Starting phenix.real_space_refine on Fri Jul 26 03:00:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnk_33317/07_2024/7xnk_33317_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnk_33317/07_2024/7xnk_33317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnk_33317/07_2024/7xnk_33317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnk_33317/07_2024/7xnk_33317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnk_33317/07_2024/7xnk_33317_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnk_33317/07_2024/7xnk_33317_neut_trim.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 S 88 5.16 5 C 10224 2.51 5 N 2700 2.21 5 O 2832 1.98 5 H 15652 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 174": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 228": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 237": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 243": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 293": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 360": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 366": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 511": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 539": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 174": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 228": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 237": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 243": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 293": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 360": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 366": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 511": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 539": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 174": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 228": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 237": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 243": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 293": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 360": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 366": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 511": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 539": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 174": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 228": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 237": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 243": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 293": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 360": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 366": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 511": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 539": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 31500 Number of models: 1 Model: "" Number of chains: 12 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: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Classifications: {'peptide': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Classifications: {'peptide': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Classifications: {'peptide': 1} Time building chain proxies: 13.38, per 1000 atoms: 0.42 Number of scatterers: 31500 At special positions: 0 Unit cell: (112.554, 113.568, 121.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 88 16.00 O 2832 8.00 N 2700 7.00 C 10224 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 - 3.50 Amino acid : False - 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: 25.43 Conformation dependent library (CDL) restraints added in 3.7 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: 100 helices and 4 sheets defined 77.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 120 through 143 Processing helix chain 'A' and resid 150 through 178 removed outlier: 3.891A pdb=" N PHE A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 195 Processing helix chain 'A' and resid 196 through 217 Processing helix chain 'A' and resid 224 through 237 removed outlier: 4.084A pdb=" N PHE A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 removed outlier: 3.522A pdb=" N VAL A 241 " --> pdb=" O MET A 238 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.532A pdb=" N THR A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) 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: 4.112A pdb=" N GLY A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.792A pdb=" N ALA A 370 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 533 removed outlier: 3.714A pdb=" N THR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 533 " --> pdb=" O PHE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 564 removed outlier: 3.834A pdb=" N ASP A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 22 removed outlier: 3.823A pdb=" N PHE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 removed outlier: 4.244A pdb=" N VAL B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 removed outlier: 3.788A pdb=" N GLU B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 79 through 92 removed outlier: 3.696A pdb=" N GLU B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.610A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.777A pdb=" N ARG B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 4.252A 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 150 through 178 removed outlier: 3.891A pdb=" N PHE C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C 161 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 195 Processing helix chain 'C' and resid 196 through 217 Processing helix chain 'C' and resid 224 through 237 removed outlier: 4.084A pdb=" N PHE C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 241 removed outlier: 3.521A pdb=" N VAL C 241 " --> pdb=" O MET C 238 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.531A pdb=" N THR C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) 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: 4.111A pdb=" N GLY C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 366 through 385 removed outlier: 3.793A pdb=" N ALA C 370 " --> pdb=" O ARG C 366 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU C 385 " --> pdb=" O CYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 533 removed outlier: 3.714A pdb=" N THR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 533 " --> pdb=" O PHE C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 564 removed outlier: 3.835A pdb=" N ASP C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 22 removed outlier: 3.824A pdb=" N PHE D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 40 removed outlier: 4.244A pdb=" N VAL D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 55 removed outlier: 3.788A pdb=" N GLU D 55 " --> pdb=" O ASP D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 75 Processing helix chain 'D' and resid 79 through 92 removed outlier: 3.696A pdb=" N GLU D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 113 removed outlier: 3.611A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 129 removed outlier: 3.777A pdb=" N ARG D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 4.252A 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 150 through 178 removed outlier: 3.891A pdb=" N PHE E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP E 158 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE E 161 " --> pdb=" O PHE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 195 Processing helix chain 'E' and resid 196 through 217 Processing helix chain 'E' and resid 224 through 237 removed outlier: 4.084A pdb=" N PHE E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 241 removed outlier: 3.522A pdb=" N VAL E 241 " --> pdb=" O MET E 238 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.532A pdb=" N THR E 311 " --> pdb=" O VAL E 307 " (cutoff:3.500A) 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: 4.112A pdb=" N GLY E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 366 through 385 removed outlier: 3.792A pdb=" N ALA E 370 " --> pdb=" O ARG E 366 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU E 385 " --> pdb=" O CYS E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 533 removed outlier: 3.714A pdb=" N THR E 513 " --> pdb=" O HIS E 509 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG E 533 " --> pdb=" O PHE E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 564 removed outlier: 3.835A pdb=" N ASP E 564 " --> pdb=" O GLN E 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 22 removed outlier: 3.824A pdb=" N PHE F 20 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 40 removed outlier: 4.244A pdb=" N VAL F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU F 40 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 removed outlier: 3.788A pdb=" N GLU F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 79 through 92 removed outlier: 3.695A pdb=" N GLU F 84 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 113 removed outlier: 3.611A pdb=" N LEU F 106 " --> pdb=" O SER F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 129 removed outlier: 3.777A pdb=" N ARG F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) removed outlier: 4.252A 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 150 through 178 removed outlier: 3.891A pdb=" N PHE G 157 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE G 161 " --> pdb=" O PHE G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 195 Processing helix chain 'G' and resid 196 through 217 Processing helix chain 'G' and resid 224 through 237 removed outlier: 4.085A pdb=" N PHE G 232 " --> pdb=" O ARG G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 241 removed outlier: 3.521A pdb=" N VAL G 241 " --> pdb=" O MET G 238 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.532A pdb=" N THR G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) 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: 4.113A pdb=" N GLY G 345 " --> pdb=" O ALA G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 364 No H-bonds generated for 'chain 'G' and resid 362 through 364' Processing helix chain 'G' and resid 366 through 385 removed outlier: 3.792A pdb=" N ALA G 370 " --> pdb=" O ARG G 366 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU G 385 " --> pdb=" O CYS G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 509 through 533 removed outlier: 3.714A pdb=" N THR G 513 " --> pdb=" O HIS G 509 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG G 533 " --> pdb=" O PHE G 529 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 564 removed outlier: 3.835A pdb=" N ASP G 564 " --> pdb=" O GLN G 560 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 22 removed outlier: 3.824A pdb=" N PHE H 20 " --> pdb=" O ALA H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 4.244A pdb=" N VAL H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 55 removed outlier: 3.788A pdb=" N GLU H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 79 through 92 removed outlier: 3.696A pdb=" N GLU H 84 " --> pdb=" O THR H 80 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 113 removed outlier: 3.610A pdb=" N LEU H 106 " --> pdb=" O SER H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 129 removed outlier: 3.776A pdb=" N ARG H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) removed outlier: 4.252A 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 101 Processing sheet with id=AA2, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'F' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 101 1065 hydrogen bonds defined for protein. 3171 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: 11.36 Time building geometry restraints manager: 26.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 15626 1.02 - 1.21: 30 1.21 - 1.41: 6978 1.41 - 1.61: 9058 1.61 - 1.81: 144 Bond restraints: 31836 Sorted by residual: 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 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 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=" 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=" CBE I0S C 701 " pdb=" SBF I0S C 701 " ideal model delta sigma weight residual 1.717 1.584 0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 31831 not shown) Histogram of bond angle deviations from ideal: 59.35 - 79.37: 41 79.37 - 99.38: 52 99.38 - 119.40: 43991 119.40 - 139.42: 13187 139.42 - 159.44: 1 Bond angle restraints: 57272 Sorted by residual: angle pdb=" C ALA F 58 " pdb=" N ASP F 59 " pdb=" H ASP F 59 " ideal model delta sigma weight residual 124.81 67.44 57.37 3.00e+00 1.11e-01 3.66e+02 angle pdb=" C ASP F 25 " pdb=" N GLY F 26 " pdb=" H GLY F 26 " ideal model delta sigma weight residual 124.39 68.85 55.53 3.00e+00 1.11e-01 3.43e+02 angle pdb=" CA ASP F 59 " pdb=" N ASP F 59 " pdb=" H ASP F 59 " ideal model delta sigma weight residual 114.51 59.35 55.16 3.00e+00 1.11e-01 3.38e+02 angle pdb=" C ASP D 25 " pdb=" N GLY D 26 " pdb=" H GLY D 26 " ideal model delta sigma weight residual 124.39 70.44 53.95 3.00e+00 1.11e-01 3.23e+02 angle pdb=" CA GLY D 26 " pdb=" N GLY D 26 " pdb=" H GLY D 26 " ideal model delta sigma weight residual 114.09 60.66 53.42 3.00e+00 1.11e-01 3.17e+02 ... (remaining 57267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.18: 14533 34.18 - 68.36: 332 68.36 - 102.55: 19 102.55 - 136.73: 4 136.73 - 170.91: 8 Dihedral angle restraints: 14896 sinusoidal: 7980 harmonic: 6916 Sorted by residual: dihedral pdb=" CA ARG H 75 " pdb=" C ARG H 75 " pdb=" N LYS H 76 " pdb=" CA LYS H 76 " ideal model delta harmonic sigma weight residual 180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ARG D 75 " pdb=" C ARG D 75 " pdb=" N LYS D 76 " pdb=" CA LYS D 76 " ideal model delta harmonic sigma weight residual -180.00 -156.47 -23.53 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ARG B 75 " pdb=" C ARG B 75 " pdb=" N LYS B 76 " pdb=" CA LYS B 76 " ideal model delta harmonic sigma weight residual -180.00 -156.47 -23.53 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 14893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 2266 0.155 - 0.311: 146 0.311 - 0.466: 12 0.466 - 0.622: 4 0.622 - 0.777: 4 Chirality restraints: 2432 Sorted by residual: chirality pdb=" CB THR B 29 " pdb=" CA THR B 29 " pdb=" OG1 THR B 29 " pdb=" CG2 THR B 29 " both_signs ideal model delta sigma weight residual False 2.55 1.77 0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" CB THR H 29 " pdb=" CA THR H 29 " pdb=" OG1 THR H 29 " pdb=" CG2 THR H 29 " both_signs ideal model delta sigma weight residual False 2.55 1.78 0.78 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" CB THR D 29 " pdb=" CA THR D 29 " pdb=" OG1 THR D 29 " pdb=" CG2 THR D 29 " both_signs ideal model delta sigma weight residual False 2.55 1.78 0.78 2.00e-01 2.50e+01 1.50e+01 ... (remaining 2429 not shown) Planarity restraints: 4664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 61 " -0.022 2.00e-02 2.50e+03 2.17e-02 7.04e+00 pdb=" CG ASN H 61 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN H 61 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN H 61 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN H 61 " 0.030 2.00e-02 2.50e+03 pdb="HD22 ASN H 61 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 61 " 0.022 2.00e-02 2.50e+03 2.14e-02 6.89e+00 pdb=" CG ASN D 61 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN D 61 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN D 61 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN D 61 " -0.030 2.00e-02 2.50e+03 pdb="HD22 ASN D 61 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY H 24 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" N ASP H 25 " 0.043 2.00e-02 2.50e+03 pdb=" CA ASP H 25 " -0.011 2.00e-02 2.50e+03 pdb=" H ASP H 25 " -0.020 2.00e-02 2.50e+03 ... (remaining 4661 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.21: 2093 2.21 - 2.94: 81869 2.94 - 3.68: 108506 3.68 - 4.41: 166533 4.41 - 5.14: 268394 Nonbonded interactions: 627395 Sorted by model distance: nonbonded pdb=" H LEU F 40 " pdb=" HA LEU F 40 " model vdw 1.478 1.816 nonbonded pdb=" H ASP F 59 " pdb=" HA ASP F 59 " model vdw 1.513 1.816 nonbonded pdb=" H GLN F 9 " pdb=" HA GLN F 9 " model vdw 1.523 1.816 nonbonded pdb=" H GLY F 26 " pdb=" HA3 GLY F 26 " model vdw 1.524 1.816 nonbonded pdb=" H ILE F 28 " pdb=" HA ILE F 28 " model vdw 1.548 1.816 ... (remaining 627390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.120 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: 0.490 Extract box with map and model: 1.320 Check model and map are aligned: 0.230 Set scattering table: 0.330 Process input model: 103.120 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 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 : 0.020 0.169 16184 Z= 1.312 Angle : 1.100 15.849 21880 Z= 0.588 Chirality : 0.088 0.777 2432 Planarity : 0.005 0.062 2748 Dihedral : 12.810 170.912 5888 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.73 % Allowed : 0.24 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.17), residues: 1936 helix: -1.09 (0.11), residues: 1480 sheet: None (None), residues: 0 loop : -0.74 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 305 HIS 0.005 0.002 HIS G 126 PHE 0.024 0.004 PHE C 332 TYR 0.023 0.003 TYR C 299 ARG 0.009 0.001 ARG E 174 *********************** 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 591 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 579 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 191 LEU cc_start: 0.8884 (tp) cc_final: 0.8682 (mp) REVERT: A 228 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7168 (tmt170) REVERT: A 523 PHE cc_start: 0.8147 (m-10) cc_final: 0.7877 (m-10) REVERT: A 537 ASP cc_start: 0.8235 (t0) cc_final: 0.7537 (p0) REVERT: A 540 ASP cc_start: 0.8523 (m-30) cc_final: 0.8235 (m-30) REVERT: A 550 LEU cc_start: 0.8829 (mp) cc_final: 0.8582 (pp) REVERT: B 79 ASP cc_start: 0.7089 (t70) cc_final: 0.6811 (t70) REVERT: B 80 THR cc_start: 0.8041 (m) cc_final: 0.7744 (p) REVERT: B 116 LYS cc_start: 0.8757 (mttt) cc_final: 0.8453 (mttp) REVERT: C 191 LEU cc_start: 0.8977 (tp) cc_final: 0.8747 (mp) REVERT: C 228 ARG cc_start: 0.7566 (mtt180) cc_final: 0.7199 (tmt170) REVERT: C 288 VAL cc_start: 0.9147 (p) cc_final: 0.8887 (t) REVERT: C 537 ASP cc_start: 0.8214 (t0) cc_final: 0.7618 (p0) REVERT: C 540 ASP cc_start: 0.8519 (m-30) cc_final: 0.8217 (m-30) REVERT: C 543 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7864 (mt-10) REVERT: C 550 LEU cc_start: 0.8832 (mp) cc_final: 0.8592 (pp) REVERT: D 72 MET cc_start: 0.6731 (ttp) cc_final: 0.6485 (ttp) REVERT: D 116 LYS cc_start: 0.8593 (mttt) cc_final: 0.7996 (mttp) REVERT: E 228 ARG cc_start: 0.7593 (mtt180) cc_final: 0.7231 (tmt170) REVERT: E 288 VAL cc_start: 0.9063 (p) cc_final: 0.8809 (t) REVERT: E 537 ASP cc_start: 0.8226 (t0) cc_final: 0.7524 (p0) REVERT: E 550 LEU cc_start: 0.8869 (mp) cc_final: 0.8576 (pp) REVERT: F 79 ASP cc_start: 0.6592 (t70) cc_final: 0.6317 (t70) REVERT: G 105 HIS cc_start: 0.6767 (t-90) cc_final: 0.6506 (t-170) REVERT: G 228 ARG cc_start: 0.7626 (mtt180) cc_final: 0.7366 (tmt170) REVERT: G 288 VAL cc_start: 0.9186 (p) cc_final: 0.8857 (t) REVERT: G 537 ASP cc_start: 0.8190 (t0) cc_final: 0.7535 (p0) REVERT: G 540 ASP cc_start: 0.8442 (m-30) cc_final: 0.8113 (m-30) REVERT: G 543 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8061 (mt-10) REVERT: G 550 LEU cc_start: 0.8866 (mp) cc_final: 0.8579 (pp) REVERT: H 116 LYS cc_start: 0.8609 (mttt) cc_final: 0.7974 (mttp) outliers start: 12 outliers final: 4 residues processed: 586 average time/residue: 3.0590 time to fit residues: 1957.1706 Evaluate side-chains 379 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 375 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain H residue 27 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 174 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 321 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN E 289 ASN F 54 ASN F 112 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN H 144 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16184 Z= 0.191 Angle : 0.662 20.620 21880 Z= 0.354 Chirality : 0.087 1.627 2432 Planarity : 0.004 0.057 2748 Dihedral : 10.557 171.058 2271 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.49 % Allowed : 14.75 % Favored : 82.77 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1936 helix: 0.71 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -0.37 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 379 HIS 0.006 0.001 HIS H 108 PHE 0.016 0.001 PHE F 90 TYR 0.010 0.001 TYR C 545 ARG 0.010 0.001 ARG H 127 *********************** 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 448 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 407 time to evaluate : 2.446 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 191 LEU cc_start: 0.8852 (tp) cc_final: 0.8614 (mp) REVERT: A 228 ARG cc_start: 0.7591 (mtt180) cc_final: 0.7259 (tmt170) REVERT: A 555 ARG cc_start: 0.7226 (mtp85) cc_final: 0.6606 (ttm-80) REVERT: B 52 MET cc_start: 0.7199 (mtp) cc_final: 0.6656 (mtp) REVERT: B 127 ARG cc_start: 0.8657 (mtm110) cc_final: 0.8440 (mtm110) REVERT: B 140 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: C 191 LEU cc_start: 0.8857 (tp) cc_final: 0.8630 (mp) REVERT: C 228 ARG cc_start: 0.7439 (mtt180) cc_final: 0.7178 (tmt170) REVERT: C 290 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: D 72 MET cc_start: 0.6787 (ttp) cc_final: 0.6523 (ttp) REVERT: D 116 LYS cc_start: 0.8750 (mttt) cc_final: 0.8082 (mttp) REVERT: E 228 ARG cc_start: 0.7551 (mtt180) cc_final: 0.7308 (tmt170) REVERT: E 555 ARG cc_start: 0.7233 (mtp85) cc_final: 0.6810 (ttm-80) REVERT: F 73 MET cc_start: 0.6018 (mmp) cc_final: 0.5429 (mmp) REVERT: F 81 ASP cc_start: 0.8746 (m-30) cc_final: 0.8494 (m-30) REVERT: F 116 LYS cc_start: 0.8842 (mttt) cc_final: 0.8564 (mptt) REVERT: G 228 ARG cc_start: 0.7585 (mtt180) cc_final: 0.7326 (tmt170) REVERT: G 509 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.5847 (m-70) REVERT: H 73 MET cc_start: 0.5985 (mmp) cc_final: 0.5329 (mmt) REVERT: H 79 ASP cc_start: 0.6690 (t70) cc_final: 0.6447 (t70) REVERT: H 87 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7438 (ttm-80) REVERT: H 127 ARG cc_start: 0.8475 (mtm110) cc_final: 0.8204 (mtm110) REVERT: H 144 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8224 (mt0) outliers start: 41 outliers final: 16 residues processed: 423 average time/residue: 2.9480 time to fit residues: 1368.3622 Evaluate side-chains 348 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 329 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain G residue 388 ASP Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 16184 Z= 0.483 Angle : 0.730 20.616 21880 Z= 0.397 Chirality : 0.091 1.626 2432 Planarity : 0.005 0.060 2748 Dihedral : 10.845 173.273 2267 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.82 % Allowed : 16.57 % Favored : 79.61 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 1936 helix: 1.05 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.39 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 379 HIS 0.006 0.001 HIS E 509 PHE 0.018 0.002 PHE F 20 TYR 0.029 0.002 TYR D 139 ARG 0.010 0.001 ARG H 75 *********************** 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 404 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 341 time to evaluate : 2.297 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: A 191 LEU cc_start: 0.8967 (tp) cc_final: 0.8606 (mm) REVERT: A 228 ARG cc_start: 0.7686 (mtt180) cc_final: 0.7465 (tmt170) REVERT: A 537 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7678 (m-30) REVERT: B 23 ASP cc_start: 0.5432 (OUTLIER) cc_final: 0.5063 (m-30) REVERT: B 52 MET cc_start: 0.7272 (mtp) cc_final: 0.7054 (mtp) REVERT: B 73 MET cc_start: 0.6127 (mmp) cc_final: 0.5500 (mmt) REVERT: B 96 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7350 (m-30) REVERT: B 116 LYS cc_start: 0.8890 (mttt) cc_final: 0.8650 (mttp) REVERT: C 191 LEU cc_start: 0.8973 (tp) cc_final: 0.8613 (mm) REVERT: C 290 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: D 20 PHE cc_start: 0.6866 (m-80) cc_final: 0.6577 (m-80) REVERT: D 77 MET cc_start: 0.5588 (OUTLIER) cc_final: 0.4597 (ppp) REVERT: D 116 LYS cc_start: 0.8950 (mttt) cc_final: 0.8720 (mttp) REVERT: D 141 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: E 170 GLU cc_start: 0.7725 (tt0) cc_final: 0.7397 (tt0) REVERT: E 228 ARG cc_start: 0.7749 (mtt180) cc_final: 0.7508 (tmt170) REVERT: F 37 MET cc_start: 0.8123 (mtm) cc_final: 0.7911 (mtm) REVERT: F 73 MET cc_start: 0.6210 (mmp) cc_final: 0.5949 (mmp) REVERT: F 81 ASP cc_start: 0.8580 (m-30) cc_final: 0.8361 (m-30) REVERT: F 96 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7167 (m-30) REVERT: F 116 LYS cc_start: 0.8974 (mttt) cc_final: 0.8259 (mptt) REVERT: G 509 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.5846 (m-70) REVERT: H 96 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7523 (m-30) REVERT: H 116 LYS cc_start: 0.8902 (mttt) cc_final: 0.8659 (mttp) outliers start: 63 outliers final: 30 residues processed: 365 average time/residue: 2.7564 time to fit residues: 1109.9673 Evaluate side-chains 355 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 316 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 540 ASP Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 388 ASP Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 540 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 140 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 117 optimal weight: 0.4980 chunk 175 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 91 optimal weight: 0.3980 chunk 166 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16184 Z= 0.162 Angle : 0.604 20.621 21880 Z= 0.322 Chirality : 0.087 1.649 2432 Planarity : 0.004 0.054 2748 Dihedral : 9.805 168.551 2265 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.06 % Allowed : 19.48 % Favored : 78.46 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.19), residues: 1936 helix: 1.63 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -0.04 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 379 HIS 0.004 0.001 HIS E 509 PHE 0.027 0.001 PHE B 20 TYR 0.008 0.001 TYR C 545 ARG 0.013 0.001 ARG H 127 *********************** 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 378 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 344 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 191 LEU cc_start: 0.8890 (tp) cc_final: 0.8675 (mp) REVERT: A 228 ARG cc_start: 0.7547 (mtt180) cc_final: 0.7280 (tmt170) REVERT: B 52 MET cc_start: 0.7295 (mtp) cc_final: 0.6956 (ttm) REVERT: B 116 LYS cc_start: 0.8879 (mttt) cc_final: 0.8625 (mttp) REVERT: C 191 LEU cc_start: 0.8876 (tp) cc_final: 0.8657 (mp) REVERT: D 116 LYS cc_start: 0.8943 (mttt) cc_final: 0.8725 (mttp) REVERT: E 228 ARG cc_start: 0.7559 (mtt180) cc_final: 0.7295 (tmt170) REVERT: F 73 MET cc_start: 0.6168 (mmp) cc_final: 0.5846 (mmt) REVERT: F 81 ASP cc_start: 0.8572 (m-30) cc_final: 0.8316 (m-30) REVERT: F 116 LYS cc_start: 0.8960 (mttt) cc_final: 0.8211 (mptt) REVERT: G 509 HIS cc_start: 0.7334 (OUTLIER) cc_final: 0.5836 (m-70) REVERT: H 72 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6877 (ttm) REVERT: H 73 MET cc_start: 0.6045 (mmp) cc_final: 0.5395 (mmt) REVERT: H 87 ARG cc_start: 0.7999 (ttm110) cc_final: 0.7711 (ttm-80) REVERT: H 116 LYS cc_start: 0.8864 (mttt) cc_final: 0.8621 (mttp) outliers start: 34 outliers final: 12 residues processed: 362 average time/residue: 2.9479 time to fit residues: 1190.6813 Evaluate side-chains 331 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 317 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 537 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 76 optimal weight: 0.0670 chunk 158 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16184 Z= 0.192 Angle : 0.608 20.787 21880 Z= 0.325 Chirality : 0.089 1.664 2432 Planarity : 0.004 0.068 2748 Dihedral : 9.798 167.275 2265 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.49 % Allowed : 20.51 % Favored : 77.00 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.19), residues: 1936 helix: 1.88 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : 0.13 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 379 HIS 0.004 0.001 HIS E 509 PHE 0.023 0.001 PHE B 20 TYR 0.010 0.001 TYR D 139 ARG 0.015 0.001 ARG F 127 *********************** 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 370 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 329 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.8888 (tp) cc_final: 0.8673 (mp) REVERT: A 228 ARG cc_start: 0.7558 (mtt180) cc_final: 0.7285 (tmt170) REVERT: B 73 MET cc_start: 0.6046 (mmp) cc_final: 0.5375 (mmt) REVERT: B 116 LYS cc_start: 0.8932 (mttt) cc_final: 0.8662 (mttp) REVERT: C 191 LEU cc_start: 0.8919 (tp) cc_final: 0.8706 (mp) REVERT: C 539 ARG cc_start: 0.8164 (tmm-80) cc_final: 0.7902 (tmm-80) REVERT: D 63 THR cc_start: 0.8011 (p) cc_final: 0.7787 (t) REVERT: D 116 LYS cc_start: 0.8960 (mttt) cc_final: 0.8726 (mttp) REVERT: E 228 ARG cc_start: 0.7573 (mtt180) cc_final: 0.7329 (tmt170) REVERT: F 73 MET cc_start: 0.6098 (mmp) cc_final: 0.5758 (mmp) REVERT: F 81 ASP cc_start: 0.8546 (m-30) cc_final: 0.8317 (m-30) REVERT: F 116 LYS cc_start: 0.8952 (mttt) cc_final: 0.8190 (mptt) REVERT: H 72 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6833 (ttm) REVERT: H 73 MET cc_start: 0.6210 (mmp) cc_final: 0.5499 (mmt) REVERT: H 116 LYS cc_start: 0.8912 (mttt) cc_final: 0.8666 (mttp) outliers start: 41 outliers final: 23 residues processed: 353 average time/residue: 2.8941 time to fit residues: 1122.5816 Evaluate side-chains 342 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 318 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 388 ASP Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 GLN G 359 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16184 Z= 0.313 Angle : 0.653 20.915 21880 Z= 0.352 Chirality : 0.090 1.644 2432 Planarity : 0.005 0.078 2748 Dihedral : 10.002 167.680 2265 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.22 % Allowed : 20.39 % Favored : 76.40 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.19), residues: 1936 helix: 1.77 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : 0.07 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.003 0.001 HIS E 509 PHE 0.023 0.002 PHE B 20 TYR 0.019 0.001 TYR F 139 ARG 0.015 0.001 ARG F 127 *********************** 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 384 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 331 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.8946 (tp) cc_final: 0.8728 (mp) REVERT: A 228 ARG cc_start: 0.7636 (mtt180) cc_final: 0.7390 (tmt170) REVERT: B 13 PHE cc_start: 0.7653 (m-80) cc_final: 0.7389 (m-80) REVERT: B 73 MET cc_start: 0.6071 (mmp) cc_final: 0.5416 (mmt) REVERT: B 116 LYS cc_start: 0.9028 (mttt) cc_final: 0.8764 (mttp) REVERT: C 191 LEU cc_start: 0.8951 (tp) cc_final: 0.8735 (mp) REVERT: D 63 THR cc_start: 0.8147 (p) cc_final: 0.7881 (t) REVERT: D 75 ARG cc_start: 0.7180 (ppt-90) cc_final: 0.6980 (ppt-90) REVERT: D 77 MET cc_start: 0.5739 (OUTLIER) cc_final: 0.4845 (ppp) REVERT: D 116 LYS cc_start: 0.8978 (mttt) cc_final: 0.8756 (mttp) REVERT: E 228 ARG cc_start: 0.7718 (mtt180) cc_final: 0.7384 (tmt170) REVERT: F 72 MET cc_start: 0.6678 (ttp) cc_final: 0.6412 (mtm) REVERT: F 73 MET cc_start: 0.6295 (mmp) cc_final: 0.5907 (mmt) REVERT: F 116 LYS cc_start: 0.8969 (mttt) cc_final: 0.8612 (mptt) REVERT: H 72 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6739 (ttm) REVERT: H 73 MET cc_start: 0.6210 (mmp) cc_final: 0.5469 (mmt) REVERT: H 87 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7823 (ttm-80) REVERT: H 116 LYS cc_start: 0.8922 (mttt) cc_final: 0.8681 (mttp) outliers start: 53 outliers final: 37 residues processed: 361 average time/residue: 2.7504 time to fit residues: 1095.8589 Evaluate side-chains 355 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 316 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain G residue 148 TYR Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 388 ASP Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 119 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 135 optimal weight: 0.0170 chunk 156 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 85 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16184 Z= 0.194 Angle : 0.617 20.777 21880 Z= 0.329 Chirality : 0.089 1.641 2432 Planarity : 0.004 0.087 2748 Dihedral : 9.712 165.793 2265 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.61 % Allowed : 22.21 % Favored : 75.18 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.19), residues: 1936 helix: 1.99 (0.14), residues: 1468 sheet: None (None), residues: 0 loop : 0.32 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 379 HIS 0.004 0.001 HIS E 509 PHE 0.021 0.001 PHE B 20 TYR 0.010 0.001 TYR C 545 ARG 0.015 0.001 ARG F 127 *********************** 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 377 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 334 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.8918 (tp) cc_final: 0.8682 (mp) REVERT: A 228 ARG cc_start: 0.7604 (mtt180) cc_final: 0.7369 (tmt170) REVERT: B 116 LYS cc_start: 0.9026 (mttt) cc_final: 0.8764 (mttp) REVERT: C 191 LEU cc_start: 0.8921 (tp) cc_final: 0.8711 (mp) REVERT: C 214 CYS cc_start: 0.7921 (t) cc_final: 0.7588 (t) REVERT: D 116 LYS cc_start: 0.8973 (mttt) cc_final: 0.8747 (mttp) REVERT: E 228 ARG cc_start: 0.7687 (mtt180) cc_final: 0.7357 (tmt170) REVERT: F 116 LYS cc_start: 0.8953 (mttt) cc_final: 0.8608 (mptt) REVERT: G 191 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8321 (mp) REVERT: H 72 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6790 (ttm) REVERT: H 73 MET cc_start: 0.6248 (mmp) cc_final: 0.5480 (mmt) REVERT: H 87 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7834 (ttm-80) REVERT: H 116 LYS cc_start: 0.8968 (mttt) cc_final: 0.8571 (mttp) outliers start: 43 outliers final: 25 residues processed: 360 average time/residue: 2.8765 time to fit residues: 1142.2378 Evaluate side-chains 352 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 325 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 145 optimal weight: 0.3980 chunk 168 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN F 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16184 Z= 0.192 Angle : 0.621 20.705 21880 Z= 0.330 Chirality : 0.089 1.671 2432 Planarity : 0.004 0.094 2748 Dihedral : 9.586 163.882 2265 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.37 % Allowed : 22.63 % Favored : 75.00 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.20), residues: 1936 helix: 2.11 (0.14), residues: 1468 sheet: None (None), residues: 0 loop : 0.45 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 379 HIS 0.004 0.001 HIS E 509 PHE 0.033 0.001 PHE F 13 TYR 0.013 0.001 TYR G 545 ARG 0.018 0.001 ARG F 127 *********************** 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 365 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 326 time to evaluate : 2.500 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 191 LEU cc_start: 0.8899 (tp) cc_final: 0.8665 (mp) REVERT: B 73 MET cc_start: 0.5933 (mmp) cc_final: 0.5569 (tpt) REVERT: B 116 LYS cc_start: 0.9008 (mttt) cc_final: 0.8738 (mttp) REVERT: C 191 LEU cc_start: 0.8899 (tp) cc_final: 0.8692 (mp) REVERT: C 214 CYS cc_start: 0.7835 (t) cc_final: 0.7500 (t) REVERT: D 116 LYS cc_start: 0.8970 (mttt) cc_final: 0.8743 (mttp) REVERT: E 228 ARG cc_start: 0.7542 (mtt180) cc_final: 0.7318 (tmt170) REVERT: F 72 MET cc_start: 0.6932 (ttp) cc_final: 0.6496 (mtm) REVERT: F 85 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8464 (mm-30) REVERT: F 116 LYS cc_start: 0.8956 (mttt) cc_final: 0.8615 (mptt) REVERT: G 170 GLU cc_start: 0.7551 (tt0) cc_final: 0.7166 (tt0) REVERT: G 191 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8322 (mp) REVERT: H 73 MET cc_start: 0.6240 (mmp) cc_final: 0.5493 (mmt) REVERT: H 87 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7682 (mtm110) REVERT: H 116 LYS cc_start: 0.8969 (mttt) cc_final: 0.8579 (mttp) outliers start: 39 outliers final: 24 residues processed: 347 average time/residue: 2.7999 time to fit residues: 1069.9053 Evaluate side-chains 341 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 316 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN C 289 ASN C 359 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.6212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16184 Z= 0.344 Angle : 0.674 20.777 21880 Z= 0.363 Chirality : 0.090 1.643 2432 Planarity : 0.005 0.106 2748 Dihedral : 9.958 166.587 2264 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.37 % Allowed : 23.36 % Favored : 74.27 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.19), residues: 1936 helix: 1.87 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : 0.34 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 379 HIS 0.004 0.001 HIS E 509 PHE 0.018 0.002 PHE B 20 TYR 0.021 0.002 TYR H 139 ARG 0.018 0.001 ARG F 127 *********************** 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 358 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 319 time to evaluate : 2.622 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 191 LEU cc_start: 0.8956 (tp) cc_final: 0.8721 (mp) REVERT: B 73 MET cc_start: 0.5903 (mmp) cc_final: 0.5486 (mmt) REVERT: B 116 LYS cc_start: 0.9032 (mttt) cc_final: 0.8778 (mttp) REVERT: B 127 ARG cc_start: 0.8321 (mtm110) cc_final: 0.8051 (mtm110) REVERT: C 191 LEU cc_start: 0.8962 (tp) cc_final: 0.8756 (mp) REVERT: C 214 CYS cc_start: 0.7809 (t) cc_final: 0.7518 (t) REVERT: C 530 GLN cc_start: 0.8585 (tt0) cc_final: 0.8331 (tp-100) REVERT: D 77 MET cc_start: 0.5589 (OUTLIER) cc_final: 0.4796 (pp-130) REVERT: D 116 LYS cc_start: 0.8984 (mttt) cc_final: 0.8644 (mttp) REVERT: E 228 ARG cc_start: 0.7583 (mtt180) cc_final: 0.7349 (tmt170) REVERT: F 72 MET cc_start: 0.6279 (ttp) cc_final: 0.6077 (mtm) REVERT: F 116 LYS cc_start: 0.8999 (mttt) cc_final: 0.8631 (mptt) REVERT: F 127 ARG cc_start: 0.8598 (mtm110) cc_final: 0.8340 (mtm110) REVERT: G 170 GLU cc_start: 0.7576 (tt0) cc_final: 0.7193 (tt0) REVERT: G 191 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8366 (mp) REVERT: H 73 MET cc_start: 0.6262 (mmp) cc_final: 0.5509 (mmt) REVERT: H 116 LYS cc_start: 0.9052 (mttt) cc_final: 0.8655 (mttp) outliers start: 39 outliers final: 29 residues processed: 345 average time/residue: 2.7156 time to fit residues: 1037.6515 Evaluate side-chains 343 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 312 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 148 TYR Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 388 ASP Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 119 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 152 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN F 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16184 Z= 0.174 Angle : 0.640 20.701 21880 Z= 0.338 Chirality : 0.089 1.671 2432 Planarity : 0.004 0.099 2748 Dihedral : 9.497 163.292 2264 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.21 % Allowed : 24.64 % Favored : 74.15 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.19), residues: 1936 helix: 2.11 (0.14), residues: 1468 sheet: None (None), residues: 0 loop : 0.47 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 379 HIS 0.003 0.001 HIS E 509 PHE 0.021 0.001 PHE B 20 TYR 0.013 0.001 TYR C 545 ARG 0.018 0.001 ARG F 127 ********************** 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 338 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 318 time to evaluate : 2.598 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 191 LEU cc_start: 0.8909 (tp) cc_final: 0.8682 (mp) REVERT: B 14 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7794 (mmmm) REVERT: B 73 MET cc_start: 0.6104 (mmp) cc_final: 0.5515 (mmt) REVERT: B 116 LYS cc_start: 0.9017 (mttt) cc_final: 0.8760 (mttp) REVERT: B 127 ARG cc_start: 0.8307 (mtm110) cc_final: 0.8077 (mtm110) REVERT: C 214 CYS cc_start: 0.7720 (t) cc_final: 0.7424 (t) REVERT: D 23 ASP cc_start: 0.5966 (m-30) cc_final: 0.5681 (m-30) REVERT: D 116 LYS cc_start: 0.9000 (mttt) cc_final: 0.8609 (mttp) REVERT: E 228 ARG cc_start: 0.7531 (mtt180) cc_final: 0.7303 (tmt170) REVERT: E 534 LYS cc_start: 0.8404 (mmmm) cc_final: 0.8169 (mmtt) REVERT: F 72 MET cc_start: 0.6305 (ttp) cc_final: 0.6081 (mtm) REVERT: F 116 LYS cc_start: 0.8973 (mttt) cc_final: 0.8599 (mptt) REVERT: F 127 ARG cc_start: 0.8589 (mtm110) cc_final: 0.8323 (mtm110) REVERT: G 191 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8323 (mp) REVERT: H 73 MET cc_start: 0.6182 (mmp) cc_final: 0.5433 (mmt) REVERT: H 87 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7840 (ttm-80) REVERT: H 116 LYS cc_start: 0.9033 (mttt) cc_final: 0.8637 (mttp) outliers start: 20 outliers final: 14 residues processed: 333 average time/residue: 2.8258 time to fit residues: 1039.9516 Evaluate side-chains 327 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 312 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 152 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 133 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.177634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.106654 restraints weight = 60716.996| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.16 r_work: 0.3159 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16184 Z= 0.166 Angle : 0.630 20.697 21880 Z= 0.334 Chirality : 0.089 1.669 2432 Planarity : 0.004 0.095 2748 Dihedral : 9.241 159.240 2264 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.09 % Allowed : 24.82 % Favored : 74.09 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.19), residues: 1936 helix: 2.28 (0.14), residues: 1472 sheet: None (None), residues: 0 loop : 0.45 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 379 HIS 0.003 0.000 HIS E 509 PHE 0.021 0.001 PHE B 20 TYR 0.012 0.001 TYR C 545 ARG 0.017 0.001 ARG F 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17165.89 seconds wall clock time: 294 minutes 42.84 seconds (17682.84 seconds total)