Starting phenix.real_space_refine on Mon Sep 14 16:22:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xnl_33318/09_2026/7xnl_33318_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnl_33318/09_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_33318/09_2026/7xnl_33318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnl_33318/09_2026/7xnl_33318.map" model { file = "/net/cci-nas-00/data/ceres_data/7xnl_33318/09_2026/7xnl_33318_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnl_33318/09_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-2.2.1-6174/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, 36 Unusual residues: {' K': 4} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 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: 6.32, per 1000 atoms: 0.20 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: 3.50 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.67 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: 8.50 Time building geometry restraints manager: 4.74 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.220 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 34.340 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.110 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.870 ------------------------------------------------------------------------------- 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 : 0.706 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: 0.3867 time to fit residues: 348.8568 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 : 0.879 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.172741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.117555 restraints weight = 76325.687| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.51 r_work: 0.3371 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3893 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= 0.134 Angle : 0.531 4.808 22140 Z= 0.294 Chirality : 0.035 0.114 2460 Planarity : 0.004 0.041 2756 Dihedral : 11.097 175.341 2332 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.55 % Allowed : 10.44 % Favored : 89.02 % 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: -0.27 (0.18), residues: 1936 helix: 0.24 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -1.28 (0.30), residues: 436 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 0.018 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 0.00280 / 0.13 (16372) covalent geometry : angle 0.53099 / 0.29 (22140) hydrogen bonds : bond 0.04853 / 3.21 ( 1080) hydrogen bonds : angle 4.34369 / 3.18 ( 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: 9 poor density : 486 time to evaluate : 0.886 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: 0.8701 (ttm-80) cc_final: 0.8484 (ttt90) REVERT: A 537 ASP cc_start: 0.7073 (p0) cc_final: 0.6810 (p0) REVERT: B 28 ILE cc_start: 0.6008 (mm) cc_final: 0.5606 (tp) REVERT: B 29 THR cc_start: 0.7314 (m) cc_final: 0.7087 (p) REVERT: B 38 ARG cc_start: 0.7696 (mtt180) cc_final: 0.7433 (mtt180) REVERT: B 77 MET cc_start: 0.8072 (ppp) cc_final: 0.7840 (ppp) REVERT: B 85 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8003 (tp30) REVERT: B 142 PHE cc_start: 0.7910 (m-80) cc_final: 0.7705 (m-80) REVERT: B 145 MET cc_start: 0.8060 (ttp) cc_final: 0.7392 (tmm) REVERT: C 537 ASP cc_start: 0.7116 (p0) cc_final: 0.6862 (p0) REVERT: D 28 ILE cc_start: 0.6015 (mm) cc_final: 0.5613 (tp) REVERT: D 29 THR cc_start: 0.7310 (m) cc_final: 0.7081 (p) REVERT: D 100 TYR cc_start: 0.8708 (m-80) cc_final: 0.8261 (m-10) REVERT: D 142 PHE cc_start: 0.7894 (m-80) cc_final: 0.7681 (m-80) REVERT: D 145 MET cc_start: 0.8080 (ttp) cc_final: 0.7401 (tmm) REVERT: E 519 ARG cc_start: 0.8697 (ttm-80) cc_final: 0.8351 (mtp85) REVERT: E 531 GLN cc_start: 0.8302 (mt0) cc_final: 0.7972 (pt0) REVERT: E 537 ASP cc_start: 0.6987 (p0) cc_final: 0.6743 (p0) REVERT: F 28 ILE cc_start: 0.5997 (mm) cc_final: 0.5594 (tp) REVERT: F 29 THR cc_start: 0.7305 (m) cc_final: 0.7081 (p) REVERT: F 145 MET cc_start: 0.8073 (ttp) cc_final: 0.7366 (tmm) REVERT: G 356 GLN cc_start: 0.8686 (mm110) cc_final: 0.8426 (mm-40) REVERT: G 537 ASP cc_start: 0.7114 (p0) cc_final: 0.6836 (p0) REVERT: G 555 ARG cc_start: 0.8255 (tpp80) cc_final: 0.8018 (mmm160) REVERT: H 28 ILE cc_start: 0.6019 (mm) cc_final: 0.5597 (tp) REVERT: H 29 THR cc_start: 0.7308 (m) cc_final: 0.7080 (p) REVERT: H 100 TYR cc_start: 0.8739 (m-80) cc_final: 0.8285 (m-10) REVERT: H 142 PHE cc_start: 0.7871 (m-80) cc_final: 0.7662 (m-80) REVERT: H 145 MET cc_start: 0.7765 (ttp) cc_final: 0.7292 (tmm) outliers start: 9 outliers final: 7 residues processed: 492 average time/residue: 0.3692 time to fit residues: 253.3543 Evaluate side-chains 431 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 424 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASN 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: 0.8980 chunk 40 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 144 GLN D 144 GLN F 144 GLN G 547 GLN H 144 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.168464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110957 restraints weight = 76161.957| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.50 r_work: 0.3271 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16372 Z= 0.200 Angle : 0.535 5.261 22140 Z= 0.299 Chirality : 0.037 0.118 2460 Planarity : 0.004 0.060 2756 Dihedral : 10.622 173.803 2332 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.91 % Allowed : 11.89 % Favored : 87.20 % 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: 0.46 (0.19), residues: 1936 helix: 0.75 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.05 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 127 TYR 0.016 0.002 TYR G 299 PHE 0.020 0.002 PHE B 20 TRP 0.010 0.001 TRP E 176 HIS 0.007 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (16372) covalent geometry : angle 0.53526 / 0.30 (22140) hydrogen bonds : bond 0.04569 / 3.01 ( 1080) hydrogen bonds : angle 4.17686 / 3.07 ( 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 449 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 434 time to evaluate : 0.828 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: B 28 ILE cc_start: 0.6139 (mm) cc_final: 0.5745 (tp) REVERT: B 75 ARG cc_start: 0.6379 (ttp-110) cc_final: 0.5991 (ptp-170) REVERT: B 127 ARG cc_start: 0.9005 (ptm-80) cc_final: 0.8687 (tmm-80) REVERT: B 145 MET cc_start: 0.8156 (ttp) cc_final: 0.7660 (ttp) REVERT: D 28 ILE cc_start: 0.6152 (mm) cc_final: 0.5716 (tp) REVERT: D 29 THR cc_start: 0.7456 (m) cc_final: 0.7224 (p) REVERT: D 75 ARG cc_start: 0.6158 (ttp-110) cc_final: 0.5829 (ptp-170) REVERT: D 100 TYR cc_start: 0.8832 (m-80) cc_final: 0.8322 (m-10) REVERT: D 127 ARG cc_start: 0.9031 (ptm-80) cc_final: 0.8705 (tmm-80) REVERT: D 145 MET cc_start: 0.8225 (ttp) cc_final: 0.7724 (ttp) REVERT: E 382 TYR cc_start: 0.7387 (t80) cc_final: 0.7096 (t80) REVERT: F 28 ILE cc_start: 0.6116 (mm) cc_final: 0.5723 (tp) REVERT: F 75 ARG cc_start: 0.6595 (ttp-110) cc_final: 0.6012 (ptp-170) REVERT: F 127 ARG cc_start: 0.8979 (ptm-80) cc_final: 0.8639 (tmm-80) REVERT: F 145 MET cc_start: 0.8202 (ttp) cc_final: 0.7704 (ttp) REVERT: G 555 ARG cc_start: 0.8255 (tpp80) cc_final: 0.8032 (mmm160) REVERT: H 28 ILE cc_start: 0.6143 (mm) cc_final: 0.5729 (tp) REVERT: H 100 TYR cc_start: 0.8842 (m-80) cc_final: 0.8327 (m-10) REVERT: H 127 ARG cc_start: 0.9099 (ptm-80) cc_final: 0.8838 (tmm-80) REVERT: H 145 MET cc_start: 0.7889 (ttp) cc_final: 0.7660 (tmm) outliers start: 15 outliers final: 12 residues processed: 442 average time/residue: 0.3315 time to fit residues: 209.7920 Evaluate side-chains 418 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 406 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 508 GLU Chi-restraints excluded: chain D residue 80 THR 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 F residue 80 THR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain H residue 80 THR 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: 9.9990 chunk 46 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 144 GLN C 386 ASN D 144 GLN E 386 ASN F 144 GLN H 144 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.168984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.111953 restraints weight = 75318.957| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.47 r_work: 0.3288 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16372 Z= 0.135 Angle : 0.478 4.446 22140 Z= 0.265 Chirality : 0.035 0.114 2460 Planarity : 0.003 0.042 2756 Dihedral : 10.358 174.748 2332 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.91 % Allowed : 13.23 % Favored : 85.86 % 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: 1.10 (0.19), residues: 1936 helix: 1.18 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.75 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 519 TYR 0.012 0.001 TYR C 545 PHE 0.019 0.001 PHE H 20 TRP 0.009 0.001 TRP E 176 HIS 0.006 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (16372) covalent geometry : angle 0.47812 / 0.27 (22140) hydrogen bonds : bond 0.04085 / 2.70 ( 1080) hydrogen bonds : angle 3.90390 / 2.86 ( 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 450 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 435 time to evaluate : 1.271 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: A 210 MET cc_start: 0.8592 (mtp) cc_final: 0.8339 (mtp) REVERT: A 382 TYR cc_start: 0.7274 (t80) cc_final: 0.6953 (t80) REVERT: A 519 ARG cc_start: 0.8794 (ttm110) cc_final: 0.8485 (ttm-80) REVERT: B 28 ILE cc_start: 0.6013 (mm) cc_final: 0.5606 (tp) REVERT: B 29 THR cc_start: 0.7446 (m) cc_final: 0.7228 (p) REVERT: B 127 ARG cc_start: 0.9022 (ptm-80) cc_final: 0.8774 (tmm-80) REVERT: B 145 MET cc_start: 0.8092 (ttp) cc_final: 0.7508 (tmm) REVERT: C 516 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8274 (p) REVERT: D 28 ILE cc_start: 0.6000 (mm) cc_final: 0.5573 (tp) REVERT: D 29 THR cc_start: 0.7524 (m) cc_final: 0.7301 (p) REVERT: D 100 TYR cc_start: 0.8754 (m-80) cc_final: 0.8214 (m-10) REVERT: D 112 ASN cc_start: 0.8358 (m-40) cc_final: 0.8134 (m110) REVERT: D 127 ARG cc_start: 0.9031 (ptm-80) cc_final: 0.8778 (tmm-80) REVERT: D 145 MET cc_start: 0.8142 (ttp) cc_final: 0.7531 (tmm) REVERT: E 210 MET cc_start: 0.8537 (mtp) cc_final: 0.8300 (mtp) REVERT: E 382 TYR cc_start: 0.7338 (t80) cc_final: 0.6999 (t80) REVERT: F 28 ILE cc_start: 0.5767 (mm) cc_final: 0.5376 (tp) REVERT: F 29 THR cc_start: 0.7463 (m) cc_final: 0.7246 (p) REVERT: F 127 ARG cc_start: 0.8989 (ptm-80) cc_final: 0.8723 (tmm-80) REVERT: F 145 MET cc_start: 0.8166 (ttp) cc_final: 0.7689 (ttp) REVERT: G 210 MET cc_start: 0.8595 (mtp) cc_final: 0.8350 (mtp) REVERT: G 555 ARG cc_start: 0.8250 (tpp80) cc_final: 0.7961 (mmm160) REVERT: H 28 ILE cc_start: 0.6066 (mm) cc_final: 0.5668 (tp) REVERT: H 100 TYR cc_start: 0.8777 (m-80) cc_final: 0.8238 (m-10) REVERT: H 127 ARG cc_start: 0.9097 (ptm-80) cc_final: 0.8757 (tmm-80) REVERT: H 145 MET cc_start: 0.7950 (ttp) cc_final: 0.7586 (tmm) outliers start: 15 outliers final: 12 residues processed: 444 average time/residue: 0.3199 time to fit residues: 203.6195 Evaluate side-chains 428 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 415 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 516 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 20 PHE Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain H residue 80 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 190 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 386 ASN G 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.167847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.111401 restraints weight = 74635.877| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.35 r_work: 0.3285 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5516 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= 0.141 Angle : 0.479 4.417 22140 Z= 0.265 Chirality : 0.035 0.132 2460 Planarity : 0.003 0.045 2756 Dihedral : 10.290 175.666 2332 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.79 % Allowed : 14.56 % 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: 1.46 (0.19), residues: 1936 helix: 1.42 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.53 (0.34), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 519 TYR 0.012 0.001 TYR C 545 PHE 0.018 0.001 PHE B 20 TRP 0.007 0.001 TRP E 176 HIS 0.007 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16372) covalent geometry : angle 0.47860 / 0.26 (22140) hydrogen bonds : bond 0.03962 / 2.62 ( 1080) hydrogen bonds : angle 3.83786 / 2.81 ( 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 440 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 427 time to evaluate : 0.870 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: A 210 MET cc_start: 0.8600 (mtp) cc_final: 0.8286 (mtp) REVERT: A 382 TYR cc_start: 0.7332 (t80) cc_final: 0.7011 (t80) REVERT: A 519 ARG cc_start: 0.8794 (ttm110) cc_final: 0.8574 (ttm110) REVERT: A 555 ARG cc_start: 0.7216 (mmm160) cc_final: 0.6553 (ttm110) REVERT: B 28 ILE cc_start: 0.5843 (mm) cc_final: 0.5491 (tp) REVERT: B 29 THR cc_start: 0.7463 (m) cc_final: 0.7246 (p) REVERT: B 127 ARG cc_start: 0.9061 (ptm-80) cc_final: 0.8796 (tmm-80) REVERT: B 145 MET cc_start: 0.8169 (ttp) cc_final: 0.7635 (tmm) REVERT: D 100 TYR cc_start: 0.8777 (m-80) cc_final: 0.8178 (m-10) REVERT: D 127 ARG cc_start: 0.9078 (ptm-80) cc_final: 0.8806 (tmm-80) REVERT: D 145 MET cc_start: 0.8213 (ttp) cc_final: 0.7642 (tmm) REVERT: E 210 MET cc_start: 0.8521 (mtp) cc_final: 0.8266 (mtp) REVERT: E 382 TYR cc_start: 0.7397 (t80) cc_final: 0.7048 (t80) REVERT: F 29 THR cc_start: 0.7495 (m) cc_final: 0.7284 (p) REVERT: F 127 ARG cc_start: 0.9028 (ptm-80) cc_final: 0.8758 (tmm-80) REVERT: F 145 MET cc_start: 0.8301 (ttp) cc_final: 0.7906 (ttp) REVERT: G 210 MET cc_start: 0.8586 (mtp) cc_final: 0.8271 (mtp) REVERT: G 555 ARG cc_start: 0.8321 (tpp80) cc_final: 0.8000 (mmm160) REVERT: H 73 MET cc_start: 0.6123 (mmm) cc_final: 0.5765 (mmm) REVERT: H 100 TYR cc_start: 0.8775 (m-80) cc_final: 0.8160 (m-80) REVERT: H 127 ARG cc_start: 0.9031 (ptm-80) cc_final: 0.8799 (tmm-80) REVERT: H 145 MET cc_start: 0.8281 (ttp) cc_final: 0.7786 (tmm) outliers start: 13 outliers final: 11 residues processed: 434 average time/residue: 0.3263 time to fit residues: 203.1291 Evaluate side-chains 427 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 416 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS 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 E residue 105 HIS Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 291 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 155 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 386 ASN G 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.166322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109578 restraints weight = 74813.584| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.34 r_work: 0.3258 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16372 Z= 0.180 Angle : 0.506 4.450 22140 Z= 0.281 Chirality : 0.036 0.116 2460 Planarity : 0.003 0.055 2756 Dihedral : 10.313 175.603 2332 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.21 % Allowed : 14.62 % Favored : 84.16 % 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: 1.40 (0.19), residues: 1936 helix: 1.37 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.51 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 519 TYR 0.015 0.002 TYR C 299 PHE 0.019 0.002 PHE H 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 0.00407 / 0.18 (16372) covalent geometry : angle 0.50641 / 0.28 (22140) hydrogen bonds : bond 0.04145 / 2.73 ( 1080) hydrogen bonds : angle 3.94261 / 2.89 ( 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 441 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 421 time to evaluate : 0.909 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: 0.8616 (mtp) cc_final: 0.8326 (mtp) REVERT: A 382 TYR cc_start: 0.7343 (t80) cc_final: 0.7036 (t80) REVERT: A 517 ILE cc_start: 0.9076 (mm) cc_final: 0.8863 (mm) REVERT: A 519 ARG cc_start: 0.8818 (ttm110) cc_final: 0.8602 (ttm110) REVERT: B 127 ARG cc_start: 0.9055 (ptm-80) cc_final: 0.8798 (tmm-80) REVERT: B 145 MET cc_start: 0.8312 (ttp) cc_final: 0.7833 (tmm) REVERT: D 28 ILE cc_start: 0.6141 (mm) cc_final: 0.5774 (tp) REVERT: D 100 TYR cc_start: 0.8793 (m-80) cc_final: 0.8064 (m-80) REVERT: D 127 ARG cc_start: 0.9079 (ptm-80) cc_final: 0.8843 (tmm-80) REVERT: D 145 MET cc_start: 0.8352 (ttp) cc_final: 0.7830 (tmm) REVERT: E 210 MET cc_start: 0.8532 (mtp) cc_final: 0.8253 (mtp) REVERT: E 382 TYR cc_start: 0.7414 (t80) cc_final: 0.7082 (t80) REVERT: E 520 MET cc_start: 0.8859 (mtm) cc_final: 0.8606 (mpp) REVERT: F 127 ARG cc_start: 0.9029 (ptm-80) cc_final: 0.8801 (tmm-80) REVERT: F 145 MET cc_start: 0.8277 (ttp) cc_final: 0.7904 (ttp) REVERT: G 210 MET cc_start: 0.8593 (mtp) cc_final: 0.8294 (mtp) REVERT: G 555 ARG cc_start: 0.8305 (tpp80) cc_final: 0.7790 (mmm160) REVERT: H 100 TYR cc_start: 0.8797 (m-80) cc_final: 0.8065 (m-80) REVERT: H 127 ARG cc_start: 0.9060 (ptm-80) cc_final: 0.8839 (tmm-80) REVERT: H 145 MET cc_start: 0.8303 (ttp) cc_final: 0.7851 (tmm) outliers start: 20 outliers final: 15 residues processed: 431 average time/residue: 0.3293 time to fit residues: 204.5749 Evaluate side-chains 428 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 413 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 C residue 291 SER Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 80 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 117 optimal weight: 0.0070 chunk 49 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 174 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 118 optimal weight: 0.1980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.169428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113875 restraints weight = 74593.415| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.41 r_work: 0.3312 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5890 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= 0.101 Angle : 0.459 4.623 22140 Z= 0.251 Chirality : 0.034 0.121 2460 Planarity : 0.003 0.061 2756 Dihedral : 9.919 176.190 2332 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.03 % Allowed : 14.44 % Favored : 84.53 % 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: 2.16 (0.20), residues: 1936 helix: 1.87 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : 0.05 (0.34), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 519 TYR 0.011 0.001 TYR C 545 PHE 0.018 0.001 PHE F 20 TRP 0.006 0.001 TRP G 176 HIS 0.007 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (16372) covalent geometry : angle 0.45944 / 0.25 (22140) hydrogen bonds : bond 0.03603 / 2.38 ( 1080) hydrogen bonds : angle 3.64231 / 2.66 ( 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 468 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 451 time to evaluate : 0.853 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 210 MET cc_start: 0.8628 (mtp) cc_final: 0.8397 (mtp) REVERT: A 382 TYR cc_start: 0.7442 (t80) cc_final: 0.7082 (t80) REVERT: B 127 ARG cc_start: 0.9049 (ptm-80) cc_final: 0.8770 (tmm-80) REVERT: B 144 GLN cc_start: 0.8621 (mm110) cc_final: 0.8350 (mm-40) REVERT: B 145 MET cc_start: 0.8282 (ttp) cc_final: 0.7833 (tmm) REVERT: C 382 TYR cc_start: 0.7320 (t80) cc_final: 0.7072 (t80) REVERT: C 385 GLU cc_start: 0.6876 (pm20) cc_final: 0.6660 (pm20) REVERT: D 100 TYR cc_start: 0.8714 (m-80) cc_final: 0.8094 (m-10) REVERT: D 127 ARG cc_start: 0.9078 (ptm-80) cc_final: 0.8777 (tmm-80) REVERT: D 145 MET cc_start: 0.8322 (ttp) cc_final: 0.7878 (tmm) REVERT: E 210 MET cc_start: 0.8541 (mtp) cc_final: 0.8320 (mtp) REVERT: E 382 TYR cc_start: 0.7398 (t80) cc_final: 0.6974 (t80) REVERT: F 29 THR cc_start: 0.7614 (m) cc_final: 0.7395 (p) REVERT: F 125 MET cc_start: 0.9110 (ttt) cc_final: 0.8796 (ttt) REVERT: F 144 GLN cc_start: 0.8631 (mm110) cc_final: 0.8364 (mm-40) REVERT: F 145 MET cc_start: 0.8273 (ttp) cc_final: 0.7457 (tmm) REVERT: G 210 MET cc_start: 0.8577 (mtp) cc_final: 0.8331 (mtp) REVERT: G 382 TYR cc_start: 0.7737 (t80) cc_final: 0.7445 (t80) REVERT: G 555 ARG cc_start: 0.8339 (tpp80) cc_final: 0.7826 (mmm160) REVERT: H 29 THR cc_start: 0.7599 (m) cc_final: 0.7372 (p) REVERT: H 100 TYR cc_start: 0.8734 (m-80) cc_final: 0.8100 (m-10) REVERT: H 127 ARG cc_start: 0.9043 (ptm-80) cc_final: 0.8762 (tmm-80) REVERT: H 145 MET cc_start: 0.8171 (ttp) cc_final: 0.7719 (tmm) outliers start: 17 outliers final: 15 residues processed: 461 average time/residue: 0.3187 time to fit residues: 213.1107 Evaluate side-chains 434 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 419 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL 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 291 SER 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 20 PHE 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 H residue 20 PHE Chi-restraints excluded: chain H residue 131 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 136 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 386 ASN ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.169270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113532 restraints weight = 74842.973| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.36 r_work: 0.3315 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.6015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16372 Z= 0.112 Angle : 0.481 6.822 22140 Z= 0.262 Chirality : 0.034 0.151 2460 Planarity : 0.003 0.062 2756 Dihedral : 9.872 175.011 2332 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.15 % Allowed : 15.17 % Favored : 83.68 % 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: 2.19 (0.20), residues: 1936 helix: 1.90 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : 0.02 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 519 TYR 0.010 0.001 TYR E 545 PHE 0.016 0.001 PHE F 20 TRP 0.006 0.001 TRP G 176 HIS 0.009 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (16372) covalent geometry : angle 0.48077 / 0.26 (22140) hydrogen bonds : bond 0.03590 / 2.37 ( 1080) hydrogen bonds : angle 3.65410 / 2.66 ( 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 452 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 433 time to evaluate : 1.044 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: A 210 MET cc_start: 0.8624 (mtp) cc_final: 0.8411 (mtp) REVERT: A 382 TYR cc_start: 0.7603 (t80) cc_final: 0.7204 (t80) REVERT: B 127 ARG cc_start: 0.9062 (ptm-80) cc_final: 0.8790 (tmm-80) REVERT: B 145 MET cc_start: 0.8222 (ttp) cc_final: 0.7785 (tmm) REVERT: C 382 TYR cc_start: 0.7354 (t80) cc_final: 0.7028 (t80) REVERT: C 555 ARG cc_start: 0.7389 (mmm160) cc_final: 0.6015 (ttm110) REVERT: D 100 TYR cc_start: 0.8727 (m-80) cc_final: 0.8077 (m-10) REVERT: D 127 ARG cc_start: 0.9060 (ptm-80) cc_final: 0.8778 (tmm-80) REVERT: D 145 MET cc_start: 0.8270 (ttp) cc_final: 0.7836 (tmm) REVERT: E 210 MET cc_start: 0.8530 (mtp) cc_final: 0.8325 (mtp) REVERT: E 531 GLN cc_start: 0.8346 (mt0) cc_final: 0.7807 (pt0) REVERT: F 145 MET cc_start: 0.7930 (ttp) cc_final: 0.7668 (tmm) REVERT: G 210 MET cc_start: 0.8576 (mtp) cc_final: 0.8348 (mtp) REVERT: G 382 TYR cc_start: 0.7781 (t80) cc_final: 0.7405 (t80) REVERT: G 385 GLU cc_start: 0.6975 (pm20) cc_final: 0.6730 (pm20) REVERT: G 555 ARG cc_start: 0.8336 (tpp80) cc_final: 0.7785 (mmm160) REVERT: H 100 TYR cc_start: 0.8741 (m-80) cc_final: 0.8089 (m-10) REVERT: H 127 ARG cc_start: 0.9047 (ptm-80) cc_final: 0.8771 (tmm-80) outliers start: 19 outliers final: 17 residues processed: 446 average time/residue: 0.3328 time to fit residues: 213.8944 Evaluate side-chains 438 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 421 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE 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 291 SER Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain F residue 20 PHE 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: 7.9990 chunk 120 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 155 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 386 ASN ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.169494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113833 restraints weight = 74789.467| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.44 r_work: 0.3313 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16372 Z= 0.114 Angle : 0.486 6.170 22140 Z= 0.264 Chirality : 0.034 0.140 2460 Planarity : 0.004 0.087 2756 Dihedral : 9.841 174.651 2332 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.09 % Allowed : 15.23 % Favored : 83.68 % 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: 2.23 (0.20), residues: 1936 helix: 1.96 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.06 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 519 TYR 0.025 0.001 TYR E 382 PHE 0.016 0.001 PHE F 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 0.00254 / 0.11 (16372) covalent geometry : angle 0.48614 / 0.26 (22140) hydrogen bonds : bond 0.03534 / 2.34 ( 1080) hydrogen bonds : angle 3.64247 / 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 450 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 432 time to evaluate : 0.845 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: 0.8626 (mtp) cc_final: 0.8415 (mtp) REVERT: A 382 TYR cc_start: 0.7598 (t80) cc_final: 0.7238 (t80) REVERT: B 127 ARG cc_start: 0.9060 (ptm-80) cc_final: 0.8781 (tmm-80) REVERT: B 144 GLN cc_start: 0.8672 (mm110) cc_final: 0.8472 (mm-40) REVERT: B 145 MET cc_start: 0.8234 (ttp) cc_final: 0.7796 (tmm) REVERT: C 382 TYR cc_start: 0.7357 (t80) cc_final: 0.7025 (t80) REVERT: C 555 ARG cc_start: 0.7358 (mmm160) cc_final: 0.5955 (ttm110) REVERT: D 22 LYS cc_start: 0.5253 (mttt) cc_final: 0.5009 (mttp) REVERT: D 100 TYR cc_start: 0.8724 (m-80) cc_final: 0.8064 (m-10) REVERT: D 127 ARG cc_start: 0.9067 (ptm-80) cc_final: 0.8790 (tmm-80) REVERT: D 145 MET cc_start: 0.8264 (ttp) cc_final: 0.7831 (tmm) REVERT: E 531 GLN cc_start: 0.8348 (mt0) cc_final: 0.7802 (pt0) REVERT: F 145 MET cc_start: 0.8070 (ttp) cc_final: 0.7700 (tmm) REVERT: G 210 MET cc_start: 0.8578 (mtp) cc_final: 0.8351 (mtp) REVERT: G 382 TYR cc_start: 0.7803 (t80) cc_final: 0.7413 (t80) REVERT: G 555 ARG cc_start: 0.8363 (tpp80) cc_final: 0.7871 (mmm160) REVERT: H 100 TYR cc_start: 0.8748 (m-80) cc_final: 0.8087 (m-10) REVERT: H 127 ARG cc_start: 0.9040 (ptm-80) cc_final: 0.8765 (tmm-80) outliers start: 18 outliers final: 17 residues processed: 444 average time/residue: 0.3346 time to fit residues: 212.9580 Evaluate side-chains 437 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 420 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE 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 291 SER Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 138 ILE 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: 0.7980 chunk 162 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 171 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 134 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 386 ASN ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.169893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115426 restraints weight = 74780.830| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.94 r_work: 0.3296 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 16372 Z= 0.109 Angle : 0.492 6.272 22140 Z= 0.266 Chirality : 0.034 0.115 2460 Planarity : 0.004 0.079 2756 Dihedral : 9.751 174.572 2332 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.85 % Allowed : 15.66 % Favored : 83.50 % 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: 2.37 (0.20), residues: 1936 helix: 2.06 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.05 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 519 TYR 0.023 0.001 TYR E 382 PHE 0.015 0.001 PHE F 20 TRP 0.006 0.001 TRP G 176 HIS 0.009 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (16372) covalent geometry : angle 0.49244 / 0.27 (22140) hydrogen bonds : bond 0.03458 / 2.29 ( 1080) hydrogen bonds : angle 3.60664 / 2.62 ( 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 445 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 431 time to evaluate : 0.864 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: 0.8551 (mtp) cc_final: 0.8341 (mtp) REVERT: A 382 TYR cc_start: 0.7546 (t80) cc_final: 0.7187 (t80) REVERT: B 127 ARG cc_start: 0.9069 (ptm-80) cc_final: 0.8786 (tmm-80) REVERT: B 145 MET cc_start: 0.8223 (ttp) cc_final: 0.7788 (tmm) REVERT: C 382 TYR cc_start: 0.7291 (t80) cc_final: 0.7009 (t80) REVERT: C 555 ARG cc_start: 0.7178 (mmm160) cc_final: 0.6024 (ttm110) REVERT: D 22 LYS cc_start: 0.5218 (mttt) cc_final: 0.4964 (mttp) REVERT: D 100 TYR cc_start: 0.8702 (m-80) cc_final: 0.8013 (m-10) REVERT: D 127 ARG cc_start: 0.9073 (ptm-80) cc_final: 0.8799 (tmm-80) REVERT: D 145 MET cc_start: 0.8266 (ttp) cc_final: 0.7793 (tmm) REVERT: E 531 GLN cc_start: 0.8301 (mt0) cc_final: 0.7762 (pt0) REVERT: G 210 MET cc_start: 0.8518 (mtp) cc_final: 0.8286 (mtp) REVERT: H 100 TYR cc_start: 0.8677 (m-80) cc_final: 0.7993 (m-10) REVERT: H 127 ARG cc_start: 0.9040 (ptm-80) cc_final: 0.8766 (tmm-80) outliers start: 14 outliers final: 13 residues processed: 440 average time/residue: 0.3306 time to fit residues: 208.3113 Evaluate side-chains 429 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 416 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain F residue 137 VAL 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: 6.9990 chunk 79 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.167376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110749 restraints weight = 75374.315| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.35 r_work: 0.3280 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.6314 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= 0.172 Angle : 0.537 7.009 22140 Z= 0.293 Chirality : 0.036 0.121 2460 Planarity : 0.004 0.065 2756 Dihedral : 10.047 174.244 2332 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.09 % Allowed : 16.14 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.10 (0.19), residues: 1936 helix: 1.89 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.22 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 38 TYR 0.023 0.002 TYR E 382 PHE 0.015 0.001 PHE G 296 TRP 0.007 0.001 TRP A 176 HIS 0.011 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (16372) covalent geometry : angle 0.53737 / 0.29 (22140) hydrogen bonds : bond 0.03854 / 2.54 ( 1080) hydrogen bonds : angle 3.81093 / 2.77 ( 3192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11798.50 seconds wall clock time: 199 minutes 50.31 seconds (11990.31 seconds total)