504 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: symmetry clash REVERT: C 197 MET cc_start: 0.9041 (mmm) cc_final: 0.8837 (mtp) REVERT: C 279 ASN cc_start: 0.8392 (t0) cc_final: 0.8138 (t0) REVERT: C 344 GLN cc_start: 0.8334 (pp30) cc_final: 0.7637 (pp30) REVERT: D 153 ARG cc_start: 0.8058 (mtt90) cc_final: 0.7620 (mtt-85) REVERT: D 207 ASP cc_start: 0.8395 (m-30) cc_final: 0.7703 (p0) REVERT: D 279 ASN cc_start: 0.8553 (t0) cc_final: 0.8103 (t0) REVERT: D 344 GLN cc_start: 0.8372 (pp30) cc_final: 0.7673 (pp30) REVERT: E 47 PHE cc_start: 0.7722 (t80) cc_final: 0.7408 (t80) REVERT: E 226 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7364 (pp20) REVERT: E 279 ASN cc_start: 0.8297 (t0) cc_final: 0.8063 (t0) REVERT: E 344 GLN cc_start: 0.8431 (pp30) cc_final: 0.7721 (pp30) outliers start: 20 outliers final: 10 residues processed: 155 average time/residue: 0.6388 time to fit residues: 108.7157 Evaluate side-chains 154 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 416 LYS 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 E residue 226 GLU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 416 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [19, 107, 76, 5, 71, 137, 38, 16, 2, 152, 81] chunk 19 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 38 optimal weight: 0.0870 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 0.0370 chunk 152 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 overall best weight: 0.8438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3330 r_free = 0.3330 target = 0.100746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.072215 restraints weight = 22434.960| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.70 r_work: 0.2660 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15225 Z= 0.106 Angle : 0.523 9.470 20560 Z= 0.262 Chirality : 0.042 0.241 2310 Planarity : 0.003 0.026 2495 Dihedral : 8.187 57.979 2745 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.52 % Allowed : 12.89 % Favored : 85.59 % 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: 1.42 (0.20), residues: 1725 helix: 2.47 (0.21), residues: 585 sheet: 0.89 (0.28), residues: 355 loop : -0.19 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 414 TYR 0.019 0.001 TYR A 335 PHE 0.011 0.001 PHE A 329 TRP 0.009 0.001 TRP E 102 HIS 0.001 0.000 HIS E 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (15200) covalent geometry : angle 0.49868 / 0.26 (20510) SS BOND : bond 0.00358 / 0.21 ( 10) SS BOND : angle 1.08542 / 0.63 ( 20) hydrogen bonds : bond 0.04030 / 2.62 ( 745) hydrogen bonds : angle 4.07293 / 2.82 ( 2550) Misc. bond : bond 0.00015 / 0.01 ( 5) link_NAG-ASN : bond 0.00488 / 0.27 ( 10) link_NAG-ASN : angle 4.07827 / 3.04 ( 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 173 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.588 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: symmetry clash REVERT: A 153 ARG cc_start: 0.8074 (mtt-85) cc_final: 0.7659 (mtt-85) REVERT: A 304 SER cc_start: 0.9110 (p) cc_final: 0.8818 (m) REVERT: B 344 GLN cc_start: 0.8474 (pp30) cc_final: 0.7711 (pp30) REVERT: C 279 ASN cc_start: 0.8396 (t0) cc_final: 0.8146 (t0) REVERT: C 344 GLN cc_start: 0.8400 (pp30) cc_final: 0.7675 (pp30) REVERT: D 153 ARG cc_start: 0.8075 (mtt90) cc_final: 0.7655 (mtt-85) REVERT: D 174 MET cc_start: 0.9447 (OUTLIER) cc_final: 0.9203 (mtt) REVERT: D 225 GLU cc_start: 0.8044 (mp0) cc_final: 0.7833 (mp0) REVERT: D 279 ASN cc_start: 0.8555 (t0) cc_final: 0.8097 (t0) REVERT: D 344 GLN cc_start: 0.8447 (pp30) cc_final: 0.7739 (pp30) REVERT: E 47 PHE cc_start: 0.7987 (t80) cc_final: 0.7724 (t80) REVERT: E 225 GLU cc_start: 0.8258 (mp0) cc_final: 0.8029 (pm20) REVERT: E 279 ASN cc_start: 0.8305 (t0) cc_final: 0.8073 (t0) REVERT: E 344 GLN cc_start: 0.8467 (pp30) cc_final: 0.7704 (pp30) outliers start: 24 outliers final: 9 residues processed: 161 average time/residue: 0.6462 time to fit residues: 113.8269 Evaluate side-chains 152 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 238 THR 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 174 MET Chi-restraints excluded: chain D residue 226 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [166, 74, 146, 157, 89, 11, 109, 65, 151, 33, 148] chunk 166 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 146 optimal weight: 0.4980 chunk 157 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 109 optimal weight: 0.0870 chunk 65 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3346 r_free = 0.3346 target = 0.101327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.072867 restraints weight = 22537.081| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.69 r_work: 0.2684 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15225 Z= 0.099 Angle : 0.510 9.515 20560 Z= 0.255 Chirality : 0.042 0.240 2310 Planarity : 0.003 0.026 2495 Dihedral : 7.931 59.725 2745 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.40 % Allowed : 13.65 % 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: 1.53 (0.20), residues: 1725 helix: 2.57 (0.21), residues: 585 sheet: 1.05 (0.28), residues: 350 loop : -0.18 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 414 TYR 0.018 0.001 TYR C 335 PHE 0.011 0.001 PHE A 329 TRP 0.009 0.001 TRP E 102 HIS 0.001 0.000 HIS E 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (15200) covalent geometry : angle 0.48811 / 0.25 (20510) SS BOND : bond 0.00337 / 0.20 ( 10) SS BOND : angle 1.02818 / 0.60 ( 20) hydrogen bonds : bond 0.03816 / 2.49 ( 745) hydrogen bonds : angle 3.93479 / 2.73 ( 2550) Misc. bond : bond 0.00012 / 0.01 ( 5) link_NAG-ASN : bond 0.00476 / 0.27 ( 10) link_NAG-ASN : angle 3.82347 / 2.84 ( 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 168 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.573 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 153 ARG cc_start: 0.8085 (mtt-85) cc_final: 0.7668 (mtt-85) REVERT: A 304 SER cc_start: 0.9076 (p) cc_final: 0.8837 (m) REVERT: B 153 ARG cc_start: 0.8085 (mtt-85) cc_final: 0.7613 (mtt-85) REVERT: B 344 GLN cc_start: 0.8468 (pp30) cc_final: 0.7717 (pp30) REVERT: C 279 ASN cc_start: 0.8391 (t0) cc_final: 0.8147 (t0) REVERT: C 344 GLN cc_start: 0.8340 (pp30) cc_final: 0.7593 (pp30) REVERT: D 153 ARG cc_start: 0.8097 (mtt90) cc_final: 0.7673 (mtt-85) REVERT: D 174 MET cc_start: 0.9449 (OUTLIER) cc_final: 0.9167 (mtt) REVERT: D 279 ASN cc_start: 0.8547 (t0) cc_final: 0.8095 (t0) REVERT: D 304 SER cc_start: 0.8983 (p) cc_final: 0.8672 (m) REVERT: D 344 GLN cc_start: 0.8440 (pp30) cc_final: 0.7739 (pp30) REVERT: E 279 ASN cc_start: 0.8325 (t0) cc_final: 0.8085 (t0) REVERT: E 344 GLN cc_start: 0.8422 (pp30) cc_final: 0.7686 (pp30) outliers start: 22 outliers final: 9 residues processed: 155 average time/residue: 0.6557 time to fit residues: 110.8373 Evaluate side-chains 153 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 CYS 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 238 THR Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain D residue 174 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [15, 0, 83, 50, 155, 34, 60, 35, 119, 61, 95] chunk 15 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 119 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3311 r_free = 0.3311 target = 0.098950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.069921 restraints weight = 22514.386| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.70 r_work: 0.2632 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15225 Z= 0.163 Angle : 0.552 9.588 20560 Z= 0.278 Chirality : 0.044 0.250 2310 Planarity : 0.003 0.026 2495 Dihedral : 8.107 55.210 2745 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.40 % Allowed : 13.84 % 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: 1.53 (0.20), residues: 1725 helix: 2.50 (0.21), residues: 585 sheet: 1.02 (0.28), residues: 355 loop : -0.11 (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 0.013 0.001 PHE D 133 TRP 0.009 0.001 TRP A 102 HIS 0.001 0.000 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (15200) covalent geometry : angle 0.52988 / 0.27 (20510) SS BOND : bond 0.00452 / 0.27 ( 10) SS BOND : angle 1.25422 / 0.74 ( 20) hydrogen bonds : bond 0.04343 / 2.85 ( 745) hydrogen bonds : angle 4.16185 / 2.89 ( 2550) Misc. bond : bond 0.00043 / 0.02 ( 5) link_NAG-ASN : bond 0.00342 / 0.19 ( 10) link_NAG-ASN : angle 3.95159 / 2.95 ( 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 169 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.469 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 153 ARG cc_start: 0.8130 (mtt-85) cc_final: 0.7823 (mtt-85) REVERT: A 174 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8108 (mmm) REVERT: A 304 SER cc_start: 0.9119 (p) cc_final: 0.8904 (m) REVERT: A 344 GLN cc_start: 0.8416 (pp30) cc_final: 0.7701 (pp30) REVERT: B 153 ARG cc_start: 0.8088 (mtt-85) cc_final: 0.7602 (mtt-85) REVERT: B 344 GLN cc_start: 0.8482 (pp30) cc_final: 0.7723 (pp30) REVERT: C 153 ARG cc_start: 0.8088 (mtt90) cc_final: 0.7879 (mtt-85) REVERT: C 279 ASN cc_start: 0.8415 (t0) cc_final: 0.8154 (t0) REVERT: C 344 GLN cc_start: 0.8311 (pp30) cc_final: 0.7565 (pp30) REVERT: D 153 ARG cc_start: 0.8149 (mtt90) cc_final: 0.7701 (mtt-85) REVERT: D 174 MET cc_start: 0.9437 (OUTLIER) cc_final: 0.9155 (mtt) REVERT: D 225 GLU cc_start: 0.8114 (mp0) cc_final: 0.7887 (mp0) REVERT: D 279 ASN cc_start: 0.8576 (t0) cc_final: 0.8068 (t0) REVERT: D 304 SER cc_start: 0.9007 (p) cc_final: 0.8709 (m) REVERT: D 344 GLN cc_start: 0.8387 (pp30) cc_final: 0.7648 (pp30) REVERT: E 279 ASN cc_start: 0.8353 (t0) cc_final: 0.8117 (t0) REVERT: E 344 GLN cc_start: 0.8382 (pp30) cc_final: 0.7615 (pp30) outliers start: 22 outliers final: 13 residues processed: 154 average time/residue: 0.6603 time to fit residues: 111.0198 Evaluate side-chains 161 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 416 LYS 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 238 THR Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 261 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [80, 115, 35, 10, 19, 149, 165, 130, 59, 88, 81] chunk 80 optimal weight: 2.9990 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: 1.9990 chunk 165 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3319 r_free = 0.3319 target = 0.099515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.070520 restraints weight = 22630.888| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.72 r_work: 0.2644 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15225 Z= 0.131 Angle : 0.532 9.549 20560 Z= 0.267 Chirality : 0.043 0.244 2310 Planarity : 0.003 0.025 2495 Dihedral : 7.989 59.292 2745 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.33 % Allowed : 13.84 % Favored : 84.83 % 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: 1.59 (0.20), residues: 1725 helix: 2.58 (0.21), residues: 585 sheet: 1.09 (0.28), residues: 355 loop : -0.11 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.020 0.001 TYR A 335 PHE 0.011 0.001 PHE A 329 TRP 0.009 0.001 TRP E 102 HIS 0.001 0.000 HIS C 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (15200) covalent geometry : angle 0.50989 / 0.26 (20510) SS BOND : bond 0.00403 / 0.24 ( 10) SS BOND : angle 1.13050 / 0.67 ( 20) hydrogen bonds : bond 0.04110 / 2.69 ( 745) hydrogen bonds : angle 4.06103 / 2.82 ( 2550) Misc. bond : bond 0.00029 / 0.02 ( 5) link_NAG-ASN : bond 0.00423 / 0.24 ( 10) link_NAG-ASN : angle 3.89053 / 2.90 ( 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 168 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.537 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 153 ARG cc_start: 0.8127 (mtt-85) cc_final: 0.7813 (mtt-85) REVERT: A 174 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8059 (mmm) REVERT: A 304 SER cc_start: 0.9108 (p) cc_final: 0.8898 (m) REVERT: A 344 GLN cc_start: 0.8425 (pp30) cc_final: 0.7677 (pp30) REVERT: B 153 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7617 (mtt-85) REVERT: B 344 GLN cc_start: 0.8488 (pp30) cc_final: 0.7713 (pp30) REVERT: C 153 ARG cc_start: 0.8088 (mtt90) cc_final: 0.7879 (mtt-85) REVERT: C 279 ASN cc_start: 0.8430 (t0) cc_final: 0.8185 (t0) REVERT: C 344 GLN cc_start: 0.8340 (pp30) cc_final: 0.7603 (pp30) REVERT: D 153 ARG cc_start: 0.8142 (mtt90) cc_final: 0.7694 (mtt-85) REVERT: D 174 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.9156 (mtt) REVERT: D 279 ASN cc_start: 0.8549 (t0) cc_final: 0.8074 (t0) REVERT: D 304 SER cc_start: 0.9004 (OUTLIER) cc_final: 0.8706 (m) REVERT: D 344 GLN cc_start: 0.8405 (pp30) cc_final: 0.7632 (pp30) REVERT: E 279 ASN cc_start: 0.8352 (t0) cc_final: 0.8108 (t0) REVERT: E 344 GLN cc_start: 0.8388 (pp30) cc_final: 0.7616 (pp30) outliers start: 21 outliers final: 14 residues processed: 155 average time/residue: 0.6450 time to fit residues: 109.1370 Evaluate side-chains 162 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 416 LYS 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 D residue 174 MET Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 304 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: [136, 100, 146, 164, 137, 109, 90, 110, 129, 93, 94] chunk 136 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 146 optimal weight: 7.9990 chunk 164 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3312 r_free = 0.3312 target = 0.099021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.070009 restraints weight = 22637.237| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.71 r_work: 0.2635 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15225 Z= 0.145 Angle : 0.545 9.568 20560 Z= 0.275 Chirality : 0.043 0.246 2310 Planarity : 0.003 0.026 2495 Dihedral : 7.966 58.371 2745 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.33 % Allowed : 13.97 % Favored : 84.70 % 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: 1.59 (0.20), residues: 1725 helix: 2.57 (0.21), residues: 585 sheet: 1.09 (0.28), residues: 355 loop : -0.11 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.021 0.001 TYR A 335 PHE 0.012 0.001 PHE D 133 TRP 0.009 0.001 TRP D 102 HIS 0.001 0.000 HIS C 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (15200) covalent geometry : angle 0.52346 / 0.27 (20510) SS BOND : bond 0.00430 / 0.26 ( 10) SS BOND : angle 1.19407 / 0.71 ( 20) hydrogen bonds : bond 0.04226 / 2.77 ( 745) hydrogen bonds : angle 4.10603 / 2.85 ( 2550) Misc. bond : bond 0.00033 / 0.02 ( 5) link_NAG-ASN : bond 0.00391 / 0.22 ( 10) link_NAG-ASN : angle 3.86769 / 2.88 ( 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 169 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.530 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: symmetry clash REVERT: A 153 ARG cc_start: 0.8137 (mtt-85) cc_final: 0.7812 (mtt-85) REVERT: A 174 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8035 (mmm) REVERT: A 225 GLU cc_start: 0.8131 (mp0) cc_final: 0.7928 (mp0) REVERT: A 304 SER cc_start: 0.9107 (p) cc_final: 0.8904 (m) REVERT: A 344 GLN cc_start: 0.8388 (pp30) cc_final: 0.7655 (pp30) REVERT: B 153 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.7611 (mtt-85) REVERT: B 225 GLU cc_start: 0.8306 (mp0) cc_final: 0.8051 (mp0) REVERT: B 344 GLN cc_start: 0.8495 (pp30) cc_final: 0.7711 (pp30) REVERT: C 279 ASN cc_start: 0.8419 (t0) cc_final: 0.8173 (t0) REVERT: C 344 GLN cc_start: 0.8319 (pp30) cc_final: 0.7573 (pp30) REVERT: D 153 ARG cc_start: 0.8160 (mtt90) cc_final: 0.7697 (mtt-85) REVERT: D 174 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.9135 (mtt) REVERT: D 225 GLU cc_start: 0.8116 (mp0) cc_final: 0.7891 (mp0) REVERT: D 279 ASN cc_start: 0.8584 (t0) cc_final: 0.8065 (t0) REVERT: D 304 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8712 (m) REVERT: D 344 GLN cc_start: 0.8366 (pp30) cc_final: 0.7613 (pp30) REVERT: E 279 ASN cc_start: 0.8354 (t0) cc_final: 0.8121 (t0) REVERT: E 344 GLN cc_start: 0.8354 (pp30) cc_final: 0.7560 (pp30) outliers start: 21 outliers final: 17 residues processed: 153 average time/residue: 0.6574 time to fit residues: 109.9358 Evaluate side-chains 165 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 416 LYS 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 174 MET Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 238 THR 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: [45, 109, 99, 76, 161, 75, 112, 16, 115, 34, 130] chunk 45 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 161 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 130 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3336 r_free = 0.3336 target = 0.100608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.072002 restraints weight = 22574.457| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.70 r_work: 0.2673 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15225 Z= 0.101 Angle : 0.519 9.520 20560 Z= 0.260 Chirality : 0.042 0.239 2310 Planarity : 0.003 0.025 2495 Dihedral : 7.636 58.251 2745 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.08 % Allowed : 14.29 % Favored : 84.63 % 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: 1.66 (0.20), residues: 1725 helix: 2.67 (0.21), residues: 585 sheet: 1.12 (0.29), residues: 355 loop : -0.10 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 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 0.002 0.000 HIS C 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (15200) covalent geometry : angle 0.49914 / 0.26 (20510) SS BOND : bond 0.00331 / 0.20 ( 10) SS BOND : angle 1.03617 / 0.61 ( 20) hydrogen bonds : bond 0.03783 / 2.47 ( 745) hydrogen bonds : angle 3.91086 / 2.71 ( 2550) Misc. bond : bond 0.00015 / 0.01 ( 5) link_NAG-ASN : bond 0.00511 / 0.29 ( 10) link_NAG-ASN : angle 3.65634 / 2.72 ( 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 165 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.498 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: symmetry clash REVERT: A 153 ARG cc_start: 0.8125 (mtt-85) cc_final: 0.7806 (mtt-85) REVERT: A 304 SER cc_start: 0.9081 (p) cc_final: 0.8878 (m) REVERT: A 344 GLN cc_start: 0.8370 (pp30) cc_final: 0.7651 (pp30) REVERT: B 153 ARG cc_start: 0.8069 (mtt-85) cc_final: 0.7603 (mtt-85) REVERT: B 344 GLN cc_start: 0.8491 (pp30) cc_final: 0.7734 (pp30) REVERT: C 225 GLU cc_start: 0.8251 (mp0) cc_final: 0.8000 (mp0) REVERT: C 279 ASN cc_start: 0.8416 (t0) cc_final: 0.8168 (t0) REVERT: C 344 GLN cc_start: 0.8316 (pp30) cc_final: 0.7567 (pp30) REVERT: D 153 ARG cc_start: 0.8119 (mtt90) cc_final: 0.7668 (mtt-85) REVERT: D 174 MET cc_start: 0.9438 (OUTLIER) cc_final: 0.9128 (mtt) REVERT: D 225 GLU cc_start: 0.8107 (mp0) cc_final: 0.7876 (mp0) REVERT: D 279 ASN cc_start: 0.8547 (t0) cc_final: 0.8071 (t0) REVERT: D 304 SER cc_start: 0.8984 (p) cc_final: 0.8697 (m) REVERT: D 344 GLN cc_start: 0.8370 (pp30) cc_final: 0.7638 (pp30) REVERT: E 279 ASN cc_start: 0.8354 (t0) cc_final: 0.8124 (t0) REVERT: E 344 GLN cc_start: 0.8292 (pp30) cc_final: 0.7536 (pp30) outliers start: 17 outliers final: 15 residues processed: 153 average time/residue: 0.6514 time to fit residues: 109.0544 Evaluate side-chains 162 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 416 LYS 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 174 MET Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 261 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: [112, 64, 123, 46, 63, 49, 81, 6, 32, 17, 39] chunk 112 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 81 optimal weight: 0.0050 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.100851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.072221 restraints weight = 22454.101| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.69 r_work: 0.2677 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15225 Z= 0.104 Angle : 0.516 9.560 20560 Z= 0.259 Chirality : 0.042 0.241 2310 Planarity : 0.003 0.026 2495 Dihedral : 7.436 56.168 2745 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.27 % Allowed : 14.29 % Favored : 84.44 % 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: 2.74 (0.21), residues: 590 sheet: 1.23 (0.29), residues: 350 loop : -0.11 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 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 C 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (15200) covalent geometry : angle 0.49770 / 0.25 (20510) SS BOND : bond 0.00350 / 0.21 ( 10) SS BOND : angle 1.05923 / 0.63 ( 20) hydrogen bonds : bond 0.03741 / 2.44 ( 745) hydrogen bonds : angle 3.88540 / 2.69 ( 2550) Misc. bond : bond 0.00019 / 0.01 ( 5) link_NAG-ASN : bond 0.00475 / 0.27 ( 10) link_NAG-ASN : angle 3.52496 / 2.62 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4727.03 seconds wall clock time: 81 minutes 14.89 seconds (4874.89 seconds total)