Starting phenix.real_space_refine on Tue Jun 24 15:35:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cy8_27070/06_2025/8cy8_27070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cy8_27070/06_2025/8cy8_27070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cy8_27070/06_2025/8cy8_27070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cy8_27070/06_2025/8cy8_27070.map" model { file = "/net/cci-nas-00/data/ceres_data/8cy8_27070/06_2025/8cy8_27070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cy8_27070/06_2025/8cy8_27070.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.095 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 192 5.16 5 C 18264 2.51 5 N 4884 2.21 5 O 5460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28800 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "B" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "C" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "D" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "E" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "F" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "G" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "H" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "I" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "J" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "K" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "L" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.57, per 1000 atoms: 0.61 Number of scatterers: 28800 At special positions: 0 Unit cell: (153.34, 150.88, 138.58, 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 192 16.00 O 5460 8.00 N 4884 7.00 C 18264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.50 Conformation dependent library (CDL) restraints added in 3.6 seconds 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6816 Finding SS restraints... Secondary structure from input PDB file: 233 helices and 12 sheets defined 67.9% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 Processing helix chain 'A' and resid 13 through 18 removed outlier: 3.704A pdb=" N LYS A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 13 through 18' Processing helix chain 'A' and resid 27 through 39 removed outlier: 3.614A pdb=" N ALA A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 86 through 95 Processing helix chain 'A' and resid 96 through 99 Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 134 through 141 Processing helix chain 'A' and resid 161 through 173 Processing helix chain 'A' and resid 184 through 199 Processing helix chain 'A' and resid 201 through 218 Processing helix chain 'A' and resid 221 through 230 removed outlier: 3.759A pdb=" N PHE A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 243 removed outlier: 4.114A pdb=" N ILE A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 253 through 268 Proline residue: A 265 - end of helix Processing helix chain 'A' and resid 269 through 285 Processing helix chain 'A' and resid 286 through 298 Processing helix chain 'A' and resid 300 through 312 removed outlier: 3.687A pdb=" N ASP A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 324 removed outlier: 3.691A pdb=" N ALA A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 11 Processing helix chain 'B' and resid 13 through 18 removed outlier: 3.525A pdb=" N LYS B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 13 through 18' Processing helix chain 'B' and resid 27 through 39 removed outlier: 3.785A pdb=" N ALA B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 75 Processing helix chain 'B' and resid 86 through 95 Processing helix chain 'B' and resid 96 through 99 Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 161 through 173 Processing helix chain 'B' and resid 184 through 199 Processing helix chain 'B' and resid 201 through 218 Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 232 through 243 removed outlier: 4.190A pdb=" N ILE B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 253 through 268 Proline residue: B 265 - end of helix Processing helix chain 'B' and resid 269 through 285 Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'B' and resid 300 through 312 removed outlier: 3.729A pdb=" N ASP B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'C' and resid 7 through 11 Processing helix chain 'C' and resid 13 through 18 removed outlier: 3.708A pdb=" N LYS C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 18 " --> pdb=" O ASN C 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 13 through 18' Processing helix chain 'C' and resid 27 through 39 removed outlier: 3.724A pdb=" N ALA C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 86 through 95 removed outlier: 3.502A pdb=" N ASN C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 99 Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 134 through 141 Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 184 through 199 Processing helix chain 'C' and resid 201 through 218 Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 232 through 243 removed outlier: 4.094A pdb=" N ILE C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 253 through 268 Proline residue: C 265 - end of helix Processing helix chain 'C' and resid 269 through 285 Processing helix chain 'C' and resid 286 through 298 Processing helix chain 'C' and resid 300 through 312 removed outlier: 3.775A pdb=" N ASP C 312 " --> pdb=" O LYS C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 324 removed outlier: 3.664A pdb=" N ALA C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 11 Processing helix chain 'D' and resid 13 through 18 removed outlier: 3.842A pdb=" N LYS D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER D 18 " --> pdb=" O ASN D 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 13 through 18' Processing helix chain 'D' and resid 27 through 39 removed outlier: 3.760A pdb=" N ALA D 32 " --> pdb=" O SER D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 86 through 95 Processing helix chain 'D' and resid 96 through 99 Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 184 through 199 Processing helix chain 'D' and resid 201 through 218 Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 232 through 243 removed outlier: 4.200A pdb=" N ILE D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 253 through 268 Proline residue: D 265 - end of helix Processing helix chain 'D' and resid 269 through 285 Processing helix chain 'D' and resid 286 through 298 Processing helix chain 'D' and resid 300 through 312 removed outlier: 3.763A pdb=" N ASP D 312 " --> pdb=" O LYS D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 324 removed outlier: 3.708A pdb=" N ALA D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 11 Processing helix chain 'E' and resid 12 through 18 removed outlier: 4.408A pdb=" N ILE E 16 " --> pdb=" O ASP E 12 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER E 18 " --> pdb=" O ASN E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 39 removed outlier: 3.746A pdb=" N ALA E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 75 Processing helix chain 'E' and resid 86 through 95 Processing helix chain 'E' and resid 96 through 99 Processing helix chain 'E' and resid 110 through 115 Processing helix chain 'E' and resid 134 through 141 Processing helix chain 'E' and resid 161 through 173 removed outlier: 3.510A pdb=" N ILE E 173 " --> pdb=" O TYR E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 199 Processing helix chain 'E' and resid 201 through 218 Processing helix chain 'E' and resid 221 through 230 Processing helix chain 'E' and resid 232 through 243 removed outlier: 4.156A pdb=" N ILE E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'E' and resid 253 through 268 Proline residue: E 265 - end of helix Processing helix chain 'E' and resid 269 through 285 Processing helix chain 'E' and resid 286 through 298 Processing helix chain 'E' and resid 300 through 312 removed outlier: 3.700A pdb=" N ASP E 312 " --> pdb=" O LYS E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 324 removed outlier: 3.685A pdb=" N ALA E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 12 removed outlier: 6.934A pdb=" N ASP F 12 " --> pdb=" O LYS F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 18 removed outlier: 3.623A pdb=" N LYS F 17 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER F 18 " --> pdb=" O ASN F 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 13 through 18' Processing helix chain 'F' and resid 27 through 39 removed outlier: 3.850A pdb=" N ALA F 32 " --> pdb=" O SER F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 75 Processing helix chain 'F' and resid 83 through 95 removed outlier: 4.747A pdb=" N ALA F 88 " --> pdb=" O ASP F 84 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASP F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 99 Processing helix chain 'F' and resid 110 through 115 Processing helix chain 'F' and resid 134 through 141 Processing helix chain 'F' and resid 161 through 173 Processing helix chain 'F' and resid 184 through 199 Processing helix chain 'F' and resid 201 through 218 Processing helix chain 'F' and resid 221 through 230 Processing helix chain 'F' and resid 232 through 243 removed outlier: 4.109A pdb=" N ILE F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 252 Processing helix chain 'F' and resid 253 through 268 Proline residue: F 265 - end of helix Processing helix chain 'F' and resid 269 through 285 Processing helix chain 'F' and resid 286 through 298 Processing helix chain 'F' and resid 300 through 312 removed outlier: 3.710A pdb=" N ASP F 312 " --> pdb=" O LYS F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 324 removed outlier: 3.710A pdb=" N ALA F 324 " --> pdb=" O ARG F 320 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 11 Processing helix chain 'G' and resid 13 through 18 removed outlier: 3.848A pdb=" N LYS G 17 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER G 18 " --> pdb=" O ASN G 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 13 through 18' Processing helix chain 'G' and resid 27 through 39 removed outlier: 3.810A pdb=" N ALA G 32 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP G 39 " --> pdb=" O MET G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 75 Processing helix chain 'G' and resid 86 through 95 Processing helix chain 'G' and resid 96 through 99 Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 134 through 141 Processing helix chain 'G' and resid 161 through 173 Processing helix chain 'G' and resid 184 through 199 Processing helix chain 'G' and resid 201 through 218 Processing helix chain 'G' and resid 221 through 230 Processing helix chain 'G' and resid 232 through 243 removed outlier: 4.093A pdb=" N ILE G 236 " --> pdb=" O GLU G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 252 Processing helix chain 'G' and resid 253 through 268 Proline residue: G 265 - end of helix Processing helix chain 'G' and resid 269 through 285 Processing helix chain 'G' and resid 286 through 298 Processing helix chain 'G' and resid 300 through 312 removed outlier: 3.769A pdb=" N ASP G 312 " --> pdb=" O LYS G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 324 removed outlier: 3.686A pdb=" N ALA G 324 " --> pdb=" O ARG G 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 11 Processing helix chain 'H' and resid 13 through 18 removed outlier: 3.769A pdb=" N LYS H 17 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER H 18 " --> pdb=" O ASN H 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 13 through 18' Processing helix chain 'H' and resid 27 through 39 removed outlier: 3.750A pdb=" N ALA H 32 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 75 Processing helix chain 'H' and resid 83 through 95 removed outlier: 4.721A pdb=" N ALA H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASP H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 99 Processing helix chain 'H' and resid 110 through 115 Processing helix chain 'H' and resid 134 through 141 Processing helix chain 'H' and resid 161 through 173 Processing helix chain 'H' and resid 184 through 199 Processing helix chain 'H' and resid 201 through 218 Processing helix chain 'H' and resid 221 through 230 Processing helix chain 'H' and resid 232 through 243 removed outlier: 4.170A pdb=" N ILE H 236 " --> pdb=" O GLU H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 252 Processing helix chain 'H' and resid 253 through 268 Proline residue: H 265 - end of helix Processing helix chain 'H' and resid 269 through 285 Processing helix chain 'H' and resid 286 through 298 Processing helix chain 'H' and resid 300 through 312 removed outlier: 3.675A pdb=" N ASP H 312 " --> pdb=" O LYS H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 323 Processing helix chain 'I' and resid 7 through 12 removed outlier: 6.902A pdb=" N ASP I 12 " --> pdb=" O LYS I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 18 removed outlier: 3.509A pdb=" N LYS I 17 " --> pdb=" O LEU I 13 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER I 18 " --> pdb=" O ASN I 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 13 through 18' Processing helix chain 'I' and resid 27 through 38 removed outlier: 3.671A pdb=" N ALA I 32 " --> pdb=" O SER I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 41 No H-bonds generated for 'chain 'I' and resid 39 through 41' Processing helix chain 'I' and resid 67 through 75 Processing helix chain 'I' and resid 86 through 95 Processing helix chain 'I' and resid 96 through 99 Processing helix chain 'I' and resid 110 through 115 Processing helix chain 'I' and resid 134 through 141 Processing helix chain 'I' and resid 161 through 173 Processing helix chain 'I' and resid 184 through 199 Processing helix chain 'I' and resid 201 through 218 Processing helix chain 'I' and resid 221 through 230 Processing helix chain 'I' and resid 232 through 243 removed outlier: 4.132A pdb=" N ILE I 236 " --> pdb=" O GLU I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 244 through 252 Processing helix chain 'I' and resid 253 through 268 Proline residue: I 265 - end of helix Processing helix chain 'I' and resid 269 through 285 Processing helix chain 'I' and resid 286 through 298 Processing helix chain 'I' and resid 300 through 312 removed outlier: 3.696A pdb=" N ASP I 312 " --> pdb=" O LYS I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 324 removed outlier: 3.682A pdb=" N ALA I 324 " --> pdb=" O ARG I 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 11 Processing helix chain 'J' and resid 13 through 18 Processing helix chain 'J' and resid 27 through 38 removed outlier: 3.772A pdb=" N ALA J 32 " --> pdb=" O SER J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 41 No H-bonds generated for 'chain 'J' and resid 39 through 41' Processing helix chain 'J' and resid 67 through 75 Processing helix chain 'J' and resid 86 through 95 Processing helix chain 'J' and resid 96 through 99 Processing helix chain 'J' and resid 110 through 115 Processing helix chain 'J' and resid 134 through 141 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 184 through 199 Processing helix chain 'J' and resid 201 through 218 Processing helix chain 'J' and resid 221 through 230 Processing helix chain 'J' and resid 232 through 243 removed outlier: 4.132A pdb=" N ILE J 236 " --> pdb=" O GLU J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 244 through 252 Processing helix chain 'J' and resid 253 through 268 Proline residue: J 265 - end of helix Processing helix chain 'J' and resid 269 through 285 Processing helix chain 'J' and resid 286 through 298 Processing helix chain 'J' and resid 300 through 312 removed outlier: 3.695A pdb=" N ASP J 312 " --> pdb=" O LYS J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 324 removed outlier: 3.696A pdb=" N ALA J 324 " --> pdb=" O ARG J 320 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 11 Processing helix chain 'K' and resid 13 through 18 removed outlier: 3.773A pdb=" N LYS K 17 " --> pdb=" O LEU K 13 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER K 18 " --> pdb=" O ASN K 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 13 through 18' Processing helix chain 'K' and resid 27 through 38 removed outlier: 3.770A pdb=" N ALA K 32 " --> pdb=" O SER K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 41 No H-bonds generated for 'chain 'K' and resid 39 through 41' Processing helix chain 'K' and resid 67 through 75 Processing helix chain 'K' and resid 83 through 95 removed outlier: 4.765A pdb=" N ALA K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 99 Processing helix chain 'K' and resid 110 through 115 Processing helix chain 'K' and resid 134 through 141 Processing helix chain 'K' and resid 161 through 173 removed outlier: 3.505A pdb=" N ILE K 173 " --> pdb=" O TYR K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 199 removed outlier: 3.544A pdb=" N GLU K 196 " --> pdb=" O ASP K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 218 Processing helix chain 'K' and resid 221 through 230 Processing helix chain 'K' and resid 232 through 243 removed outlier: 4.082A pdb=" N ILE K 236 " --> pdb=" O GLU K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 252 Processing helix chain 'K' and resid 253 through 268 Proline residue: K 265 - end of helix Processing helix chain 'K' and resid 269 through 285 Processing helix chain 'K' and resid 286 through 298 Processing helix chain 'K' and resid 300 through 312 removed outlier: 3.793A pdb=" N ASP K 312 " --> pdb=" O LYS K 308 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 324 removed outlier: 3.684A pdb=" N ALA K 324 " --> pdb=" O ARG K 320 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 13 through 18 removed outlier: 3.853A pdb=" N LYS L 17 " --> pdb=" O LEU L 13 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER L 18 " --> pdb=" O ASN L 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 13 through 18' Processing helix chain 'L' and resid 27 through 38 removed outlier: 3.701A pdb=" N ALA L 32 " --> pdb=" O SER L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 41 No H-bonds generated for 'chain 'L' and resid 39 through 41' Processing helix chain 'L' and resid 67 through 75 Processing helix chain 'L' and resid 83 through 95 removed outlier: 4.723A pdb=" N ALA L 88 " --> pdb=" O ASP L 84 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASP L 89 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 99 Processing helix chain 'L' and resid 110 through 115 Processing helix chain 'L' and resid 134 through 141 Processing helix chain 'L' and resid 161 through 173 Processing helix chain 'L' and resid 184 through 199 Processing helix chain 'L' and resid 201 through 218 Processing helix chain 'L' and resid 221 through 230 Processing helix chain 'L' and resid 232 through 243 removed outlier: 4.115A pdb=" N ILE L 236 " --> pdb=" O GLU L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 252 Processing helix chain 'L' and resid 253 through 268 Proline residue: L 265 - end of helix Processing helix chain 'L' and resid 269 through 285 Processing helix chain 'L' and resid 286 through 298 Processing helix chain 'L' and resid 300 through 312 removed outlier: 3.802A pdb=" N ASP L 312 " --> pdb=" O LYS L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 324 removed outlier: 3.678A pdb=" N ALA L 324 " --> pdb=" O ARG L 320 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 6.742A pdb=" N CYS A 150 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 78 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS A 20 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N MET A 79 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA A 22 " --> pdb=" O MET A 79 " (cutoff:3.500A) removed outlier: 9.399A pdb=" N MET A 66 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A 46 " --> pdb=" O MET A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 6 removed outlier: 6.730A pdb=" N CYS B 150 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE B 78 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N MET B 66 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 46 " --> pdb=" O MET B 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 5 through 6 removed outlier: 6.700A pdb=" N CYS C 150 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE C 78 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LYS C 20 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N MET C 79 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA C 22 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 9.535A pdb=" N MET C 66 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE C 46 " --> pdb=" O MET C 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 5 through 6 removed outlier: 6.742A pdb=" N CYS D 150 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE D 78 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS D 20 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N MET D 79 " --> pdb=" O LYS D 20 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA D 22 " --> pdb=" O MET D 79 " (cutoff:3.500A) removed outlier: 9.563A pdb=" N MET D 66 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE D 46 " --> pdb=" O MET D 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 5 through 6 removed outlier: 6.322A pdb=" N ILE E 78 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N MET E 66 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE E 46 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6 removed outlier: 6.703A pdb=" N CYS F 150 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE F 78 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LYS F 20 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N MET F 79 " --> pdb=" O LYS F 20 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA F 22 " --> pdb=" O MET F 79 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N MET F 66 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE F 46 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 5 through 6 removed outlier: 6.752A pdb=" N CYS G 150 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE G 78 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS G 20 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N MET G 79 " --> pdb=" O LYS G 20 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA G 22 " --> pdb=" O MET G 79 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N MET G 66 " --> pdb=" O VAL G 44 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE G 46 " --> pdb=" O MET G 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 5 through 6 removed outlier: 6.728A pdb=" N CYS H 150 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE H 78 " --> pdb=" O ALA H 106 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LYS H 20 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N MET H 79 " --> pdb=" O LYS H 20 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA H 22 " --> pdb=" O MET H 79 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N MET H 66 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE H 46 " --> pdb=" O MET H 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 5 through 6 removed outlier: 6.710A pdb=" N CYS I 150 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE I 78 " --> pdb=" O ALA I 106 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LYS I 20 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N MET I 79 " --> pdb=" O LYS I 20 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA I 22 " --> pdb=" O MET I 79 " (cutoff:3.500A) removed outlier: 9.463A pdb=" N MET I 66 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE I 46 " --> pdb=" O MET I 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 5 through 6 removed outlier: 6.704A pdb=" N CYS J 150 " --> pdb=" O ILE J 181 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE J 78 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N MET J 66 " --> pdb=" O VAL J 44 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE J 46 " --> pdb=" O MET J 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 5 through 6 removed outlier: 6.706A pdb=" N CYS K 150 " --> pdb=" O ILE K 181 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE K 78 " --> pdb=" O ALA K 106 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LYS K 20 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N MET K 79 " --> pdb=" O LYS K 20 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA K 22 " --> pdb=" O MET K 79 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N MET K 66 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE K 46 " --> pdb=" O MET K 66 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 6 removed outlier: 6.755A pdb=" N CYS L 150 " --> pdb=" O ILE L 181 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE L 78 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N MET L 66 " --> pdb=" O VAL L 44 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE L 46 " --> pdb=" O MET L 66 " (cutoff:3.500A) 1701 hydrogen bonds defined for protein. 4947 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: 10.33 Time building geometry restraints manager: 7.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4992 1.30 - 1.43: 6974 1.43 - 1.55: 16942 1.55 - 1.68: 0 1.68 - 1.81: 336 Bond restraints: 29244 Sorted by residual: bond pdb=" CG GLN E 197 " pdb=" CD GLN E 197 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.74e+00 bond pdb=" CB ASP D 125 " pdb=" CG ASP D 125 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.72e+00 bond pdb=" CG GLN C 197 " pdb=" CD GLN C 197 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.62e+00 bond pdb=" CB ASP I 125 " pdb=" CG ASP I 125 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.56e+00 bond pdb=" CB ASP L 125 " pdb=" CG ASP L 125 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.55e+00 ... (remaining 29239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 37846 1.75 - 3.50: 1310 3.50 - 5.24: 133 5.24 - 6.99: 52 6.99 - 8.74: 19 Bond angle restraints: 39360 Sorted by residual: angle pdb=" CG MET A 35 " pdb=" SD MET A 35 " pdb=" CE MET A 35 " ideal model delta sigma weight residual 100.90 94.46 6.44 2.20e+00 2.07e-01 8.56e+00 angle pdb=" CB MET C 35 " pdb=" CG MET C 35 " pdb=" SD MET C 35 " ideal model delta sigma weight residual 112.70 120.89 -8.19 3.00e+00 1.11e-01 7.46e+00 angle pdb=" CB MET I 79 " pdb=" CG MET I 79 " pdb=" SD MET I 79 " ideal model delta sigma weight residual 112.70 120.51 -7.81 3.00e+00 1.11e-01 6.78e+00 angle pdb=" CB MET D 79 " pdb=" CG MET D 79 " pdb=" SD MET D 79 " ideal model delta sigma weight residual 112.70 120.42 -7.72 3.00e+00 1.11e-01 6.62e+00 angle pdb=" CG MET F 35 " pdb=" SD MET F 35 " pdb=" CE MET F 35 " ideal model delta sigma weight residual 100.90 95.26 5.64 2.20e+00 2.07e-01 6.57e+00 ... (remaining 39355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16341 17.99 - 35.98: 1068 35.98 - 53.97: 176 53.97 - 71.96: 46 71.96 - 89.95: 21 Dihedral angle restraints: 17652 sinusoidal: 7008 harmonic: 10644 Sorted by residual: dihedral pdb=" CB GLU E 295 " pdb=" CG GLU E 295 " pdb=" CD GLU E 295 " pdb=" OE1 GLU E 295 " ideal model delta sinusoidal sigma weight residual 0.00 89.95 -89.95 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU A 295 " pdb=" CG GLU A 295 " pdb=" CD GLU A 295 " pdb=" OE1 GLU A 295 " ideal model delta sinusoidal sigma weight residual 0.00 88.96 -88.96 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU D 295 " pdb=" CG GLU D 295 " pdb=" CD GLU D 295 " pdb=" OE1 GLU D 295 " ideal model delta sinusoidal sigma weight residual 0.00 -87.38 87.38 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 17649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1798 0.033 - 0.065: 1509 0.065 - 0.098: 748 0.098 - 0.130: 343 0.130 - 0.163: 54 Chirality restraints: 4452 Sorted by residual: chirality pdb=" CA GLU D 94 " pdb=" N GLU D 94 " pdb=" C GLU D 94 " pdb=" CB GLU D 94 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CA GLU J 94 " pdb=" N GLU J 94 " pdb=" C GLU J 94 " pdb=" CB GLU J 94 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ILE A 268 " pdb=" N ILE A 268 " pdb=" C ILE A 268 " pdb=" CB ILE A 268 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 4449 not shown) Planarity restraints: 5076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS F 31 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C HIS F 31 " 0.033 2.00e-02 2.50e+03 pdb=" O HIS F 31 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA F 32 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA J 130 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO J 131 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO J 131 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 131 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 264 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 265 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 265 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 265 " -0.023 5.00e-02 4.00e+02 ... (remaining 5073 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1175 2.72 - 3.26: 28044 3.26 - 3.81: 43574 3.81 - 4.35: 55462 4.35 - 4.90: 97441 Nonbonded interactions: 225696 Sorted by model distance: nonbonded pdb=" O ALA C 32 " pdb=" ND2 ASN C 36 " model vdw 2.171 3.120 nonbonded pdb=" N GLY D 123 " pdb=" OE1 GLU D 158 " model vdw 2.204 3.120 nonbonded pdb=" OE1 GLU C 190 " pdb=" OH TYR D 220 " model vdw 2.209 3.040 nonbonded pdb=" N GLY J 123 " pdb=" OE1 GLU J 158 " model vdw 2.217 3.120 nonbonded pdb=" N GLY F 123 " pdb=" OE1 GLU F 158 " model vdw 2.219 3.120 ... (remaining 225691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 330) selection = (chain 'B' and resid 3 through 330) selection = chain 'C' selection = (chain 'D' and resid 3 through 330) selection = (chain 'E' and resid 3 through 330) selection = (chain 'F' and resid 3 through 330) selection = (chain 'G' and resid 3 through 330) selection = (chain 'H' and resid 3 through 330) selection = (chain 'I' and resid 3 through 330) selection = (chain 'J' and resid 3 through 330) selection = (chain 'K' and resid 3 through 330) selection = (chain 'L' and resid 3 through 330) } 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: 27.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.160 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 62.850 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 0.061 29244 Z= 0.427 Angle : 0.785 8.737 39360 Z= 0.423 Chirality : 0.056 0.163 4452 Planarity : 0.006 0.045 5076 Dihedral : 12.769 89.946 10836 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.14), residues: 3672 helix: 1.32 (0.11), residues: 2208 sheet: 1.60 (0.24), residues: 492 loop : 0.39 (0.22), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP E 328 HIS 0.011 0.002 HIS F 31 PHE 0.020 0.003 PHE I 288 TYR 0.021 0.003 TYR J 241 ARG 0.008 0.001 ARG G 38 Details of bonding type rmsd hydrogen bonds : bond 0.24326 ( 1701) hydrogen bonds : angle 6.06150 ( 4947) covalent geometry : bond 0.01050 (29244) covalent geometry : angle 0.78539 (39360) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 3.546 Fit side-chains revert: symmetry clash REVERT: A 31 HIS cc_start: 0.6524 (t-90) cc_final: 0.5918 (t-90) REVERT: A 35 MET cc_start: 0.7362 (mpp) cc_final: 0.6895 (mpt) REVERT: A 66 MET cc_start: 0.7447 (pmm) cc_final: 0.7148 (pmm) REVERT: A 128 MET cc_start: 0.8992 (ttp) cc_final: 0.8770 (ttp) REVERT: B 66 MET cc_start: 0.7511 (pmm) cc_final: 0.7296 (pmm) REVERT: B 224 MET cc_start: 0.8412 (mmp) cc_final: 0.8092 (mmp) REVERT: C 36 ASN cc_start: 0.8214 (m-40) cc_final: 0.7785 (m110) REVERT: C 188 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7880 (tp30) REVERT: C 224 MET cc_start: 0.8303 (mmp) cc_final: 0.8091 (mmp) REVERT: D 36 ASN cc_start: 0.8036 (m110) cc_final: 0.7770 (m-40) REVERT: E 36 ASN cc_start: 0.7946 (m110) cc_final: 0.7437 (m110) REVERT: F 36 ASN cc_start: 0.8203 (m110) cc_final: 0.7860 (m110) REVERT: H 36 ASN cc_start: 0.7749 (m110) cc_final: 0.7331 (m110) REVERT: H 66 MET cc_start: 0.7462 (pmm) cc_final: 0.7123 (pmm) REVERT: J 224 MET cc_start: 0.8357 (mmp) cc_final: 0.8068 (mmp) REVERT: J 247 ASP cc_start: 0.7571 (t70) cc_final: 0.7369 (t0) REVERT: K 66 MET cc_start: 0.7504 (pmm) cc_final: 0.7222 (pmm) REVERT: L 36 ASN cc_start: 0.7994 (m110) cc_final: 0.7607 (m110) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 1.5832 time to fit residues: 943.4076 Evaluate side-chains 441 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 10.0000 chunk 281 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 291 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 337 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN C 242 GLN F 242 GLN G 242 GLN H 31 HIS H 242 GLN I 242 GLN I 311 ASN J 242 GLN L 242 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.162976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120824 restraints weight = 33413.592| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.00 r_work: 0.3235 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29244 Z= 0.125 Angle : 0.489 7.731 39360 Z= 0.264 Chirality : 0.043 0.138 4452 Planarity : 0.004 0.036 5076 Dihedral : 4.615 77.399 4008 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.03 % Allowed : 7.51 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.14), residues: 3672 helix: 1.53 (0.11), residues: 2244 sheet: 1.64 (0.23), residues: 492 loop : 0.19 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 328 HIS 0.006 0.001 HIS F 31 PHE 0.011 0.001 PHE E 288 TYR 0.008 0.001 TYR D 115 ARG 0.003 0.000 ARG I 297 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 1701) hydrogen bonds : angle 4.35334 ( 4947) covalent geometry : bond 0.00295 (29244) covalent geometry : angle 0.48941 (39360) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 460 time to evaluate : 3.124 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.9045 (ttp) cc_final: 0.8818 (ttp) REVERT: B 35 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6547 (mpt) REVERT: B 66 MET cc_start: 0.7486 (pmm) cc_final: 0.6984 (pmm) REVERT: B 101 GLU cc_start: 0.7021 (mp0) cc_final: 0.6718 (mp0) REVERT: B 274 LYS cc_start: 0.8464 (mptt) cc_final: 0.8165 (mtmt) REVERT: C 36 ASN cc_start: 0.7621 (m-40) cc_final: 0.7233 (m110) REVERT: C 316 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8150 (mm-30) REVERT: D 35 MET cc_start: 0.6916 (mpt) cc_final: 0.6713 (mpt) REVERT: D 36 ASN cc_start: 0.7421 (m110) cc_final: 0.6928 (m110) REVERT: D 66 MET cc_start: 0.7104 (pmm) cc_final: 0.6866 (pmt) REVERT: D 79 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7382 (tpp) REVERT: E 36 ASN cc_start: 0.7735 (m110) cc_final: 0.7243 (m-40) REVERT: E 192 ASP cc_start: 0.8356 (t70) cc_final: 0.8039 (t0) REVERT: F 36 ASN cc_start: 0.7791 (m110) cc_final: 0.7436 (m110) REVERT: G 66 MET cc_start: 0.7450 (pmm) cc_final: 0.6998 (pmm) REVERT: G 192 ASP cc_start: 0.8315 (t70) cc_final: 0.7891 (t0) REVERT: H 31 HIS cc_start: 0.6864 (t-90) cc_final: 0.6477 (t70) REVERT: H 36 ASN cc_start: 0.7474 (m110) cc_final: 0.6870 (m110) REVERT: H 66 MET cc_start: 0.7418 (pmm) cc_final: 0.6958 (pmm) REVERT: I 66 MET cc_start: 0.7242 (pmm) cc_final: 0.7008 (pmt) REVERT: K 66 MET cc_start: 0.7565 (pmm) cc_final: 0.7159 (pmm) REVERT: L 36 ASN cc_start: 0.7610 (m110) cc_final: 0.7175 (m110) REVERT: L 325 MET cc_start: 0.5840 (OUTLIER) cc_final: 0.5060 (mpt) outliers start: 31 outliers final: 2 residues processed: 464 average time/residue: 1.6504 time to fit residues: 885.7674 Evaluate side-chains 454 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 449 time to evaluate : 4.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain L residue 325 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 357 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 339 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS F 242 GLN G 31 HIS G 242 GLN I 242 GLN L 242 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.163259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121130 restraints weight = 33471.096| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.03 r_work: 0.3202 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 29244 Z= 0.146 Angle : 0.499 9.123 39360 Z= 0.269 Chirality : 0.044 0.138 4452 Planarity : 0.003 0.035 5076 Dihedral : 4.393 64.608 4008 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.32 % Allowed : 9.42 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.14), residues: 3672 helix: 1.64 (0.11), residues: 2220 sheet: 1.60 (0.24), residues: 492 loop : 0.05 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 328 HIS 0.005 0.001 HIS A 31 PHE 0.012 0.002 PHE E 288 TYR 0.010 0.001 TYR D 115 ARG 0.002 0.000 ARG I 297 Details of bonding type rmsd hydrogen bonds : bond 0.04967 ( 1701) hydrogen bonds : angle 4.28221 ( 4947) covalent geometry : bond 0.00355 (29244) covalent geometry : angle 0.49942 (39360) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 451 time to evaluate : 3.024 Fit side-chains REVERT: A 128 MET cc_start: 0.9079 (ttp) cc_final: 0.8878 (ttp) REVERT: B 35 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6712 (mpt) REVERT: B 66 MET cc_start: 0.7564 (pmm) cc_final: 0.7096 (pmm) REVERT: B 274 LYS cc_start: 0.8510 (mptt) cc_final: 0.8194 (mtmt) REVERT: C 36 ASN cc_start: 0.7826 (m-40) cc_final: 0.7396 (m110) REVERT: C 271 GLU cc_start: 0.7865 (mp0) cc_final: 0.7565 (mt-10) REVERT: C 316 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8155 (mm-30) REVERT: D 36 ASN cc_start: 0.7517 (m110) cc_final: 0.7070 (m110) REVERT: D 66 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6381 (pmm) REVERT: D 79 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7501 (tpp) REVERT: D 180 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7438 (mp) REVERT: E 36 ASN cc_start: 0.7748 (m110) cc_final: 0.7226 (m-40) REVERT: E 128 MET cc_start: 0.9130 (ttm) cc_final: 0.8847 (ttp) REVERT: E 192 ASP cc_start: 0.8406 (t70) cc_final: 0.8067 (t0) REVERT: E 271 GLU cc_start: 0.7739 (mp0) cc_final: 0.7442 (mt-10) REVERT: F 36 ASN cc_start: 0.7880 (m110) cc_final: 0.7437 (m110) REVERT: G 35 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6705 (mpt) REVERT: G 66 MET cc_start: 0.7465 (pmm) cc_final: 0.6957 (pmm) REVERT: G 192 ASP cc_start: 0.8342 (t70) cc_final: 0.7953 (t0) REVERT: G 242 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7678 (mp-120) REVERT: G 250 TYR cc_start: 0.8027 (t80) cc_final: 0.7537 (m-10) REVERT: H 36 ASN cc_start: 0.7583 (m110) cc_final: 0.7095 (m110) REVERT: H 66 MET cc_start: 0.7461 (pmm) cc_final: 0.6881 (pmm) REVERT: H 271 GLU cc_start: 0.7938 (mp0) cc_final: 0.7619 (mt-10) REVERT: I 66 MET cc_start: 0.7277 (pmm) cc_final: 0.7066 (pmt) REVERT: I 266 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8583 (mttt) REVERT: J 48 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8360 (mt) REVERT: J 266 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8581 (mttt) REVERT: K 31 HIS cc_start: 0.6777 (t-90) cc_final: 0.6468 (m170) REVERT: K 84 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7282 (t70) REVERT: K 271 GLU cc_start: 0.7906 (mp0) cc_final: 0.7611 (mt-10) REVERT: L 36 ASN cc_start: 0.7675 (m110) cc_final: 0.7256 (m110) REVERT: L 325 MET cc_start: 0.5835 (OUTLIER) cc_final: 0.5024 (mpt) outliers start: 40 outliers final: 5 residues processed: 463 average time/residue: 1.8271 time to fit residues: 978.2779 Evaluate side-chains 458 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 442 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 242 GLN Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain L residue 325 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 10.0000 chunk 328 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 273 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 255 optimal weight: 0.0770 chunk 89 optimal weight: 0.8980 chunk 171 optimal weight: 0.0870 chunk 207 optimal weight: 3.9990 chunk 316 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 ASN B 242 GLN D 161 ASN F 242 GLN G 242 GLN I 242 GLN J 14 ASN J 242 GLN L 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.168124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126248 restraints weight = 33804.965| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.00 r_work: 0.3289 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29244 Z= 0.089 Angle : 0.432 8.167 39360 Z= 0.231 Chirality : 0.042 0.134 4452 Planarity : 0.003 0.033 5076 Dihedral : 4.062 52.255 4008 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.46 % Allowed : 9.99 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.14), residues: 3672 helix: 1.88 (0.11), residues: 2256 sheet: 1.68 (0.24), residues: 492 loop : 0.40 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 328 HIS 0.004 0.000 HIS F 31 PHE 0.008 0.001 PHE E 288 TYR 0.006 0.001 TYR K 115 ARG 0.002 0.000 ARG G 38 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 1701) hydrogen bonds : angle 4.09364 ( 4947) covalent geometry : bond 0.00197 (29244) covalent geometry : angle 0.43238 (39360) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 488 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7801 (mt-10) REVERT: B 66 MET cc_start: 0.7592 (pmm) cc_final: 0.7004 (pmm) REVERT: B 274 LYS cc_start: 0.8354 (mptt) cc_final: 0.8072 (mtmt) REVERT: C 36 ASN cc_start: 0.7707 (m-40) cc_final: 0.7118 (m110) REVERT: C 66 MET cc_start: 0.7113 (pmt) cc_final: 0.6758 (pmm) REVERT: C 250 TYR cc_start: 0.8058 (t80) cc_final: 0.7418 (m-10) REVERT: D 36 ASN cc_start: 0.7368 (m110) cc_final: 0.6814 (m110) REVERT: D 48 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8339 (mt) REVERT: D 66 MET cc_start: 0.7147 (pmm) cc_final: 0.6883 (pmt) REVERT: D 79 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7271 (tpp) REVERT: D 101 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6434 (mm-30) REVERT: D 180 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7388 (mp) REVERT: E 36 ASN cc_start: 0.7689 (m110) cc_final: 0.7206 (m-40) REVERT: E 128 MET cc_start: 0.9107 (ttm) cc_final: 0.8840 (ttp) REVERT: E 192 ASP cc_start: 0.8250 (t70) cc_final: 0.7912 (t0) REVERT: E 242 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7996 (mm-40) REVERT: F 36 ASN cc_start: 0.7715 (m110) cc_final: 0.7299 (m110) REVERT: F 192 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7805 (t0) REVERT: G 66 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.6950 (pmm) REVERT: G 76 ASP cc_start: 0.7415 (m-30) cc_final: 0.7084 (t0) REVERT: G 192 ASP cc_start: 0.8175 (t70) cc_final: 0.7808 (t0) REVERT: G 247 ASP cc_start: 0.7683 (t70) cc_final: 0.7206 (t0) REVERT: G 250 TYR cc_start: 0.7968 (t80) cc_final: 0.7460 (m-10) REVERT: H 35 MET cc_start: 0.6537 (mmm) cc_final: 0.6315 (mmm) REVERT: H 36 ASN cc_start: 0.7504 (m110) cc_final: 0.7004 (m110) REVERT: H 66 MET cc_start: 0.7513 (pmm) cc_final: 0.6875 (pmm) REVERT: I 266 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8489 (mttt) REVERT: J 48 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8436 (mt) REVERT: J 76 ASP cc_start: 0.7537 (m-30) cc_final: 0.7129 (t0) REVERT: K 31 HIS cc_start: 0.6667 (t-90) cc_final: 0.6346 (m170) REVERT: K 66 MET cc_start: 0.7411 (pmt) cc_final: 0.6745 (pmm) REVERT: L 36 ASN cc_start: 0.7536 (m110) cc_final: 0.7104 (m110) REVERT: L 101 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6243 (mm-30) REVERT: L 192 ASP cc_start: 0.8100 (t70) cc_final: 0.7815 (t0) REVERT: L 250 TYR cc_start: 0.8108 (t80) cc_final: 0.7582 (m-10) outliers start: 44 outliers final: 8 residues processed: 502 average time/residue: 1.4382 time to fit residues: 840.6267 Evaluate side-chains 453 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 436 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain L residue 101 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 313 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 350 optimal weight: 5.9990 chunk 233 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 293 optimal weight: 0.9990 chunk 314 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 327 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN B 161 ASN B 197 GLN B 242 GLN C 209 GLN D 161 ASN F 242 GLN H 242 GLN I 242 GLN J 242 GLN L 242 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.163008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121068 restraints weight = 33626.450| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.15 r_work: 0.3248 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29244 Z= 0.111 Angle : 0.464 8.458 39360 Z= 0.247 Chirality : 0.042 0.133 4452 Planarity : 0.003 0.034 5076 Dihedral : 4.035 49.095 4008 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.39 % Allowed : 10.68 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.14), residues: 3672 helix: 1.96 (0.11), residues: 2232 sheet: 1.67 (0.24), residues: 492 loop : 0.33 (0.22), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 328 HIS 0.005 0.001 HIS F 31 PHE 0.011 0.001 PHE E 288 TYR 0.008 0.001 TYR B 115 ARG 0.002 0.000 ARG F 249 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 1701) hydrogen bonds : angle 4.10127 ( 4947) covalent geometry : bond 0.00262 (29244) covalent geometry : angle 0.46386 (39360) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 441 time to evaluate : 3.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.7561 (pmm) cc_final: 0.7073 (pmm) REVERT: B 274 LYS cc_start: 0.8443 (mptt) cc_final: 0.8134 (mtmt) REVERT: C 36 ASN cc_start: 0.7682 (m-40) cc_final: 0.7181 (m110) REVERT: C 101 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6478 (mm-30) REVERT: D 36 ASN cc_start: 0.7361 (m110) cc_final: 0.6890 (m110) REVERT: D 48 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8310 (mt) REVERT: D 66 MET cc_start: 0.7140 (pmm) cc_final: 0.6388 (pmm) REVERT: D 79 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7407 (tpp) REVERT: D 101 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6446 (mm-30) REVERT: D 180 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7388 (mp) REVERT: D 192 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7791 (t0) REVERT: E 36 ASN cc_start: 0.7667 (m110) cc_final: 0.7159 (m-40) REVERT: E 128 MET cc_start: 0.9116 (ttm) cc_final: 0.8858 (ttp) REVERT: E 192 ASP cc_start: 0.8335 (t70) cc_final: 0.7996 (t0) REVERT: E 242 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8110 (mm110) REVERT: F 36 ASN cc_start: 0.7692 (m110) cc_final: 0.7263 (m110) REVERT: F 192 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7911 (t0) REVERT: G 31 HIS cc_start: 0.6877 (t70) cc_final: 0.6259 (t-90) REVERT: G 66 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6918 (pmm) REVERT: G 192 ASP cc_start: 0.8236 (t70) cc_final: 0.7833 (t0) REVERT: G 250 TYR cc_start: 0.7971 (t80) cc_final: 0.7425 (m-10) REVERT: H 35 MET cc_start: 0.6751 (mmm) cc_final: 0.6487 (mmm) REVERT: H 36 ASN cc_start: 0.7540 (m110) cc_final: 0.7048 (m110) REVERT: H 66 MET cc_start: 0.7469 (pmm) cc_final: 0.6807 (pmm) REVERT: I 266 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8576 (mttt) REVERT: J 48 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8406 (mt) REVERT: J 76 ASP cc_start: 0.7580 (m-30) cc_final: 0.7211 (t0) REVERT: J 266 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8542 (mttt) REVERT: K 84 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7194 (t70) REVERT: L 36 ASN cc_start: 0.7549 (m110) cc_final: 0.7128 (m110) REVERT: L 66 MET cc_start: 0.7193 (pmt) cc_final: 0.6922 (pmm) REVERT: L 122 LYS cc_start: 0.8286 (mmmt) cc_final: 0.7924 (tmtt) REVERT: L 192 ASP cc_start: 0.8178 (t70) cc_final: 0.7843 (t0) REVERT: L 250 TYR cc_start: 0.8112 (t80) cc_final: 0.7587 (m-10) outliers start: 42 outliers final: 8 residues processed: 458 average time/residue: 1.4525 time to fit residues: 775.5502 Evaluate side-chains 455 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 435 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 242 GLN Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 84 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 344 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 167 optimal weight: 6.9990 chunk 361 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN B 161 ASN B 197 GLN B 242 GLN D 161 ASN F 242 GLN G 242 GLN I 242 GLN J 242 GLN K 161 ASN L 242 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.159846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.118361 restraints weight = 33668.158| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.15 r_work: 0.3141 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 29244 Z= 0.241 Angle : 0.610 10.473 39360 Z= 0.321 Chirality : 0.047 0.144 4452 Planarity : 0.004 0.039 5076 Dihedral : 4.522 49.900 4008 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.59 % Allowed : 12.07 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.14), residues: 3672 helix: 1.50 (0.11), residues: 2220 sheet: 1.40 (0.24), residues: 492 loop : -0.03 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 328 HIS 0.006 0.001 HIS J 31 PHE 0.016 0.002 PHE E 288 TYR 0.015 0.002 TYR G 241 ARG 0.003 0.000 ARG E 323 Details of bonding type rmsd hydrogen bonds : bond 0.06191 ( 1701) hydrogen bonds : angle 4.35759 ( 4947) covalent geometry : bond 0.00608 (29244) covalent geometry : angle 0.60961 (39360) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 468 time to evaluate : 2.993 Fit side-chains REVERT: A 31 HIS cc_start: 0.6870 (t70) cc_final: 0.6007 (m170) REVERT: A 35 MET cc_start: 0.6633 (mmt) cc_final: 0.6291 (mmt) REVERT: A 66 MET cc_start: 0.7152 (pmt) cc_final: 0.6896 (pmm) REVERT: A 101 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6711 (mm-30) REVERT: B 35 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6635 (mpt) REVERT: B 66 MET cc_start: 0.7468 (pmm) cc_final: 0.7016 (pmm) REVERT: B 224 MET cc_start: 0.8898 (mmp) cc_final: 0.8535 (mmp) REVERT: B 271 GLU cc_start: 0.7805 (mp0) cc_final: 0.7572 (mt-10) REVERT: C 36 ASN cc_start: 0.7906 (m-40) cc_final: 0.7404 (m110) REVERT: C 38 ARG cc_start: 0.6214 (OUTLIER) cc_final: 0.5616 (ttm-80) REVERT: C 101 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6413 (mm-30) REVERT: D 36 ASN cc_start: 0.7510 (m110) cc_final: 0.7035 (m110) REVERT: D 66 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6405 (pmm) REVERT: D 79 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7522 (tpp) REVERT: D 101 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6442 (mm-30) REVERT: D 180 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7298 (mp) REVERT: D 271 GLU cc_start: 0.7857 (mp0) cc_final: 0.7589 (mt-10) REVERT: E 36 ASN cc_start: 0.7780 (m110) cc_final: 0.7279 (m-40) REVERT: E 38 ARG cc_start: 0.6293 (OUTLIER) cc_final: 0.4877 (ttm-80) REVERT: E 128 MET cc_start: 0.9209 (ttm) cc_final: 0.8921 (ttp) REVERT: E 192 ASP cc_start: 0.8487 (t70) cc_final: 0.8142 (t0) REVERT: E 271 GLU cc_start: 0.7848 (mp0) cc_final: 0.7574 (mt-10) REVERT: F 36 ASN cc_start: 0.7907 (m110) cc_final: 0.7482 (m110) REVERT: F 247 ASP cc_start: 0.7906 (t70) cc_final: 0.7512 (t70) REVERT: G 31 HIS cc_start: 0.6942 (t70) cc_final: 0.6338 (t-90) REVERT: G 66 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6704 (pmm) REVERT: G 192 ASP cc_start: 0.8425 (t70) cc_final: 0.8052 (t0) REVERT: H 35 MET cc_start: 0.6756 (mmm) cc_final: 0.6461 (mmm) REVERT: H 36 ASN cc_start: 0.7714 (m110) cc_final: 0.7189 (m110) REVERT: H 38 ARG cc_start: 0.6354 (OUTLIER) cc_final: 0.5950 (ttm-80) REVERT: H 66 MET cc_start: 0.7411 (pmm) cc_final: 0.6855 (pmm) REVERT: H 180 ILE cc_start: 0.7638 (mp) cc_final: 0.7412 (mp) REVERT: H 271 GLU cc_start: 0.7982 (mp0) cc_final: 0.7745 (mt-10) REVERT: I 247 ASP cc_start: 0.8042 (t70) cc_final: 0.7497 (t0) REVERT: I 266 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8679 (mttt) REVERT: J 48 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8336 (mt) REVERT: J 180 ILE cc_start: 0.7590 (mp) cc_final: 0.7387 (mp) REVERT: K 76 ASP cc_start: 0.7868 (t70) cc_final: 0.7440 (m-30) REVERT: K 247 ASP cc_start: 0.7988 (t70) cc_final: 0.7470 (t0) REVERT: K 271 GLU cc_start: 0.7937 (mp0) cc_final: 0.7661 (mt-10) REVERT: L 36 ASN cc_start: 0.7648 (m110) cc_final: 0.7237 (m110) REVERT: L 38 ARG cc_start: 0.6298 (OUTLIER) cc_final: 0.5414 (ttm-80) REVERT: L 101 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6129 (mm-30) REVERT: L 122 LYS cc_start: 0.8334 (mmmt) cc_final: 0.8011 (tmtt) REVERT: L 192 ASP cc_start: 0.8434 (t70) cc_final: 0.8056 (t0) REVERT: L 271 GLU cc_start: 0.7886 (mp0) cc_final: 0.7575 (mm-30) REVERT: L 281 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8409 (tptp) outliers start: 48 outliers final: 10 residues processed: 485 average time/residue: 1.3594 time to fit residues: 769.0143 Evaluate side-chains 452 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 426 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 242 GLN Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain L residue 281 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 308 optimal weight: 0.4980 chunk 146 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 330 optimal weight: 0.7980 chunk 349 optimal weight: 0.0870 chunk 244 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 312 optimal weight: 0.8980 chunk 344 optimal weight: 5.9990 chunk 313 optimal weight: 4.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 ASN B 242 GLN D 161 ASN F 242 GLN G 242 GLN H 242 GLN I 242 GLN J 14 ASN J 242 GLN K 242 GLN L 242 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.166900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125151 restraints weight = 33496.869| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.06 r_work: 0.3228 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29244 Z= 0.097 Angle : 0.472 9.655 39360 Z= 0.246 Chirality : 0.042 0.137 4452 Planarity : 0.003 0.035 5076 Dihedral : 4.086 50.900 4008 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.19 % Allowed : 12.93 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.14), residues: 3672 helix: 1.90 (0.11), residues: 2232 sheet: 1.49 (0.24), residues: 492 loop : 0.29 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 328 HIS 0.006 0.001 HIS F 31 PHE 0.009 0.001 PHE E 288 TYR 0.014 0.001 TYR G 241 ARG 0.002 0.000 ARG F 249 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 1701) hydrogen bonds : angle 4.11703 ( 4947) covalent geometry : bond 0.00218 (29244) covalent geometry : angle 0.47160 (39360) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 436 time to evaluate : 3.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.7578 (pmm) cc_final: 0.7020 (pmm) REVERT: B 274 LYS cc_start: 0.8407 (mptt) cc_final: 0.8081 (mtmt) REVERT: C 36 ASN cc_start: 0.7668 (m-40) cc_final: 0.7188 (m110) REVERT: C 101 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6386 (mm-30) REVERT: D 36 ASN cc_start: 0.7352 (m110) cc_final: 0.6870 (m110) REVERT: D 48 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8322 (mt) REVERT: D 66 MET cc_start: 0.7150 (pmm) cc_final: 0.6419 (pmm) REVERT: D 101 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6377 (mm-30) REVERT: E 36 ASN cc_start: 0.7647 (m110) cc_final: 0.7125 (m-40) REVERT: E 128 MET cc_start: 0.9129 (ttm) cc_final: 0.8873 (ttp) REVERT: E 192 ASP cc_start: 0.8298 (t70) cc_final: 0.7931 (t0) REVERT: F 36 ASN cc_start: 0.7747 (m110) cc_final: 0.7308 (m110) REVERT: G 66 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6814 (pmm) REVERT: G 192 ASP cc_start: 0.8178 (t70) cc_final: 0.7766 (t0) REVERT: G 250 TYR cc_start: 0.7883 (t80) cc_final: 0.7404 (m-10) REVERT: H 35 MET cc_start: 0.6699 (mmm) cc_final: 0.6468 (mmm) REVERT: H 36 ASN cc_start: 0.7546 (m110) cc_final: 0.6999 (m110) REVERT: H 66 MET cc_start: 0.7532 (pmm) cc_final: 0.6853 (pmm) REVERT: I 35 MET cc_start: 0.6842 (mmt) cc_final: 0.6431 (mpt) REVERT: I 266 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8527 (mttt) REVERT: J 48 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8326 (mp) REVERT: J 180 ILE cc_start: 0.7555 (mp) cc_final: 0.7354 (mp) REVERT: K 31 HIS cc_start: 0.6402 (OUTLIER) cc_final: 0.6038 (m-70) REVERT: K 66 MET cc_start: 0.7269 (pmt) cc_final: 0.6744 (pmm) REVERT: L 36 ASN cc_start: 0.7475 (m110) cc_final: 0.7022 (m110) REVERT: L 66 MET cc_start: 0.7210 (pmt) cc_final: 0.6933 (pmm) REVERT: L 101 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6024 (mm-30) REVERT: L 122 LYS cc_start: 0.8299 (mmmt) cc_final: 0.7958 (tmtt) REVERT: L 192 ASP cc_start: 0.8139 (t70) cc_final: 0.7790 (t0) REVERT: L 250 TYR cc_start: 0.8147 (t80) cc_final: 0.7601 (m-10) outliers start: 36 outliers final: 13 residues processed: 451 average time/residue: 1.5354 time to fit residues: 803.7363 Evaluate side-chains 463 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 442 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 242 GLN Chi-restraints excluded: chain I residue 242 GLN Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 242 GLN Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain L residue 242 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 361 optimal weight: 0.8980 chunk 268 optimal weight: 3.9990 chunk 360 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 303 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 237 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 161 ASN B 197 GLN D 161 ASN F 242 GLN G 242 GLN H 242 GLN I 242 GLN J 242 GLN K 242 GLN L 242 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.166156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.124910 restraints weight = 33808.643| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.19 r_work: 0.3261 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29244 Z= 0.101 Angle : 0.479 9.101 39360 Z= 0.250 Chirality : 0.042 0.147 4452 Planarity : 0.003 0.033 5076 Dihedral : 4.014 50.974 4008 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.86 % Allowed : 13.33 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.14), residues: 3672 helix: 2.02 (0.11), residues: 2232 sheet: 1.54 (0.24), residues: 492 loop : 0.38 (0.22), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 328 HIS 0.007 0.001 HIS L 31 PHE 0.009 0.001 PHE E 288 TYR 0.011 0.001 TYR L 241 ARG 0.002 0.000 ARG F 249 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 1701) hydrogen bonds : angle 4.08635 ( 4947) covalent geometry : bond 0.00229 (29244) covalent geometry : angle 0.47888 (39360) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 457 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.7577 (pmm) cc_final: 0.7016 (pmm) REVERT: B 274 LYS cc_start: 0.8420 (mptt) cc_final: 0.8087 (mtmt) REVERT: C 36 ASN cc_start: 0.7666 (m-40) cc_final: 0.7167 (m110) REVERT: C 101 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6403 (mm-30) REVERT: D 36 ASN cc_start: 0.7355 (m110) cc_final: 0.6887 (m110) REVERT: D 48 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8316 (mt) REVERT: D 66 MET cc_start: 0.7130 (pmm) cc_final: 0.6399 (pmm) REVERT: D 101 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6398 (mm-30) REVERT: E 36 ASN cc_start: 0.7614 (m110) cc_final: 0.7133 (m-40) REVERT: E 128 MET cc_start: 0.9152 (ttm) cc_final: 0.8898 (ttp) REVERT: E 192 ASP cc_start: 0.8306 (t70) cc_final: 0.7944 (t0) REVERT: F 36 ASN cc_start: 0.7855 (m110) cc_final: 0.7400 (m110) REVERT: F 192 ASP cc_start: 0.8284 (t70) cc_final: 0.8024 (t0) REVERT: G 66 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6811 (pmm) REVERT: G 76 ASP cc_start: 0.7505 (m-30) cc_final: 0.7189 (t0) REVERT: G 192 ASP cc_start: 0.8200 (t70) cc_final: 0.7794 (t0) REVERT: G 247 ASP cc_start: 0.7649 (t70) cc_final: 0.7162 (t0) REVERT: G 250 TYR cc_start: 0.7911 (t80) cc_final: 0.7399 (m-10) REVERT: H 35 MET cc_start: 0.6681 (mmm) cc_final: 0.6453 (mmm) REVERT: H 36 ASN cc_start: 0.7581 (m110) cc_final: 0.7076 (m110) REVERT: H 66 MET cc_start: 0.7515 (pmm) cc_final: 0.6831 (pmm) REVERT: I 266 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8517 (mttt) REVERT: J 48 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8273 (mp) REVERT: J 180 ILE cc_start: 0.7505 (mp) cc_final: 0.7282 (mp) REVERT: K 31 HIS cc_start: 0.6032 (OUTLIER) cc_final: 0.5495 (m-70) REVERT: K 35 MET cc_start: 0.6851 (mpt) cc_final: 0.6507 (mpt) REVERT: K 66 MET cc_start: 0.7244 (pmt) cc_final: 0.6716 (pmm) REVERT: L 36 ASN cc_start: 0.7511 (m110) cc_final: 0.7074 (m110) REVERT: L 66 MET cc_start: 0.7207 (pmt) cc_final: 0.6887 (pmm) REVERT: L 101 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6011 (mm-30) REVERT: L 128 MET cc_start: 0.8959 (ttp) cc_final: 0.8699 (ttm) REVERT: L 192 ASP cc_start: 0.8138 (t70) cc_final: 0.7785 (t0) REVERT: L 250 TYR cc_start: 0.8159 (t80) cc_final: 0.7565 (m-10) outliers start: 26 outliers final: 12 residues processed: 468 average time/residue: 1.5255 time to fit residues: 826.5666 Evaluate side-chains 455 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 435 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 242 GLN Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 266 LYS Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain L residue 242 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 340 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 chunk 358 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 161 ASN B 197 GLN B 242 GLN C 209 GLN D 161 ASN F 242 GLN G 242 GLN H 242 GLN I 242 GLN J 242 GLN L 242 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.161027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118806 restraints weight = 33680.787| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.96 r_work: 0.3183 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 29244 Z= 0.210 Angle : 0.599 9.492 39360 Z= 0.313 Chirality : 0.046 0.149 4452 Planarity : 0.004 0.039 5076 Dihedral : 4.405 47.578 4008 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.06 % Allowed : 13.69 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.14), residues: 3672 helix: 1.63 (0.11), residues: 2220 sheet: 1.33 (0.24), residues: 492 loop : 0.06 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 328 HIS 0.009 0.001 HIS L 31 PHE 0.016 0.002 PHE I 288 TYR 0.028 0.002 TYR A 241 ARG 0.005 0.000 ARG I 297 Details of bonding type rmsd hydrogen bonds : bond 0.05741 ( 1701) hydrogen bonds : angle 4.28654 ( 4947) covalent geometry : bond 0.00526 (29244) covalent geometry : angle 0.59946 (39360) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 442 time to evaluate : 3.136 Fit side-chains revert: symmetry clash REVERT: B 35 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.5971 (mpt) REVERT: B 66 MET cc_start: 0.7528 (pmm) cc_final: 0.7071 (pmm) REVERT: B 271 GLU cc_start: 0.7813 (mp0) cc_final: 0.7608 (mm-30) REVERT: C 36 ASN cc_start: 0.7915 (m-40) cc_final: 0.7448 (m110) REVERT: C 101 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6438 (mm-30) REVERT: C 271 GLU cc_start: 0.7886 (mp0) cc_final: 0.7678 (mt-10) REVERT: D 36 ASN cc_start: 0.7583 (m110) cc_final: 0.7146 (m110) REVERT: D 66 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6459 (pmm) REVERT: D 101 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6374 (mm-30) REVERT: D 271 GLU cc_start: 0.7828 (mp0) cc_final: 0.7588 (mt-10) REVERT: E 36 ASN cc_start: 0.7752 (m110) cc_final: 0.7250 (m-40) REVERT: E 128 MET cc_start: 0.9189 (ttm) cc_final: 0.8892 (ttp) REVERT: E 192 ASP cc_start: 0.8457 (t70) cc_final: 0.8147 (t0) REVERT: E 271 GLU cc_start: 0.7835 (mp0) cc_final: 0.7589 (mt-10) REVERT: F 36 ASN cc_start: 0.7970 (m110) cc_final: 0.7562 (m110) REVERT: F 192 ASP cc_start: 0.8399 (t70) cc_final: 0.8180 (t0) REVERT: F 247 ASP cc_start: 0.7908 (t70) cc_final: 0.7535 (t70) REVERT: G 66 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6808 (pmm) REVERT: G 192 ASP cc_start: 0.8411 (t70) cc_final: 0.8053 (t0) REVERT: H 35 MET cc_start: 0.6786 (mmm) cc_final: 0.6581 (mmm) REVERT: H 36 ASN cc_start: 0.7742 (m110) cc_final: 0.7252 (m110) REVERT: H 66 MET cc_start: 0.7465 (pmm) cc_final: 0.6841 (pmm) REVERT: I 35 MET cc_start: 0.6989 (mmt) cc_final: 0.6567 (mpt) REVERT: I 266 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8678 (mttt) REVERT: J 48 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8355 (mt) REVERT: J 180 ILE cc_start: 0.7631 (mp) cc_final: 0.7415 (mp) REVERT: J 281 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8134 (tttp) REVERT: K 31 HIS cc_start: 0.6104 (OUTLIER) cc_final: 0.5551 (m-70) REVERT: K 35 MET cc_start: 0.6898 (mpt) cc_final: 0.6637 (mpt) REVERT: K 76 ASP cc_start: 0.7783 (t70) cc_final: 0.7428 (m-30) REVERT: K 271 GLU cc_start: 0.7996 (mp0) cc_final: 0.7755 (mt-10) REVERT: L 36 ASN cc_start: 0.7665 (m110) cc_final: 0.7272 (m110) REVERT: L 101 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6099 (mm-30) REVERT: L 122 LYS cc_start: 0.8401 (mptp) cc_final: 0.8048 (tmtt) REVERT: L 192 ASP cc_start: 0.8346 (t70) cc_final: 0.8005 (t0) REVERT: L 271 GLU cc_start: 0.7893 (mp0) cc_final: 0.7597 (mm-30) outliers start: 32 outliers final: 10 residues processed: 457 average time/residue: 1.4352 time to fit residues: 762.2281 Evaluate side-chains 450 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 430 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 242 GLN Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 281 LYS Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain L residue 101 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 346 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 225 optimal weight: 0.6980 chunk 198 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 364 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 308 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 161 ASN B 242 GLN C 209 GLN D 161 ASN F 242 GLN G 242 GLN I 242 GLN J 242 GLN L 242 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.162025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120268 restraints weight = 33656.319| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.92 r_work: 0.3249 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29244 Z= 0.118 Angle : 0.512 9.484 39360 Z= 0.268 Chirality : 0.043 0.138 4452 Planarity : 0.003 0.035 5076 Dihedral : 4.214 52.356 4008 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.79 % Allowed : 13.99 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.14), residues: 3672 helix: 1.82 (0.11), residues: 2232 sheet: 1.38 (0.24), residues: 492 loop : 0.28 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 328 HIS 0.008 0.001 HIS F 31 PHE 0.010 0.001 PHE E 288 TYR 0.017 0.001 TYR A 241 ARG 0.004 0.000 ARG I 297 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 1701) hydrogen bonds : angle 4.16208 ( 4947) covalent geometry : bond 0.00278 (29244) covalent geometry : angle 0.51249 (39360) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 453 time to evaluate : 3.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.7533 (pmm) cc_final: 0.6983 (pmm) REVERT: B 274 LYS cc_start: 0.8400 (mptt) cc_final: 0.8061 (mtmt) REVERT: C 36 ASN cc_start: 0.7674 (m-40) cc_final: 0.7177 (m110) REVERT: C 101 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6416 (mm-30) REVERT: D 36 ASN cc_start: 0.7375 (m110) cc_final: 0.6883 (m110) REVERT: D 48 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8276 (mt) REVERT: D 66 MET cc_start: 0.7122 (pmm) cc_final: 0.6878 (pmt) REVERT: D 101 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6386 (mm-30) REVERT: E 36 ASN cc_start: 0.7664 (m110) cc_final: 0.7140 (m-40) REVERT: E 101 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6394 (mp0) REVERT: E 128 MET cc_start: 0.9174 (ttm) cc_final: 0.8903 (ttp) REVERT: E 192 ASP cc_start: 0.8307 (t70) cc_final: 0.7950 (t0) REVERT: F 36 ASN cc_start: 0.7878 (m110) cc_final: 0.7429 (m110) REVERT: F 192 ASP cc_start: 0.8284 (t70) cc_final: 0.8045 (t0) REVERT: G 66 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6705 (pmm) REVERT: G 192 ASP cc_start: 0.8203 (t70) cc_final: 0.7789 (t0) REVERT: G 247 ASP cc_start: 0.7657 (t70) cc_final: 0.7172 (t0) REVERT: G 250 TYR cc_start: 0.7903 (t80) cc_final: 0.7372 (m-10) REVERT: H 36 ASN cc_start: 0.7583 (m110) cc_final: 0.7053 (m110) REVERT: H 66 MET cc_start: 0.7495 (pmm) cc_final: 0.6837 (pmm) REVERT: H 180 ILE cc_start: 0.7543 (mp) cc_final: 0.7322 (mp) REVERT: I 247 ASP cc_start: 0.7821 (t70) cc_final: 0.7327 (t0) REVERT: I 266 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8563 (mttp) REVERT: J 48 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8352 (mt) REVERT: K 31 HIS cc_start: 0.6080 (OUTLIER) cc_final: 0.5710 (m-70) REVERT: K 76 ASP cc_start: 0.7713 (t70) cc_final: 0.7112 (t0) REVERT: L 36 ASN cc_start: 0.7531 (m110) cc_final: 0.7118 (m110) REVERT: L 66 MET cc_start: 0.7242 (pmt) cc_final: 0.6897 (pmm) REVERT: L 101 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6110 (mm-30) REVERT: L 122 LYS cc_start: 0.8385 (mptp) cc_final: 0.7979 (tmtt) REVERT: L 192 ASP cc_start: 0.8205 (t70) cc_final: 0.7810 (t0) REVERT: L 250 TYR cc_start: 0.8101 (t80) cc_final: 0.7466 (m-10) outliers start: 24 outliers final: 6 residues processed: 463 average time/residue: 1.5453 time to fit residues: 833.2102 Evaluate side-chains 434 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 419 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain I residue 266 LYS Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain L residue 101 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 271 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 161 ASN B 242 GLN D 161 ASN G 242 GLN I 242 GLN J 242 GLN L 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.162120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120443 restraints weight = 33588.530| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.87 r_work: 0.3201 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 29244 Z= 0.185 Angle : 0.587 9.611 39360 Z= 0.306 Chirality : 0.045 0.185 4452 Planarity : 0.004 0.038 5076 Dihedral : 4.372 48.640 4008 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.99 % Allowed : 14.09 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.14), residues: 3672 helix: 1.65 (0.11), residues: 2220 sheet: 1.23 (0.24), residues: 492 loop : 0.08 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 328 HIS 0.008 0.001 HIS L 31 PHE 0.014 0.002 PHE E 288 TYR 0.012 0.002 TYR G 241 ARG 0.004 0.000 ARG I 297 Details of bonding type rmsd hydrogen bonds : bond 0.05322 ( 1701) hydrogen bonds : angle 4.27344 ( 4947) covalent geometry : bond 0.00460 (29244) covalent geometry : angle 0.58711 (39360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22747.50 seconds wall clock time: 392 minutes 19.74 seconds (23539.74 seconds total)