Starting phenix.real_space_refine on Wed Feb 21 20:35:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnk_33317/02_2024/7xnk_33317_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnk_33317/02_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_33317/02_2024/7xnk_33317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnk_33317/02_2024/7xnk_33317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnk_33317/02_2024/7xnk_33317_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnk_33317/02_2024/7xnk_33317_neut_trim_updated.pdb" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 15.52, per 1000 atoms: 0.49 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: 26.56 Conformation dependent library (CDL) restraints added in 3.0 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... running ksdssp... Secondary structure from input PDB file: 92 helices and 0 sheets defined 71.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 121 through 144 removed outlier: 3.879A pdb=" N THR A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 179 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) removed outlier: 4.922A pdb=" N GLY A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 197 through 216 Processing helix chain 'A' and resid 224 through 240 removed outlier: 4.084A pdb=" N PHE A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N HIS A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 259 through 284 Processing helix chain 'A' and resid 299 through 310 Processing helix chain 'A' and resid 323 through 335 Processing helix chain 'A' and resid 337 through 340 Processing helix chain 'A' and resid 342 through 363 removed outlier: 4.494A pdb=" N LYS A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS A 363 " --> pdb=" O GLN A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.972A pdb=" N GLU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 538 through 563 Processing helix chain 'B' and resid 7 through 21 removed outlier: 3.823A pdb=" N PHE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 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 46 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 66 through 74 Processing helix chain 'B' and resid 80 through 93 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) removed outlier: 4.486A pdb=" N PHE B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 112 Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.777A pdb=" N ARG B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 Processing helix chain 'C' and resid 105 through 114 Processing helix chain 'C' and resid 121 through 144 removed outlier: 3.879A pdb=" N THR C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 179 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) removed outlier: 4.922A pdb=" N GLY C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 194 Processing helix chain 'C' and resid 197 through 216 Processing helix chain 'C' and resid 224 through 240 removed outlier: 4.084A pdb=" N PHE C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET C 238 " --> pdb=" O GLN C 234 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N HIS C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 257 Processing helix chain 'C' and resid 259 through 284 Processing helix chain 'C' and resid 299 through 310 Processing helix chain 'C' and resid 323 through 335 Processing helix chain 'C' and resid 337 through 340 Processing helix chain 'C' and resid 342 through 363 removed outlier: 4.493A pdb=" N LYS C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS C 363 " --> pdb=" O GLN C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.970A pdb=" N GLU C 385 " --> pdb=" O CYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 538 through 563 Processing helix chain 'D' and resid 7 through 21 removed outlier: 3.824A pdb=" N PHE D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 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 46 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 66 through 74 Processing helix chain 'D' and resid 80 through 93 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) removed outlier: 4.486A pdb=" N PHE D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 112 Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.777A pdb=" N ARG D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'E' and resid 105 through 114 Processing helix chain 'E' and resid 121 through 144 removed outlier: 3.879A pdb=" N THR E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 179 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) removed outlier: 4.921A pdb=" N GLY E 179 " --> pdb=" O LEU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 194 Processing helix chain 'E' and resid 197 through 216 Processing helix chain 'E' and resid 224 through 240 removed outlier: 4.084A pdb=" N PHE E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET E 238 " --> pdb=" O GLN E 234 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N HIS E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 257 Processing helix chain 'E' and resid 259 through 284 Processing helix chain 'E' and resid 299 through 310 Processing helix chain 'E' and resid 323 through 335 Processing helix chain 'E' and resid 337 through 340 Processing helix chain 'E' and resid 342 through 363 removed outlier: 4.494A pdb=" N LYS E 362 " --> pdb=" O LYS E 358 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS E 363 " --> pdb=" O GLN E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 385 removed outlier: 3.972A pdb=" N GLU E 385 " --> pdb=" O CYS E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 532 Processing helix chain 'E' and resid 538 through 563 Processing helix chain 'F' and resid 7 through 21 removed outlier: 3.824A pdb=" N PHE F 20 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 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 46 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 66 through 74 Processing helix chain 'F' and resid 80 through 93 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) removed outlier: 4.485A pdb=" N PHE F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 112 Processing helix chain 'F' and resid 119 through 128 removed outlier: 3.777A pdb=" N ARG F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'G' and resid 105 through 114 Processing helix chain 'G' and resid 121 through 144 removed outlier: 3.878A pdb=" N THR G 144 " --> pdb=" O SER G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 179 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) removed outlier: 4.921A pdb=" N GLY G 179 " --> pdb=" O LEU G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 194 Processing helix chain 'G' and resid 197 through 216 Processing helix chain 'G' and resid 224 through 240 removed outlier: 4.085A pdb=" N PHE G 232 " --> pdb=" O ARG G 228 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET G 238 " --> pdb=" O GLN G 234 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU G 239 " --> pdb=" O ILE G 235 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N HIS G 240 " --> pdb=" O LEU G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 257 Processing helix chain 'G' and resid 259 through 284 Processing helix chain 'G' and resid 299 through 310 Processing helix chain 'G' and resid 323 through 335 Processing helix chain 'G' and resid 337 through 340 Processing helix chain 'G' and resid 342 through 363 removed outlier: 4.493A pdb=" N LYS G 362 " --> pdb=" O LYS G 358 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N HIS G 363 " --> pdb=" O GLN G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 385 removed outlier: 3.972A pdb=" N GLU G 385 " --> pdb=" O CYS G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 532 Processing helix chain 'G' and resid 538 through 563 Processing helix chain 'H' and resid 7 through 21 removed outlier: 3.824A pdb=" N PHE H 20 " --> pdb=" O ALA H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 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 46 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 66 through 74 Processing helix chain 'H' and resid 80 through 93 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) removed outlier: 4.486A pdb=" N PHE H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 112 Processing helix chain 'H' and resid 119 through 128 removed outlier: 3.776A pdb=" N ARG H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 146 960 hydrogen bonds defined for protein. 2868 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: 11.86 Time building geometry restraints manager: 27.41 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: 2105 2.21 - 2.94: 81978 2.94 - 3.68: 108619 3.68 - 4.41: 166791 4.41 - 5.14: 268427 Nonbonded interactions: 627920 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 627915 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: 0.650 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: 0.440 Extract box with map and model: 4.910 Check model and map are aligned: 0.470 Set scattering table: 0.260 Process input model: 104.760 Find NCS groups from input model: 1.460 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: 0.010 Load rotamer database and sin/cos tables:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.510 ------------------------------------------------------------------------------- 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 : 2.463 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: 3.1013 time to fit residues: 1981.4471 Evaluate side-chains 379 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 375 time to evaluate : 2.402 ------------------------------------------------------------------------------- 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: 2.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 174 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.7772 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16184 Z= 0.188 Angle : 0.652 20.720 21880 Z= 0.345 Chirality : 0.088 1.627 2432 Planarity : 0.004 0.055 2748 Dihedral : 10.565 171.575 2271 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.94 % Allowed : 15.17 % Favored : 82.89 % 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: 0.51 (0.19), residues: 1936 helix: 0.67 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.44 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 379 HIS 0.007 0.001 HIS H 108 PHE 0.016 0.001 PHE D 90 TYR 0.010 0.001 TYR C 545 ARG 0.008 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 432 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 400 time to evaluate : 2.508 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: 0.8903 (tp) cc_final: 0.8624 (mm) REVERT: A 228 ARG cc_start: 0.7591 (mtt180) cc_final: 0.7256 (tmt170) REVERT: A 537 ASP cc_start: 0.7983 (t0) cc_final: 0.7377 (p0) REVERT: A 538 VAL cc_start: 0.8660 (t) cc_final: 0.8422 (t) REVERT: A 555 ARG cc_start: 0.7238 (mtp85) cc_final: 0.6622 (ttm-80) REVERT: B 52 MET cc_start: 0.7188 (mtp) cc_final: 0.6645 (mtp) REVERT: B 80 THR cc_start: 0.8057 (m) cc_final: 0.7746 (p) REVERT: B 127 ARG cc_start: 0.8680 (mtm110) cc_final: 0.8434 (mtm110) REVERT: C 191 LEU cc_start: 0.8887 (tp) cc_final: 0.8602 (mm) REVERT: C 228 ARG cc_start: 0.7439 (mtt180) cc_final: 0.7175 (tmt170) REVERT: C 290 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: C 537 ASP cc_start: 0.8011 (t0) cc_final: 0.7465 (p0) REVERT: D 116 LYS cc_start: 0.8709 (mttt) cc_final: 0.8055 (mttp) REVERT: E 228 ARG cc_start: 0.7555 (mtt180) cc_final: 0.7309 (tmt170) REVERT: E 555 ARG cc_start: 0.7244 (mtp85) cc_final: 0.6819 (ttm-80) REVERT: F 73 MET cc_start: 0.6123 (mmp) cc_final: 0.5771 (mmp) REVERT: F 79 ASP cc_start: 0.6517 (t70) cc_final: 0.6203 (t70) REVERT: F 80 THR cc_start: 0.7793 (m) cc_final: 0.7430 (p) REVERT: F 81 ASP cc_start: 0.8613 (m-30) cc_final: 0.8140 (m-30) REVERT: F 116 LYS cc_start: 0.8786 (mttt) cc_final: 0.8498 (mptt) REVERT: G 228 ARG cc_start: 0.7587 (mtt180) cc_final: 0.7324 (tmt170) REVERT: G 509 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.5852 (m-70) REVERT: G 537 ASP cc_start: 0.8000 (t0) cc_final: 0.7366 (p0) REVERT: H 79 ASP cc_start: 0.7208 (t70) cc_final: 0.6910 (t70) REVERT: H 80 THR cc_start: 0.7941 (m) cc_final: 0.7647 (p) REVERT: H 87 ARG cc_start: 0.7711 (ttm110) cc_final: 0.7506 (mtm110) REVERT: H 127 ARG cc_start: 0.8487 (mtm110) cc_final: 0.8172 (mtm110) REVERT: H 144 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8192 (mm-40) outliers start: 32 outliers final: 11 residues processed: 412 average time/residue: 2.9680 time to fit residues: 1340.7529 Evaluate side-chains 349 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 336 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 290 GLU 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 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: 2.9990 chunk 145 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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: 0.7901 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 16184 Z= 0.424 Angle : 0.698 20.623 21880 Z= 0.376 Chirality : 0.090 1.627 2432 Planarity : 0.004 0.043 2748 Dihedral : 10.684 172.900 2267 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.40 % Allowed : 16.50 % Favored : 80.10 % 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: 0.84 (0.19), residues: 1936 helix: 0.91 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.30 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 379 HIS 0.006 0.001 HIS E 509 PHE 0.017 0.002 PHE C 166 TYR 0.028 0.002 TYR D 139 ARG 0.006 0.001 ARG D 127 *********************** 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 398 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 342 time to evaluate : 4.519 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 228 ARG cc_start: 0.7661 (mtt180) cc_final: 0.7401 (tmt170) REVERT: A 537 ASP cc_start: 0.8177 (t0) cc_final: 0.7464 (p0) REVERT: B 52 MET cc_start: 0.7218 (mtp) cc_final: 0.7015 (mtp) REVERT: B 116 LYS cc_start: 0.8940 (mttt) cc_final: 0.8678 (mttp) REVERT: C 196 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8434 (ptmt) REVERT: C 290 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: C 537 ASP cc_start: 0.8191 (t0) cc_final: 0.7475 (p0) REVERT: D 77 MET cc_start: 0.5408 (OUTLIER) cc_final: 0.4074 (ppp) REVERT: D 80 THR cc_start: 0.7696 (m) cc_final: 0.7432 (p) REVERT: D 116 LYS cc_start: 0.8939 (mttt) cc_final: 0.8706 (mttp) REVERT: D 141 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: E 170 GLU cc_start: 0.7732 (tt0) cc_final: 0.7416 (tt0) REVERT: E 228 ARG cc_start: 0.7568 (mtt180) cc_final: 0.7359 (tmt170) REVERT: F 73 MET cc_start: 0.6125 (mmp) cc_final: 0.5727 (mmp) REVERT: F 80 THR cc_start: 0.7754 (m) cc_final: 0.7552 (p) REVERT: F 116 LYS cc_start: 0.8947 (mttt) cc_final: 0.8226 (mptt) REVERT: G 509 HIS cc_start: 0.7429 (OUTLIER) cc_final: 0.5997 (m-70) REVERT: G 520 MET cc_start: 0.8310 (ttm) cc_final: 0.7918 (ttm) REVERT: G 537 ASP cc_start: 0.8168 (t0) cc_final: 0.7447 (p0) REVERT: H 79 ASP cc_start: 0.7216 (t70) cc_final: 0.6890 (t70) REVERT: H 80 THR cc_start: 0.7796 (OUTLIER) cc_final: 0.7494 (p) REVERT: H 96 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7372 (m-30) outliers start: 56 outliers final: 29 residues processed: 360 average time/residue: 2.8497 time to fit residues: 1129.7263 Evaluate side-chains 349 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 313 time to evaluate : 2.415 ------------------------------------------------------------------------------- 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 540 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LYS 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 72 MET 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 388 ASP Chi-restraints excluded: chain E residue 540 ASP Chi-restraints excluded: chain F residue 27 THR 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 210 MET Chi-restraints excluded: chain G residue 388 ASP Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 528 LYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 19 optimal weight: 0.2980 chunk 83 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5256 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 : 0.611 20.703 21880 Z= 0.324 Chirality : 0.088 1.653 2432 Planarity : 0.004 0.054 2748 Dihedral : 9.985 170.471 2265 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.18 % Allowed : 19.66 % Favored : 78.16 % 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: 1.44 (0.19), residues: 1936 helix: 1.33 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.02 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 379 HIS 0.005 0.001 HIS E 509 PHE 0.015 0.001 PHE G 123 TYR 0.010 0.001 TYR D 139 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: 36 poor density : 342 time to evaluate : 2.563 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 228 ARG cc_start: 0.7560 (mtt180) cc_final: 0.7287 (tmt170) REVERT: A 537 ASP cc_start: 0.8189 (t0) cc_final: 0.7445 (p0) REVERT: B 52 MET cc_start: 0.7306 (mtp) cc_final: 0.6955 (ttm) REVERT: B 72 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.6589 (ttm) REVERT: B 73 MET cc_start: 0.5959 (mmp) cc_final: 0.5204 (mmt) REVERT: B 116 LYS cc_start: 0.8927 (mttt) cc_final: 0.8671 (mttp) REVERT: C 196 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8340 (ptmt) REVERT: C 537 ASP cc_start: 0.8206 (t0) cc_final: 0.7428 (p0) REVERT: C 545 TYR cc_start: 0.8374 (t80) cc_final: 0.8122 (t80) REVERT: D 116 LYS cc_start: 0.8941 (mttt) cc_final: 0.8723 (mttp) REVERT: E 228 ARG cc_start: 0.7566 (mtt180) cc_final: 0.7296 (tmt170) REVERT: F 37 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7572 (mtm) REVERT: F 73 MET cc_start: 0.5815 (mmp) cc_final: 0.5384 (mmp) REVERT: F 80 THR cc_start: 0.7723 (m) cc_final: 0.7419 (p) REVERT: F 81 ASP cc_start: 0.8586 (m-30) cc_final: 0.8222 (m-30) REVERT: F 116 LYS cc_start: 0.8909 (mttt) cc_final: 0.8542 (mptt) REVERT: G 373 SER cc_start: 0.9073 (p) cc_final: 0.8679 (m) REVERT: G 509 HIS cc_start: 0.7409 (OUTLIER) cc_final: 0.5955 (m-70) REVERT: H 87 ARG cc_start: 0.7973 (ttm110) cc_final: 0.7721 (ttm-80) outliers start: 36 outliers final: 17 residues processed: 357 average time/residue: 2.8770 time to fit residues: 1129.8843 Evaluate side-chains 342 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 321 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LYS 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 E residue 182 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain G residue 182 SER 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 80 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 131 ILE 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: 0.7980 chunk 2 optimal weight: 0.2980 chunk 138 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN C 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16184 Z= 0.177 Angle : 0.599 20.643 21880 Z= 0.319 Chirality : 0.088 1.655 2432 Planarity : 0.004 0.065 2748 Dihedral : 9.793 168.351 2265 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.67 % Allowed : 20.39 % Favored : 76.94 % 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: 1.85 (0.19), residues: 1936 helix: 1.64 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : 0.06 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 379 HIS 0.004 0.000 HIS E 509 PHE 0.026 0.001 PHE F 20 TYR 0.010 0.001 TYR C 545 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 377 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 333 time to evaluate : 2.331 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: A 228 ARG cc_start: 0.7558 (mtt180) cc_final: 0.7283 (tmt170) REVERT: A 537 ASP cc_start: 0.8192 (t0) cc_final: 0.7438 (p0) REVERT: B 73 MET cc_start: 0.6022 (mmp) cc_final: 0.5247 (mmt) REVERT: B 116 LYS cc_start: 0.8961 (mttt) cc_final: 0.8673 (mttp) REVERT: C 537 ASP cc_start: 0.8199 (t0) cc_final: 0.7409 (p0) REVERT: C 545 TYR cc_start: 0.8395 (t80) cc_final: 0.8092 (t80) REVERT: D 33 LEU cc_start: 0.7466 (tp) cc_final: 0.7116 (tp) REVERT: D 63 THR cc_start: 0.8210 (p) cc_final: 0.7955 (t) REVERT: D 77 MET cc_start: 0.5426 (OUTLIER) cc_final: 0.4591 (pp-130) REVERT: D 116 LYS cc_start: 0.8933 (mttt) cc_final: 0.8726 (mttp) REVERT: E 228 ARG cc_start: 0.7558 (mtt180) cc_final: 0.7316 (tmt170) REVERT: F 73 MET cc_start: 0.6061 (mmp) cc_final: 0.5761 (mmt) REVERT: F 81 ASP cc_start: 0.8516 (m-30) cc_final: 0.8259 (m-30) REVERT: F 116 LYS cc_start: 0.8902 (mttt) cc_final: 0.8127 (mptt) REVERT: G 509 HIS cc_start: 0.7402 (OUTLIER) cc_final: 0.5900 (m-70) REVERT: H 87 ARG cc_start: 0.7976 (ttm110) cc_final: 0.7761 (ttm110) outliers start: 44 outliers final: 18 residues processed: 353 average time/residue: 2.9098 time to fit residues: 1128.0580 Evaluate side-chains 332 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 312 time to evaluate : 2.681 ------------------------------------------------------------------------------- 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 230 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 230 ILE 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 E residue 136 CYS Chi-restraints excluded: chain E residue 182 SER 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 G residue 509 HIS Chi-restraints excluded: chain H residue 27 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: 0.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 185 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN C 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16184 Z= 0.213 Angle : 0.617 20.746 21880 Z= 0.327 Chirality : 0.089 1.635 2432 Planarity : 0.004 0.076 2748 Dihedral : 9.803 166.627 2265 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.73 % Allowed : 21.06 % Favored : 76.21 % 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: 2.00 (0.19), residues: 1936 helix: 1.75 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : 0.11 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.006 0.001 HIS E 509 PHE 0.023 0.001 PHE B 20 TYR 0.013 0.001 TYR H 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 361 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 316 time to evaluate : 2.627 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: A 228 ARG cc_start: 0.7547 (mtt180) cc_final: 0.7283 (tmt170) REVERT: A 530 GLN cc_start: 0.8577 (tt0) cc_final: 0.8359 (tp-100) REVERT: A 537 ASP cc_start: 0.8182 (t0) cc_final: 0.7422 (p0) REVERT: B 19 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7490 (mp) REVERT: B 73 MET cc_start: 0.6013 (mmp) cc_final: 0.5161 (mmt) REVERT: B 116 LYS cc_start: 0.8998 (mttt) cc_final: 0.8720 (mttp) REVERT: C 196 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8333 (ptmt) REVERT: C 537 ASP cc_start: 0.8200 (t0) cc_final: 0.7382 (p0) REVERT: C 545 TYR cc_start: 0.8435 (t80) cc_final: 0.8136 (t80) REVERT: D 63 THR cc_start: 0.8161 (p) cc_final: 0.7901 (t) REVERT: D 77 MET cc_start: 0.5499 (OUTLIER) cc_final: 0.4467 (pp-130) REVERT: D 116 LYS cc_start: 0.8932 (mttt) cc_final: 0.8710 (mttp) REVERT: E 228 ARG cc_start: 0.7557 (mtt180) cc_final: 0.7349 (tmt170) REVERT: F 81 ASP cc_start: 0.8503 (m-30) cc_final: 0.8246 (m-30) REVERT: F 116 LYS cc_start: 0.8931 (mttt) cc_final: 0.8576 (mptt) REVERT: G 509 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.5655 (m-70) REVERT: H 87 ARG cc_start: 0.7946 (ttm110) cc_final: 0.7578 (mtm110) outliers start: 45 outliers final: 24 residues processed: 343 average time/residue: 3.0000 time to fit residues: 1129.1623 Evaluate side-chains 339 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 311 time to evaluate : 2.469 ------------------------------------------------------------------------------- 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 230 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain D residue 77 MET 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 E residue 388 ASP Chi-restraints excluded: chain F residue 51 ASP 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 210 MET Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 388 ASP Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 63 THR 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: 0.9990 chunk 105 optimal weight: 4.9990 chunk 135 optimal weight: 20.0000 chunk 156 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN C 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5861 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= 0.187 Angle : 0.608 20.780 21880 Z= 0.323 Chirality : 0.089 1.677 2432 Planarity : 0.005 0.085 2748 Dihedral : 9.627 164.416 2265 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.03 % Allowed : 21.72 % Favored : 75.24 % 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: 1.84 (0.14), residues: 1472 sheet: None (None), residues: 0 loop : 0.31 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.004 0.001 HIS E 509 PHE 0.032 0.001 PHE F 13 TYR 0.011 0.001 TYR B 139 ARG 0.017 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 369 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 319 time to evaluate : 2.280 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: A 228 ARG cc_start: 0.7518 (mtt180) cc_final: 0.7310 (tmt170) REVERT: A 537 ASP cc_start: 0.8201 (t0) cc_final: 0.7439 (p0) REVERT: B 19 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7505 (mp) REVERT: B 116 LYS cc_start: 0.9004 (mttt) cc_final: 0.8731 (mttp) REVERT: C 196 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8335 (ptmt) REVERT: C 537 ASP cc_start: 0.8188 (t0) cc_final: 0.7305 (p0) REVERT: C 545 TYR cc_start: 0.8424 (t80) cc_final: 0.8146 (t80) REVERT: D 63 THR cc_start: 0.8266 (p) cc_final: 0.8063 (t) REVERT: D 77 MET cc_start: 0.5637 (OUTLIER) cc_final: 0.4781 (pp-130) REVERT: D 116 LYS cc_start: 0.8951 (mttt) cc_final: 0.8721 (mttp) REVERT: F 13 PHE cc_start: 0.7682 (m-80) cc_final: 0.7369 (m-80) REVERT: F 73 MET cc_start: 0.6121 (mmp) cc_final: 0.5819 (mmt) REVERT: F 81 ASP cc_start: 0.8498 (m-30) cc_final: 0.8262 (m-30) REVERT: F 85 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8628 (mm-30) REVERT: F 116 LYS cc_start: 0.8944 (mttt) cc_final: 0.8592 (mptt) REVERT: H 87 ARG cc_start: 0.7932 (ttm110) cc_final: 0.7545 (mtm110) outliers start: 50 outliers final: 29 residues processed: 348 average time/residue: 2.9861 time to fit residues: 1138.5844 Evaluate side-chains 344 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 312 time to evaluate : 2.334 ------------------------------------------------------------------------------- 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 230 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 77 MET 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 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 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 230 ILE Chi-restraints excluded: chain G residue 388 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN B 144 GLN C 289 ASN F 144 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5944 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= 0.205 Angle : 0.622 20.861 21880 Z= 0.329 Chirality : 0.089 1.684 2432 Planarity : 0.004 0.095 2748 Dihedral : 9.595 163.152 2265 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.61 % Allowed : 22.27 % Favored : 75.12 % 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: 2.25 (0.19), residues: 1936 helix: 1.90 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : 0.30 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 379 HIS 0.003 0.001 HIS E 509 PHE 0.023 0.001 PHE B 20 TYR 0.013 0.001 TYR B 139 ARG 0.017 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 362 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 319 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ARG cc_start: 0.7575 (mtt180) cc_final: 0.7367 (tmt170) REVERT: A 537 ASP cc_start: 0.8211 (t0) cc_final: 0.7379 (p0) REVERT: B 116 LYS cc_start: 0.9019 (mttt) cc_final: 0.8753 (mttp) REVERT: C 196 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8318 (ptmt) REVERT: C 537 ASP cc_start: 0.8166 (t0) cc_final: 0.7279 (p0) REVERT: C 545 TYR cc_start: 0.8448 (t80) cc_final: 0.8115 (t80) REVERT: D 77 MET cc_start: 0.5649 (OUTLIER) cc_final: 0.4817 (pp-130) REVERT: D 116 LYS cc_start: 0.9004 (mttt) cc_final: 0.8727 (mttp) REVERT: D 127 ARG cc_start: 0.8561 (mtm110) cc_final: 0.8353 (mtm110) REVERT: F 13 PHE cc_start: 0.7698 (m-80) cc_final: 0.7433 (m-80) REVERT: F 72 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6773 (mtm) REVERT: F 73 MET cc_start: 0.6062 (mmp) cc_final: 0.5748 (mmt) REVERT: F 81 ASP cc_start: 0.8492 (m-30) cc_final: 0.8233 (m-30) REVERT: F 116 LYS cc_start: 0.8921 (mttt) cc_final: 0.8583 (mptt) outliers start: 43 outliers final: 30 residues processed: 348 average time/residue: 3.0533 time to fit residues: 1183.5732 Evaluate side-chains 343 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 310 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 247 THR 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 E residue 136 CYS Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 247 THR 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 72 MET 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 230 ILE Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 388 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 7.9990 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: 10.0000 chunk 52 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 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 289 ASN C 289 ASN E 359 GLN G 359 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16184 Z= 0.308 Angle : 0.656 20.914 21880 Z= 0.351 Chirality : 0.090 1.672 2432 Planarity : 0.004 0.105 2748 Dihedral : 9.853 165.510 2264 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.55 % Allowed : 22.51 % Favored : 74.94 % 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: 1.97 (0.19), residues: 1936 helix: 1.66 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : 0.34 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.006 0.001 HIS A 509 PHE 0.024 0.002 PHE B 20 TYR 0.020 0.001 TYR D 139 ARG 0.019 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 361 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 319 time to evaluate : 2.605 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 228 ARG cc_start: 0.7579 (mtt180) cc_final: 0.7376 (tmt170) REVERT: A 537 ASP cc_start: 0.8250 (t0) cc_final: 0.7423 (p0) REVERT: B 116 LYS cc_start: 0.9021 (mttt) cc_final: 0.8758 (mttp) REVERT: C 196 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8382 (ptmt) REVERT: D 77 MET cc_start: 0.5636 (OUTLIER) cc_final: 0.4858 (pp-130) REVERT: D 116 LYS cc_start: 0.9031 (mttt) cc_final: 0.8768 (mttp) REVERT: D 127 ARG cc_start: 0.8559 (mtm110) cc_final: 0.8352 (mtm110) REVERT: E 530 GLN cc_start: 0.8555 (tt0) cc_final: 0.8354 (tp-100) REVERT: F 13 PHE cc_start: 0.7742 (m-80) cc_final: 0.7452 (m-80) REVERT: F 72 MET cc_start: 0.7174 (mtm) cc_final: 0.6939 (mtm) REVERT: F 73 MET cc_start: 0.6082 (mmp) cc_final: 0.5708 (mmt) REVERT: F 116 LYS cc_start: 0.8984 (mttt) cc_final: 0.8181 (mptt) outliers start: 42 outliers final: 32 residues processed: 345 average time/residue: 2.9230 time to fit residues: 1106.3215 Evaluate side-chains 340 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 306 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 77 MET 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 E residue 388 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 80 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 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 101 ILE Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 176 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7842 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16184 Z= 0.166 Angle : 0.627 20.674 21880 Z= 0.331 Chirality : 0.089 1.697 2432 Planarity : 0.004 0.107 2748 Dihedral : 9.379 161.124 2264 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.52 % Allowed : 24.33 % 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: 2.34 (0.19), residues: 1936 helix: 1.95 (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 0.011 0.001 TRP A 379 HIS 0.005 0.001 HIS A 509 PHE 0.022 0.001 PHE F 20 TYR 0.008 0.001 TYR C 545 ARG 0.020 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 343 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 318 time to evaluate : 2.493 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 228 ARG cc_start: 0.7552 (mtt180) cc_final: 0.7327 (tmt170) REVERT: A 528 LYS cc_start: 0.9431 (ttpt) cc_final: 0.9221 (mppt) REVERT: A 537 ASP cc_start: 0.8210 (t0) cc_final: 0.7413 (p0) REVERT: B 77 MET cc_start: 0.6260 (ppp) cc_final: 0.5795 (ptt) REVERT: B 116 LYS cc_start: 0.9001 (mttt) cc_final: 0.8733 (mttp) REVERT: C 196 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8283 (ptmt) REVERT: C 539 ARG cc_start: 0.8151 (tmm-80) cc_final: 0.7763 (tmm-80) REVERT: C 545 TYR cc_start: 0.8371 (t80) cc_final: 0.8157 (t80) REVERT: D 23 ASP cc_start: 0.5804 (m-30) cc_final: 0.5422 (m-30) REVERT: D 75 ARG cc_start: 0.6859 (ppt-90) cc_final: 0.6646 (ppt-90) REVERT: D 116 LYS cc_start: 0.9005 (mttt) cc_final: 0.8730 (mttp) REVERT: D 127 ARG cc_start: 0.8558 (mtm110) cc_final: 0.8351 (mtm110) REVERT: F 13 PHE cc_start: 0.7726 (m-80) cc_final: 0.7458 (m-80) REVERT: F 73 MET cc_start: 0.6016 (mmp) cc_final: 0.5580 (mmt) REVERT: F 116 LYS cc_start: 0.8955 (mttt) cc_final: 0.8137 (mptt) REVERT: F 127 ARG cc_start: 0.8575 (mtm110) cc_final: 0.8355 (mtm110) REVERT: H 87 ARG cc_start: 0.8049 (ttm-80) cc_final: 0.7830 (ttm-80) outliers start: 25 outliers final: 19 residues processed: 335 average time/residue: 2.9999 time to fit residues: 1101.2343 Evaluate side-chains 327 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 307 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 196 LYS 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 E residue 136 CYS Chi-restraints excluded: chain E residue 182 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 230 ILE Chi-restraints excluded: chain H residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 152 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.177107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.105273 restraints weight = 60523.203| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.18 r_work: 0.3168 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16184 Z= 0.164 Angle : 0.622 20.633 21880 Z= 0.329 Chirality : 0.089 1.675 2432 Planarity : 0.004 0.104 2748 Dihedral : 9.264 158.723 2264 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.21 % Allowed : 25.00 % Favored : 73.79 % 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: 2.53 (0.19), residues: 1936 helix: 2.09 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : 0.45 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 379 HIS 0.005 0.001 HIS A 509 PHE 0.022 0.001 PHE B 20 TYR 0.010 0.001 TYR A 545 ARG 0.019 0.001 ARG F 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17166.34 seconds wall clock time: 298 minutes 55.98 seconds (17935.98 seconds total)