Starting phenix.real_space_refine on Mon Jul 6 01:20:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xnl_33318/07_2026/7xnl_33318_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnl_33318/07_2026/7xnl_33318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xnl_33318/07_2026/7xnl_33318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnl_33318/07_2026/7xnl_33318.map" model { file = "/net/cci-nas-00/data/ceres_data/7xnl_33318/07_2026/7xnl_33318_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnl_33318/07_2026/7xnl_33318_neut_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 12 5.49 5 S 88 5.16 5 C 10324 2.51 5 N 2700 2.21 5 O 2908 1.98 5 H 15652 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31688 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5712 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 2 Chain: "B" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5712 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 2 Chain: "D" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5712 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 2 Chain: "F" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5712 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 2 Chain: "H" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 32 Ad-hoc single atom residues: {' K': 4} Classifications: {'peptide': 1} Chain breaks: 4 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Classifications: {'peptide': 1} Chain: "F" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Classifications: {'peptide': 1} Chain: "H" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.49, per 1000 atoms: 0.17 Number of scatterers: 31688 At special positions: 0 Unit cell: (114.582, 114.582, 121.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 88 16.00 P 12 15.00 O 2908 8.00 N 2700 7.00 C 10324 6.00 H 15652 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 684.6 milliseconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB I0S A 705 " pdb=" CB I0S C 701 " pdb=" CB I0S E 701 " pdb=" CB I0S G 701 " Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 80.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 104 through 115 removed outlier: 4.167A pdb=" N GLY A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 143 Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 148 through 178 removed outlier: 3.589A pdb=" N THR A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TRP A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 186 through 194 Processing helix chain 'A' and resid 196 through 217 Processing helix chain 'A' and resid 224 through 237 removed outlier: 4.388A pdb=" N PHE A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 Processing helix chain 'A' and resid 245 through 258 Processing helix chain 'A' and resid 258 through 285 Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 322 through 336 Processing helix chain 'A' and resid 337 through 340 Processing helix chain 'A' and resid 341 through 361 removed outlier: 3.990A pdb=" N GLY A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 386 removed outlier: 3.808A pdb=" N GLU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASN A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.906A pdb=" N TRP A 392 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 395 " --> pdb=" O TRP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 533 removed outlier: 3.892A pdb=" N THR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 563 removed outlier: 3.771A pdb=" N VAL A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 22 removed outlier: 3.703A pdb=" N PHE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 removed outlier: 4.253A pdb=" N VAL B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.939A pdb=" N GLU B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.591A pdb=" N ARG B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 147 Processing helix chain 'C' and resid 105 through 115 Processing helix chain 'C' and resid 120 through 143 Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 148 through 178 removed outlier: 3.590A pdb=" N THR C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 161 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 186 through 194 Processing helix chain 'C' and resid 196 through 217 Processing helix chain 'C' and resid 224 through 237 removed outlier: 4.389A pdb=" N PHE C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 241 Processing helix chain 'C' and resid 245 through 258 Processing helix chain 'C' and resid 258 through 285 Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 322 through 336 Processing helix chain 'C' and resid 337 through 340 Processing helix chain 'C' and resid 341 through 361 removed outlier: 3.990A pdb=" N GLY C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 386 removed outlier: 3.808A pdb=" N GLU C 385 " --> pdb=" O CYS C 381 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN C 386 " --> pdb=" O TYR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 395 removed outlier: 3.905A pdb=" N TRP C 392 " --> pdb=" O SER C 389 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR C 395 " --> pdb=" O TRP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 533 removed outlier: 3.892A pdb=" N THR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 563 removed outlier: 3.771A pdb=" N VAL C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 22 removed outlier: 3.703A pdb=" N PHE D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 40 removed outlier: 4.253A pdb=" N VAL D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 65 through 75 Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.939A pdb=" N GLU D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 118 through 129 removed outlier: 3.591A pdb=" N ARG D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 147 Processing helix chain 'E' and resid 105 through 115 Processing helix chain 'E' and resid 120 through 143 Processing helix chain 'E' and resid 145 through 147 No H-bonds generated for 'chain 'E' and resid 145 through 147' Processing helix chain 'E' and resid 148 through 178 removed outlier: 3.589A pdb=" N THR E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TRP E 158 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE E 161 " --> pdb=" O PHE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 186 through 194 Processing helix chain 'E' and resid 196 through 217 Processing helix chain 'E' and resid 224 through 237 removed outlier: 4.389A pdb=" N PHE E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 241 Processing helix chain 'E' and resid 245 through 258 Processing helix chain 'E' and resid 258 through 285 Processing helix chain 'E' and resid 298 through 311 Processing helix chain 'E' and resid 322 through 336 Processing helix chain 'E' and resid 337 through 340 Processing helix chain 'E' and resid 341 through 361 removed outlier: 3.990A pdb=" N GLY E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 386 removed outlier: 3.808A pdb=" N GLU E 385 " --> pdb=" O CYS E 381 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASN E 386 " --> pdb=" O TYR E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 395 removed outlier: 3.905A pdb=" N TRP E 392 " --> pdb=" O SER E 389 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR E 395 " --> pdb=" O TRP E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 533 removed outlier: 3.891A pdb=" N THR E 513 " --> pdb=" O HIS E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 563 removed outlier: 3.770A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 22 removed outlier: 3.703A pdb=" N PHE F 20 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 40 removed outlier: 4.253A pdb=" N VAL F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU F 40 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 79 through 91 removed outlier: 3.939A pdb=" N GLU F 84 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG F 91 " --> pdb=" O ARG F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 118 through 129 removed outlier: 3.591A pdb=" N ARG F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'G' and resid 105 through 115 Processing helix chain 'G' and resid 120 through 143 Processing helix chain 'G' and resid 145 through 147 No H-bonds generated for 'chain 'G' and resid 145 through 147' Processing helix chain 'G' and resid 148 through 178 removed outlier: 3.590A pdb=" N THR G 153 " --> pdb=" O ALA G 149 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE G 157 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE G 161 " --> pdb=" O PHE G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 186 through 194 Processing helix chain 'G' and resid 196 through 217 Processing helix chain 'G' and resid 224 through 237 removed outlier: 4.389A pdb=" N PHE G 232 " --> pdb=" O ARG G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 241 Processing helix chain 'G' and resid 245 through 258 Processing helix chain 'G' and resid 258 through 285 Processing helix chain 'G' and resid 298 through 311 Processing helix chain 'G' and resid 322 through 336 Processing helix chain 'G' and resid 337 through 340 Processing helix chain 'G' and resid 341 through 361 removed outlier: 3.990A pdb=" N GLY G 345 " --> pdb=" O ALA G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 386 removed outlier: 3.808A pdb=" N GLU G 385 " --> pdb=" O CYS G 381 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN G 386 " --> pdb=" O TYR G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 395 removed outlier: 3.906A pdb=" N TRP G 392 " --> pdb=" O SER G 389 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR G 395 " --> pdb=" O TRP G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 509 through 533 removed outlier: 3.891A pdb=" N THR G 513 " --> pdb=" O HIS G 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 563 removed outlier: 3.772A pdb=" N VAL G 541 " --> pdb=" O ASP G 537 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 22 removed outlier: 3.703A pdb=" N PHE H 20 " --> pdb=" O ALA H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 4.253A pdb=" N VAL H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 79 through 91 removed outlier: 3.939A pdb=" N GLU H 84 " --> pdb=" O THR H 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 94 No H-bonds generated for 'chain 'H' and resid 92 through 94' Processing helix chain 'H' and resid 103 through 113 Processing helix chain 'H' and resid 118 through 129 removed outlier: 3.591A pdb=" N ARG H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA H 129 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 147 Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 102 1080 hydrogen bonds defined for protein. 3192 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: 7.01 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15628 1.03 - 1.22: 36 1.22 - 1.42: 7000 1.42 - 1.61: 9200 1.61 - 1.81: 160 Bond restraints: 32024 Sorted by residual: bond pdb=" CAT I0S G 701 " pdb=" SBF I0S G 701 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CAT I0S A 705 " pdb=" SBF I0S A 705 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CAT I0S E 701 " pdb=" SBF I0S E 701 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CAT I0S C 701 " pdb=" SBF I0S C 701 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CBE I0S E 701 " pdb=" SBF I0S E 701 " ideal model delta sigma weight residual 1.717 1.584 0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 32019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 57034 3.17 - 6.34: 438 6.34 - 9.51: 40 9.51 - 12.68: 12 12.68 - 15.85: 8 Bond angle restraints: 57532 Sorted by residual: angle pdb=" OAQ I0S E 701 " pdb=" SAI I0S E 701 " pdb=" OAR I0S E 701 " ideal model delta sigma weight residual 119.45 103.60 15.85 3.00e+00 1.11e-01 2.79e+01 angle pdb=" OAQ I0S C 701 " pdb=" SAI I0S C 701 " pdb=" OAR I0S C 701 " ideal model delta sigma weight residual 119.45 103.61 15.84 3.00e+00 1.11e-01 2.79e+01 angle pdb=" OAQ I0S A 705 " pdb=" SAI I0S A 705 " pdb=" OAR I0S A 705 " ideal model delta sigma weight residual 119.45 103.62 15.83 3.00e+00 1.11e-01 2.79e+01 angle pdb=" OAQ I0S G 701 " pdb=" SAI I0S G 701 " pdb=" OAR I0S G 701 " ideal model delta sigma weight residual 119.45 103.62 15.83 3.00e+00 1.11e-01 2.79e+01 angle pdb=" CA I0S G 701 " pdb=" N I0S G 701 " pdb=" CAG I0S G 701 " ideal model delta sigma weight residual 121.42 107.76 13.66 3.00e+00 1.11e-01 2.07e+01 ... (remaining 57527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.18: 14640 34.18 - 68.36: 288 68.36 - 102.55: 24 102.55 - 136.73: 4 136.73 - 170.91: 8 Dihedral angle restraints: 14964 sinusoidal: 8048 harmonic: 6916 Sorted by residual: dihedral pdb=" CBB I0S E 701 " pdb=" CAZ I0S E 701 " pdb=" OBA I0S E 701 " pdb=" CBC I0S E 701 " ideal model delta sinusoidal sigma weight residual -1.02 -171.93 170.91 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CBB I0S A 705 " pdb=" CAZ I0S A 705 " pdb=" OBA I0S A 705 " pdb=" CBC I0S A 705 " ideal model delta sinusoidal sigma weight residual -1.02 -171.92 170.90 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CBB I0S G 701 " pdb=" CAZ I0S G 701 " pdb=" OBA I0S G 701 " pdb=" CBC I0S G 701 " ideal model delta sinusoidal sigma weight residual -1.02 -171.91 170.89 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 14961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1884 0.062 - 0.124: 474 0.124 - 0.186: 86 0.186 - 0.248: 12 0.248 - 0.310: 4 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CB VAL E 308 " pdb=" CA VAL E 308 " pdb=" CG1 VAL E 308 " pdb=" CG2 VAL E 308 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB VAL A 308 " pdb=" CA VAL A 308 " pdb=" CG1 VAL A 308 " pdb=" CG2 VAL A 308 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CB VAL G 308 " pdb=" CA VAL G 308 " pdb=" CG1 VAL G 308 " pdb=" CG2 VAL G 308 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 2457 not shown) Planarity restraints: 4672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 174 " -0.009 9.50e-02 1.11e+02 1.92e-02 8.10e+00 pdb=" NE ARG G 174 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG G 174 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG G 174 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 174 " -0.006 2.00e-02 2.50e+03 pdb="HH11 ARG G 174 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG G 174 " -0.020 2.00e-02 2.50e+03 pdb="HH21 ARG G 174 " -0.032 2.00e-02 2.50e+03 pdb="HH22 ARG G 174 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 174 " 0.010 9.50e-02 1.11e+02 1.91e-02 8.01e+00 pdb=" NE ARG C 174 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 174 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 174 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 174 " 0.006 2.00e-02 2.50e+03 pdb="HH11 ARG C 174 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG C 174 " 0.020 2.00e-02 2.50e+03 pdb="HH21 ARG C 174 " 0.031 2.00e-02 2.50e+03 pdb="HH22 ARG C 174 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 174 " 0.010 9.50e-02 1.11e+02 1.91e-02 7.95e+00 pdb=" NE ARG A 174 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 174 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 174 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 174 " 0.006 2.00e-02 2.50e+03 pdb="HH11 ARG A 174 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 174 " 0.020 2.00e-02 2.50e+03 pdb="HH21 ARG A 174 " 0.031 2.00e-02 2.50e+03 pdb="HH22 ARG A 174 " -0.039 2.00e-02 2.50e+03 ... (remaining 4669 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.39: 13691 2.39 - 3.08: 88976 3.08 - 3.76: 106110 3.76 - 4.45: 167068 4.45 - 5.14: 254732 Nonbonded interactions: 630577 Sorted by model distance: nonbonded pdb=" OD1 ASP C 564 " pdb="HH21 ARG E 562 " model vdw 1.700 2.450 nonbonded pdb="HH12 ARG H 107 " pdb=" OD1 ASP H 123 " model vdw 1.720 2.450 nonbonded pdb="HH12 ARG D 107 " pdb=" OD1 ASP D 123 " model vdw 1.720 2.450 nonbonded pdb="HH12 ARG F 107 " pdb=" OD1 ASP F 123 " model vdw 1.720 2.450 nonbonded pdb="HH12 ARG B 107 " pdb=" OD1 ASP B 123 " model vdw 1.720 2.450 ... (remaining 630572 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 104 through 564) selection = (chain 'C' and resid 104 through 564) selection = (chain 'E' and resid 104 through 564) selection = (chain 'G' and resid 104 through 564) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 0.880 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.210 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.860 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.014 0.133 16372 Z= 0.610 Angle : 1.058 15.849 22140 Z= 0.549 Chirality : 0.057 0.310 2460 Planarity : 0.005 0.053 2756 Dihedral : 13.022 170.912 5956 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.16), residues: 1936 helix: -1.28 (0.11), residues: 1488 sheet: None (None), residues: 0 loop : -1.62 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 243 TYR 0.025 0.003 TYR A 299 PHE 0.023 0.003 PHE A 332 TRP 0.023 0.003 TRP E 379 HIS 0.006 0.002 HIS C 126 Details of bonding type rmsd/Z covalent geometry : bond 0.01417 / 0.61 (16372) covalent geometry : angle 1.05833 / 0.55 (22140) hydrogen bonds : bond 0.13793 / 9.16 ( 1080) hydrogen bonds : angle 5.53397 / 4.06 ( 3192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 658 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 658 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 VAL cc_start: 0.9067 (p) cc_final: 0.8434 (p) REVERT: A 519 ARG cc_start: 0.8604 (ttm-80) cc_final: 0.8385 (ttt90) REVERT: B 29 THR cc_start: 0.7227 (m) cc_final: 0.7019 (p) REVERT: B 113 LEU cc_start: 0.7854 (mt) cc_final: 0.7392 (tp) REVERT: B 145 MET cc_start: 0.7921 (ttp) cc_final: 0.7303 (tmm) REVERT: C 133 VAL cc_start: 0.9038 (p) cc_final: 0.8557 (p) REVERT: C 519 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8403 (ttt90) REVERT: C 547 GLN cc_start: 0.8588 (mt0) cc_final: 0.7788 (mt0) REVERT: C 562 ARG cc_start: 0.6759 (tpt170) cc_final: 0.6544 (tpt90) REVERT: D 29 THR cc_start: 0.7214 (m) cc_final: 0.7007 (p) REVERT: D 100 TYR cc_start: 0.8659 (m-80) cc_final: 0.8454 (m-10) REVERT: D 113 LEU cc_start: 0.7846 (mt) cc_final: 0.7395 (tp) REVERT: D 145 MET cc_start: 0.7933 (ttp) cc_final: 0.7303 (tmm) REVERT: E 133 VAL cc_start: 0.9086 (p) cc_final: 0.8560 (m) REVERT: E 519 ARG cc_start: 0.8617 (ttm-80) cc_final: 0.8384 (ttt90) REVERT: F 29 THR cc_start: 0.7234 (m) cc_final: 0.7028 (p) REVERT: F 100 TYR cc_start: 0.8649 (m-80) cc_final: 0.8395 (m-10) REVERT: F 108 HIS cc_start: 0.8373 (t-90) cc_final: 0.7965 (t-90) REVERT: F 113 LEU cc_start: 0.7915 (mt) cc_final: 0.7463 (tp) REVERT: F 145 MET cc_start: 0.7898 (ttp) cc_final: 0.7300 (tmm) REVERT: G 133 VAL cc_start: 0.9013 (p) cc_final: 0.8411 (p) REVERT: G 382 TYR cc_start: 0.7264 (t80) cc_final: 0.6914 (t80) REVERT: G 519 ARG cc_start: 0.8594 (ttm-80) cc_final: 0.8391 (ttt90) REVERT: H 29 THR cc_start: 0.7217 (m) cc_final: 0.7014 (p) REVERT: H 100 TYR cc_start: 0.8670 (m-80) cc_final: 0.8453 (m-10) REVERT: H 113 LEU cc_start: 0.7882 (mt) cc_final: 0.7439 (tp) REVERT: H 145 MET cc_start: 0.7910 (ttp) cc_final: 0.7165 (tmm) outliers start: 0 outliers final: 0 residues processed: 658 average time/residue: 0.3664 time to fit residues: 330.1251 Evaluate side-chains 438 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 356 GLN A 386 ASN B 144 GLN C 240 HIS C 356 GLN C 386 ASN D 144 GLN E 386 ASN F 144 GLN G 386 ASN H 144 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.172848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117703 restraints weight = 76210.429| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.52 r_work: 0.3383 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16372 Z= 0.130 Angle : 0.528 4.405 22140 Z= 0.290 Chirality : 0.035 0.112 2460 Planarity : 0.004 0.040 2756 Dihedral : 11.009 175.833 2332 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.49 % Allowed : 10.32 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.18), residues: 1936 helix: 0.31 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -1.39 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 518 TYR 0.014 0.001 TYR C 545 PHE 0.019 0.001 PHE F 20 TRP 0.007 0.001 TRP E 176 HIS 0.006 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (16372) covalent geometry : angle 0.52784 / 0.29 (22140) hydrogen bonds : bond 0.04661 / 3.08 ( 1080) hydrogen bonds : angle 4.27613 / 3.14 ( 3192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 495 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 487 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 ARG cc_start: 0.8718 (ttm-80) cc_final: 0.8501 (ttt90) REVERT: A 537 ASP cc_start: 0.7157 (p0) cc_final: 0.6878 (p0) REVERT: B 28 ILE cc_start: 0.6020 (mm) cc_final: 0.5602 (tp) REVERT: B 29 THR cc_start: 0.7325 (m) cc_final: 0.7099 (p) REVERT: B 77 MET cc_start: 0.8049 (ppp) cc_final: 0.7833 (ppp) REVERT: B 85 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8006 (tp30) REVERT: B 142 PHE cc_start: 0.7930 (m-80) cc_final: 0.7714 (m-80) REVERT: B 145 MET cc_start: 0.8067 (ttp) cc_final: 0.7418 (tmm) REVERT: C 537 ASP cc_start: 0.7161 (p0) cc_final: 0.6901 (p0) REVERT: D 28 ILE cc_start: 0.6022 (mm) cc_final: 0.5604 (tp) REVERT: D 29 THR cc_start: 0.7324 (m) cc_final: 0.7095 (p) REVERT: D 100 TYR cc_start: 0.8709 (m-80) cc_final: 0.8278 (m-10) REVERT: D 142 PHE cc_start: 0.7934 (m-80) cc_final: 0.7720 (m-80) REVERT: D 145 MET cc_start: 0.8098 (ttp) cc_final: 0.7437 (tmm) REVERT: E 286 ASP cc_start: 0.7648 (m-30) cc_final: 0.7435 (m-30) REVERT: E 519 ARG cc_start: 0.8663 (ttm-80) cc_final: 0.8381 (ttt90) REVERT: E 531 GLN cc_start: 0.8320 (mt0) cc_final: 0.7996 (pt0) REVERT: E 537 ASP cc_start: 0.7006 (p0) cc_final: 0.6750 (p0) REVERT: F 28 ILE cc_start: 0.6011 (mm) cc_final: 0.5590 (tp) REVERT: F 29 THR cc_start: 0.7322 (m) cc_final: 0.7098 (p) REVERT: F 85 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7963 (tp30) REVERT: F 100 TYR cc_start: 0.8575 (m-80) cc_final: 0.8235 (m-10) REVERT: F 145 MET cc_start: 0.8077 (ttp) cc_final: 0.7389 (tmm) REVERT: G 356 GLN cc_start: 0.8656 (mm110) cc_final: 0.8429 (mm-40) REVERT: G 537 ASP cc_start: 0.7125 (p0) cc_final: 0.6837 (p0) REVERT: G 555 ARG cc_start: 0.8252 (tpp80) cc_final: 0.8021 (mmm160) REVERT: H 28 ILE cc_start: 0.6031 (mm) cc_final: 0.5583 (tp) REVERT: H 29 THR cc_start: 0.7324 (m) cc_final: 0.7096 (p) REVERT: H 100 TYR cc_start: 0.8721 (m-80) cc_final: 0.8284 (m-10) REVERT: H 142 PHE cc_start: 0.7940 (m-80) cc_final: 0.7735 (m-80) REVERT: H 145 MET cc_start: 0.7771 (ttp) cc_final: 0.7331 (tmm) outliers start: 8 outliers final: 6 residues processed: 492 average time/residue: 0.3202 time to fit residues: 219.6480 Evaluate side-chains 436 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 430 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 386 ASN Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain G residue 105 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 164 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 144 GLN D 144 GLN F 144 GLN H 144 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.170299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115505 restraints weight = 75699.182| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.71 r_work: 0.3305 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16372 Z= 0.150 Angle : 0.498 5.053 22140 Z= 0.277 Chirality : 0.035 0.111 2460 Planarity : 0.004 0.047 2756 Dihedral : 10.553 176.027 2332 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.42 % Allowed : 12.20 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1936 helix: 0.92 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.89 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 555 TYR 0.011 0.001 TYR C 299 PHE 0.020 0.001 PHE B 20 TRP 0.008 0.001 TRP E 176 HIS 0.007 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (16372) covalent geometry : angle 0.49801 / 0.28 (22140) hydrogen bonds : bond 0.04293 / 2.84 ( 1080) hydrogen bonds : angle 4.01574 / 2.95 ( 3192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 450 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 443 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8585 (mtp) cc_final: 0.8297 (mtp) REVERT: B 28 ILE cc_start: 0.6089 (mm) cc_final: 0.5679 (tp) REVERT: B 29 THR cc_start: 0.7386 (m) cc_final: 0.7167 (p) REVERT: B 75 ARG cc_start: 0.6438 (ttp-110) cc_final: 0.6135 (ptp-170) REVERT: B 127 ARG cc_start: 0.9012 (ptm-80) cc_final: 0.8697 (tmm-80) REVERT: B 145 MET cc_start: 0.8099 (ttp) cc_final: 0.7409 (tmm) REVERT: C 533 ARG cc_start: 0.8149 (mtp180) cc_final: 0.7626 (mmm-85) REVERT: D 28 ILE cc_start: 0.6094 (mm) cc_final: 0.5668 (tp) REVERT: D 29 THR cc_start: 0.7383 (m) cc_final: 0.7156 (p) REVERT: D 75 ARG cc_start: 0.6298 (ttp-110) cc_final: 0.6024 (ptp-170) REVERT: D 100 TYR cc_start: 0.8815 (m-80) cc_final: 0.8380 (m-10) REVERT: D 127 ARG cc_start: 0.9052 (ptm-80) cc_final: 0.8719 (tmm-80) REVERT: D 145 MET cc_start: 0.8129 (ttp) cc_final: 0.7424 (tmm) REVERT: E 382 TYR cc_start: 0.7370 (t80) cc_final: 0.7072 (t80) REVERT: F 28 ILE cc_start: 0.6074 (mm) cc_final: 0.5661 (tp) REVERT: F 29 THR cc_start: 0.7379 (m) cc_final: 0.7162 (p) REVERT: F 75 ARG cc_start: 0.6742 (ttp-110) cc_final: 0.6152 (ptp-170) REVERT: F 127 ARG cc_start: 0.8962 (ptm-80) cc_final: 0.8670 (tmm-80) REVERT: F 142 PHE cc_start: 0.7981 (m-80) cc_final: 0.7721 (m-80) REVERT: F 145 MET cc_start: 0.8249 (ttp) cc_final: 0.7472 (tmm) REVERT: G 210 MET cc_start: 0.8556 (mtp) cc_final: 0.8288 (mtp) REVERT: G 356 GLN cc_start: 0.8799 (mm110) cc_final: 0.8549 (mm-40) REVERT: G 555 ARG cc_start: 0.8219 (tpp80) cc_final: 0.8018 (mmm160) REVERT: H 28 ILE cc_start: 0.6062 (mm) cc_final: 0.5625 (tp) REVERT: H 29 THR cc_start: 0.7374 (m) cc_final: 0.7150 (p) REVERT: H 75 ARG cc_start: 0.6410 (ttp-110) cc_final: 0.6054 (ptp-170) REVERT: H 100 TYR cc_start: 0.8828 (m-80) cc_final: 0.8388 (m-10) REVERT: H 127 ARG cc_start: 0.9111 (ptm-80) cc_final: 0.8740 (tmm-80) REVERT: H 142 PHE cc_start: 0.7993 (m-80) cc_final: 0.7723 (m-80) REVERT: H 145 MET cc_start: 0.7833 (ttp) cc_final: 0.7488 (tmm) outliers start: 7 outliers final: 5 residues processed: 449 average time/residue: 0.3288 time to fit residues: 209.9655 Evaluate side-chains 421 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 416 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain G residue 105 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 11 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 100 optimal weight: 0.0020 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 386 ASN B 144 GLN D 144 GLN F 144 GLN G 386 ASN H 144 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.168447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.111213 restraints weight = 74761.163| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.51 r_work: 0.3279 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16372 Z= 0.162 Angle : 0.492 4.468 22140 Z= 0.274 Chirality : 0.035 0.113 2460 Planarity : 0.003 0.040 2756 Dihedral : 10.424 175.347 2332 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.55 % Allowed : 13.29 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.19), residues: 1936 helix: 1.28 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -0.49 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 519 TYR 0.015 0.001 TYR C 299 PHE 0.019 0.002 PHE D 20 TRP 0.010 0.001 TRP C 176 HIS 0.007 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (16372) covalent geometry : angle 0.49249 / 0.27 (22140) hydrogen bonds : bond 0.04157 / 2.74 ( 1080) hydrogen bonds : angle 3.93998 / 2.90 ( 3192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 432 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 423 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8601 (mtp) cc_final: 0.8358 (mtp) REVERT: A 382 TYR cc_start: 0.7330 (t80) cc_final: 0.7021 (t80) REVERT: A 519 ARG cc_start: 0.8828 (ttm110) cc_final: 0.8569 (ttm-80) REVERT: B 28 ILE cc_start: 0.6036 (mm) cc_final: 0.5650 (tp) REVERT: B 127 ARG cc_start: 0.9019 (ptm-80) cc_final: 0.8770 (tmm-80) REVERT: B 145 MET cc_start: 0.8071 (ttp) cc_final: 0.7510 (tmm) REVERT: D 28 ILE cc_start: 0.6046 (mm) cc_final: 0.5653 (tp) REVERT: D 100 TYR cc_start: 0.8775 (m-80) cc_final: 0.8267 (m-10) REVERT: D 127 ARG cc_start: 0.9053 (ptm-80) cc_final: 0.8796 (tmm-80) REVERT: D 145 MET cc_start: 0.8177 (ttp) cc_final: 0.7572 (tmm) REVERT: E 210 MET cc_start: 0.8554 (mtp) cc_final: 0.8320 (mtp) REVERT: F 28 ILE cc_start: 0.6028 (mm) cc_final: 0.5628 (tp) REVERT: F 127 ARG cc_start: 0.9012 (ptm-80) cc_final: 0.8741 (tmm-80) REVERT: F 145 MET cc_start: 0.8234 (ttp) cc_final: 0.7789 (ttp) REVERT: G 210 MET cc_start: 0.8605 (mtp) cc_final: 0.8351 (mtp) REVERT: G 555 ARG cc_start: 0.8208 (tpp80) cc_final: 0.7878 (mmm160) REVERT: H 28 ILE cc_start: 0.6036 (mm) cc_final: 0.5629 (tp) REVERT: H 100 TYR cc_start: 0.8787 (m-80) cc_final: 0.8268 (m-10) REVERT: H 145 MET cc_start: 0.8119 (ttp) cc_final: 0.7766 (ttp) outliers start: 9 outliers final: 8 residues processed: 428 average time/residue: 0.3201 time to fit residues: 195.7340 Evaluate side-chains 416 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 408 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 165 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 47 optimal weight: 0.0670 chunk 183 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 386 ASN G 356 GLN G 386 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.168633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.111869 restraints weight = 74602.096| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.38 r_work: 0.3299 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16372 Z= 0.131 Angle : 0.469 5.259 22140 Z= 0.257 Chirality : 0.035 0.128 2460 Planarity : 0.003 0.036 2756 Dihedral : 10.219 175.990 2332 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.73 % Allowed : 13.96 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.19), residues: 1936 helix: 1.56 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -0.24 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 519 TYR 0.019 0.001 TYR E 382 PHE 0.017 0.001 PHE D 20 TRP 0.007 0.001 TRP A 176 HIS 0.007 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (16372) covalent geometry : angle 0.46862 / 0.26 (22140) hydrogen bonds : bond 0.03862 / 2.55 ( 1080) hydrogen bonds : angle 3.78326 / 2.77 ( 3192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 445 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 433 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8609 (mtp) cc_final: 0.8306 (mtp) REVERT: A 382 TYR cc_start: 0.7339 (t80) cc_final: 0.6997 (t80) REVERT: A 519 ARG cc_start: 0.8821 (ttm110) cc_final: 0.8554 (ttm110) REVERT: A 555 ARG cc_start: 0.7361 (mmm160) cc_final: 0.6561 (ttm110) REVERT: B 105 GLU cc_start: 0.8590 (tp30) cc_final: 0.8352 (tp30) REVERT: B 127 ARG cc_start: 0.9059 (ptm-80) cc_final: 0.8789 (tmm-80) REVERT: B 145 MET cc_start: 0.8169 (ttp) cc_final: 0.7639 (tmm) REVERT: D 100 TYR cc_start: 0.8760 (m-80) cc_final: 0.8150 (m-80) REVERT: D 127 ARG cc_start: 0.9070 (ptm-80) cc_final: 0.8810 (tmm-80) REVERT: D 145 MET cc_start: 0.8208 (ttp) cc_final: 0.7642 (tmm) REVERT: E 210 MET cc_start: 0.8521 (mtp) cc_final: 0.8298 (mtp) REVERT: E 382 TYR cc_start: 0.6938 (t80) cc_final: 0.6470 (t80) REVERT: F 105 GLU cc_start: 0.8568 (tp30) cc_final: 0.8291 (tp30) REVERT: F 127 ARG cc_start: 0.9022 (ptm-80) cc_final: 0.8743 (tmm-80) REVERT: F 145 MET cc_start: 0.8276 (ttp) cc_final: 0.7865 (ttp) REVERT: G 210 MET cc_start: 0.8580 (mtp) cc_final: 0.8297 (mtp) REVERT: G 544 GLN cc_start: 0.9209 (pt0) cc_final: 0.9006 (pt0) REVERT: G 555 ARG cc_start: 0.8340 (tpp80) cc_final: 0.8007 (mmm160) REVERT: H 100 TYR cc_start: 0.8773 (m-80) cc_final: 0.8162 (m-80) REVERT: H 145 MET cc_start: 0.8150 (ttp) cc_final: 0.7782 (tmm) outliers start: 12 outliers final: 10 residues processed: 439 average time/residue: 0.2918 time to fit residues: 183.9998 Evaluate side-chains 420 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 410 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 165 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 155 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.166744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109884 restraints weight = 74951.790| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.38 r_work: 0.3266 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16372 Z= 0.181 Angle : 0.503 4.452 22140 Z= 0.278 Chirality : 0.036 0.122 2460 Planarity : 0.003 0.043 2756 Dihedral : 10.277 175.607 2332 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 1.21 % Allowed : 14.14 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.19), residues: 1936 helix: 1.50 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -0.30 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 519 TYR 0.015 0.002 TYR C 299 PHE 0.018 0.002 PHE D 20 TRP 0.008 0.001 TRP C 176 HIS 0.008 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (16372) covalent geometry : angle 0.50327 / 0.28 (22140) hydrogen bonds : bond 0.04082 / 2.69 ( 1080) hydrogen bonds : angle 3.91332 / 2.87 ( 3192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 436 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 416 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8629 (mtp) cc_final: 0.8338 (mtp) REVERT: A 382 TYR cc_start: 0.7371 (t80) cc_final: 0.7055 (t80) REVERT: A 519 ARG cc_start: 0.8804 (ttm110) cc_final: 0.8595 (ttm110) REVERT: B 127 ARG cc_start: 0.9067 (ptm-80) cc_final: 0.8805 (tmm-80) REVERT: B 145 MET cc_start: 0.8318 (ttp) cc_final: 0.7858 (tmm) REVERT: D 100 TYR cc_start: 0.8788 (m-80) cc_final: 0.8065 (m-80) REVERT: D 127 ARG cc_start: 0.9061 (ptm-80) cc_final: 0.8803 (tmm-80) REVERT: D 145 MET cc_start: 0.8342 (ttp) cc_final: 0.7844 (tmm) REVERT: E 210 MET cc_start: 0.8523 (mtp) cc_final: 0.8311 (mtp) REVERT: F 127 ARG cc_start: 0.9001 (ptm-80) cc_final: 0.8776 (tmm-80) REVERT: F 145 MET cc_start: 0.8268 (ttp) cc_final: 0.7719 (tmm) REVERT: G 210 MET cc_start: 0.8608 (mtp) cc_final: 0.8320 (mtp) REVERT: G 382 TYR cc_start: 0.7741 (t80) cc_final: 0.7052 (t80) REVERT: G 555 ARG cc_start: 0.8292 (tpp80) cc_final: 0.7768 (mmm160) REVERT: H 100 TYR cc_start: 0.8792 (m-80) cc_final: 0.8061 (m-80) REVERT: H 145 MET cc_start: 0.8177 (ttp) cc_final: 0.7900 (ttp) outliers start: 20 outliers final: 17 residues processed: 426 average time/residue: 0.3040 time to fit residues: 186.4997 Evaluate side-chains 415 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 398 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 80 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 117 optimal weight: 0.0050 chunk 49 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 174 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.169034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113347 restraints weight = 74493.913| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.46 r_work: 0.3310 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16372 Z= 0.106 Angle : 0.469 4.768 22140 Z= 0.255 Chirality : 0.034 0.119 2460 Planarity : 0.003 0.052 2756 Dihedral : 9.984 176.227 2332 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.15 % Allowed : 14.81 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.20), residues: 1936 helix: 1.77 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -0.04 (0.33), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 519 TYR 0.017 0.001 TYR E 382 PHE 0.017 0.001 PHE F 20 TRP 0.007 0.001 TRP G 176 HIS 0.009 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (16372) covalent geometry : angle 0.46933 / 0.26 (22140) hydrogen bonds : bond 0.03648 / 2.41 ( 1080) hydrogen bonds : angle 3.67720 / 2.68 ( 3192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 460 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 441 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8643 (mtp) cc_final: 0.8387 (mtp) REVERT: A 382 TYR cc_start: 0.7508 (t80) cc_final: 0.7213 (t80) REVERT: B 127 ARG cc_start: 0.9051 (ptm-80) cc_final: 0.8768 (tmm-80) REVERT: B 145 MET cc_start: 0.8248 (ttp) cc_final: 0.7824 (tmm) REVERT: C 382 TYR cc_start: 0.7356 (t80) cc_final: 0.7063 (t80) REVERT: C 555 ARG cc_start: 0.7435 (mmm160) cc_final: 0.5819 (ttm110) REVERT: D 100 TYR cc_start: 0.8730 (m-80) cc_final: 0.8054 (m-10) REVERT: D 127 ARG cc_start: 0.9072 (ptm-80) cc_final: 0.8818 (tmm-80) REVERT: D 145 MET cc_start: 0.8302 (ttp) cc_final: 0.7881 (tmm) REVERT: E 210 MET cc_start: 0.8536 (mtp) cc_final: 0.8283 (mtp) REVERT: F 127 ARG cc_start: 0.9028 (ptm-80) cc_final: 0.8653 (tmm-80) REVERT: F 145 MET cc_start: 0.8273 (ttp) cc_final: 0.7804 (tmm) REVERT: G 210 MET cc_start: 0.8606 (mtp) cc_final: 0.8350 (mtp) REVERT: G 382 TYR cc_start: 0.7785 (t80) cc_final: 0.7316 (t80) REVERT: G 555 ARG cc_start: 0.8354 (tpp80) cc_final: 0.7845 (mmm160) REVERT: H 100 TYR cc_start: 0.8744 (m-80) cc_final: 0.8055 (m-10) REVERT: H 109 VAL cc_start: 0.9119 (t) cc_final: 0.8898 (t) outliers start: 19 outliers final: 18 residues processed: 451 average time/residue: 0.3069 time to fit residues: 200.6740 Evaluate side-chains 426 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 408 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 80 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 136 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 159 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.169041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.113077 restraints weight = 75007.413| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.47 r_work: 0.3308 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16372 Z= 0.113 Angle : 0.481 5.129 22140 Z= 0.262 Chirality : 0.034 0.118 2460 Planarity : 0.003 0.057 2756 Dihedral : 9.931 175.595 2332 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.03 % Allowed : 15.17 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.19), residues: 1936 helix: 1.85 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -0.05 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 519 TYR 0.013 0.001 TYR E 382 PHE 0.017 0.001 PHE B 20 TRP 0.006 0.001 TRP C 176 HIS 0.009 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (16372) covalent geometry : angle 0.48103 / 0.26 (22140) hydrogen bonds : bond 0.03648 / 2.41 ( 1080) hydrogen bonds : angle 3.67592 / 2.68 ( 3192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 436 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 419 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8632 (mtp) cc_final: 0.8422 (mtp) REVERT: B 127 ARG cc_start: 0.9066 (ptm-80) cc_final: 0.8787 (tmm-80) REVERT: C 382 TYR cc_start: 0.7398 (t80) cc_final: 0.7072 (t80) REVERT: C 555 ARG cc_start: 0.7391 (mmm160) cc_final: 0.6039 (ttm110) REVERT: D 100 TYR cc_start: 0.8718 (m-80) cc_final: 0.8077 (m-10) REVERT: D 127 ARG cc_start: 0.9069 (ptm-80) cc_final: 0.8775 (tmm-80) REVERT: D 145 MET cc_start: 0.8279 (ttp) cc_final: 0.7836 (tmm) REVERT: E 210 MET cc_start: 0.8502 (mtp) cc_final: 0.8289 (mtp) REVERT: E 531 GLN cc_start: 0.8418 (mt0) cc_final: 0.7844 (pt0) REVERT: F 127 ARG cc_start: 0.8922 (ptm-80) cc_final: 0.8676 (tmm-80) REVERT: F 142 PHE cc_start: 0.7889 (m-80) cc_final: 0.7686 (m-80) REVERT: F 145 MET cc_start: 0.8312 (ttp) cc_final: 0.7860 (tmm) REVERT: G 210 MET cc_start: 0.8599 (mtp) cc_final: 0.8364 (mtp) REVERT: G 555 ARG cc_start: 0.8291 (tpp80) cc_final: 0.7731 (mmm160) REVERT: H 100 TYR cc_start: 0.8749 (m-80) cc_final: 0.8062 (m-10) outliers start: 17 outliers final: 16 residues processed: 429 average time/residue: 0.3072 time to fit residues: 191.3876 Evaluate side-chains 421 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 405 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain H residue 20 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 128 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 181 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 185 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.169569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113739 restraints weight = 74903.146| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.48 r_work: 0.3316 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16372 Z= 0.110 Angle : 0.483 6.300 22140 Z= 0.261 Chirality : 0.034 0.131 2460 Planarity : 0.003 0.062 2756 Dihedral : 9.851 175.113 2332 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.21 % Allowed : 15.17 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.19), residues: 1936 helix: 1.96 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -0.06 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 519 TYR 0.028 0.001 TYR A 382 PHE 0.016 0.001 PHE H 20 TRP 0.006 0.001 TRP A 176 HIS 0.008 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (16372) covalent geometry : angle 0.48283 / 0.26 (22140) hydrogen bonds : bond 0.03544 / 2.34 ( 1080) hydrogen bonds : angle 3.64558 / 2.65 ( 3192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 442 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 422 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8620 (mtp) cc_final: 0.8420 (mtp) REVERT: A 555 ARG cc_start: 0.7488 (mmm160) cc_final: 0.6719 (ttm110) REVERT: B 127 ARG cc_start: 0.9069 (ptm-80) cc_final: 0.8791 (tmm-80) REVERT: B 144 GLN cc_start: 0.8605 (mm110) cc_final: 0.8368 (mm-40) REVERT: C 382 TYR cc_start: 0.7423 (t80) cc_final: 0.7112 (t80) REVERT: C 555 ARG cc_start: 0.7286 (mmm160) cc_final: 0.5873 (ttm110) REVERT: D 100 TYR cc_start: 0.8730 (m-80) cc_final: 0.8100 (m-10) REVERT: D 127 ARG cc_start: 0.9077 (ptm-80) cc_final: 0.8795 (tmm-80) REVERT: D 145 MET cc_start: 0.8299 (ttp) cc_final: 0.7873 (tmm) REVERT: E 210 MET cc_start: 0.8493 (mtp) cc_final: 0.8292 (mtp) REVERT: E 531 GLN cc_start: 0.8373 (mt0) cc_final: 0.7843 (pt0) REVERT: F 127 ARG cc_start: 0.8939 (ptm-80) cc_final: 0.8725 (tmm-80) REVERT: F 142 PHE cc_start: 0.7951 (m-80) cc_final: 0.7747 (m-80) REVERT: F 145 MET cc_start: 0.8336 (ttp) cc_final: 0.7893 (tmm) REVERT: G 210 MET cc_start: 0.8588 (mtp) cc_final: 0.8361 (mtp) REVERT: H 100 TYR cc_start: 0.8752 (m-80) cc_final: 0.8110 (m-10) outliers start: 20 outliers final: 17 residues processed: 435 average time/residue: 0.3013 time to fit residues: 188.5821 Evaluate side-chains 425 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 408 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain H residue 20 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 164 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 171 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.168504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.112367 restraints weight = 74909.672| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.37 r_work: 0.3305 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16372 Z= 0.131 Angle : 0.502 6.627 22140 Z= 0.273 Chirality : 0.035 0.128 2460 Planarity : 0.004 0.065 2756 Dihedral : 9.923 174.880 2332 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 1.46 % Allowed : 15.47 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.19), residues: 1936 helix: 1.92 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -0.16 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 519 TYR 0.021 0.001 TYR A 382 PHE 0.022 0.001 PHE F 13 TRP 0.006 0.001 TRP A 176 HIS 0.010 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (16372) covalent geometry : angle 0.50225 / 0.27 (22140) hydrogen bonds : bond 0.03662 / 2.42 ( 1080) hydrogen bonds : angle 3.71431 / 2.71 ( 3192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 436 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 412 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8633 (mtp) cc_final: 0.8426 (mtp) REVERT: A 555 ARG cc_start: 0.7411 (mmm160) cc_final: 0.6551 (ttm110) REVERT: B 127 ARG cc_start: 0.9042 (ptm-80) cc_final: 0.8785 (tmm-80) REVERT: B 144 GLN cc_start: 0.8625 (mm110) cc_final: 0.8326 (mm-40) REVERT: C 382 TYR cc_start: 0.7409 (t80) cc_final: 0.7124 (t80) REVERT: C 555 ARG cc_start: 0.7307 (mmm160) cc_final: 0.5881 (ttm110) REVERT: D 100 TYR cc_start: 0.8795 (m-80) cc_final: 0.8071 (m-10) REVERT: D 125 MET cc_start: 0.9103 (ttt) cc_final: 0.8863 (ttp) REVERT: D 127 ARG cc_start: 0.9078 (ptm-80) cc_final: 0.8802 (tmm-80) REVERT: D 145 MET cc_start: 0.8272 (ttp) cc_final: 0.7841 (tmm) REVERT: E 531 GLN cc_start: 0.8320 (mt0) cc_final: 0.7781 (pt0) REVERT: F 127 ARG cc_start: 0.8944 (ptm-80) cc_final: 0.8705 (tmm-80) REVERT: F 142 PHE cc_start: 0.7925 (m-80) cc_final: 0.7716 (m-80) REVERT: F 145 MET cc_start: 0.8332 (ttp) cc_final: 0.7846 (tmm) REVERT: G 210 MET cc_start: 0.8612 (mtp) cc_final: 0.8382 (mtp) REVERT: G 555 ARG cc_start: 0.8208 (tpp-160) cc_final: 0.7666 (tpt-90) REVERT: H 100 TYR cc_start: 0.8800 (m-80) cc_final: 0.8135 (m-10) outliers start: 24 outliers final: 18 residues processed: 427 average time/residue: 0.3192 time to fit residues: 195.4297 Evaluate side-chains 428 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 410 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain H residue 20 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 26 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.168405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111532 restraints weight = 75461.515| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.45 r_work: 0.3286 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.6356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16372 Z= 0.133 Angle : 0.511 7.436 22140 Z= 0.277 Chirality : 0.035 0.117 2460 Planarity : 0.004 0.065 2756 Dihedral : 9.960 175.487 2332 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.09 % Allowed : 15.96 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.19), residues: 1936 helix: 1.94 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -0.20 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 38 TYR 0.017 0.001 TYR A 382 PHE 0.016 0.001 PHE F 13 TRP 0.007 0.001 TRP A 176 HIS 0.010 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (16372) covalent geometry : angle 0.51124 / 0.28 (22140) hydrogen bonds : bond 0.03696 / 2.44 ( 1080) hydrogen bonds : angle 3.72289 / 2.71 ( 3192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11366.32 seconds wall clock time: 192 minutes 32.58 seconds (11552.58 seconds total)