Starting phenix.real_space_refine on Wed Feb 21 23:40:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnl_33318/02_2024/7xnl_33318_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnl_33318/02_2024/7xnl_33318.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnl_33318/02_2024/7xnl_33318_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnl_33318/02_2024/7xnl_33318_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnl_33318/02_2024/7xnl_33318_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnl_33318/02_2024/7xnl_33318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnl_33318/02_2024/7xnl_33318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnl_33318/02_2024/7xnl_33318_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnl_33318/02_2024/7xnl_33318_neut_trim_updated.pdb" } resolution = 3.1 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 12 5.49 5 S 88 5.16 5 C 10324 2.51 5 N 2700 2.21 5 O 2908 1.98 5 H 15652 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 360": "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 PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 360": "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 PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 360": "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 PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 360": "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: 31688 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5712 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 2 Chain: "B" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5712 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 2 Chain: "D" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5712 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 2 Chain: "F" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5712 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 2 Chain: "H" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {' K': 4} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Classifications: {'peptide': 1} Chain: "F" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Classifications: {'peptide': 1} Chain: "H" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.84, per 1000 atoms: 0.44 Number of scatterers: 31688 At special positions: 0 Unit cell: (114.582, 114.582, 121.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 88 16.00 P 12 15.00 O 2908 8.00 N 2700 7.00 C 10324 6.00 H 15652 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 27.03 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: 96 helices and 4 sheets defined 72.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 121 through 142 Processing helix chain 'A' and resid 149 through 180 removed outlier: 3.589A pdb=" N THR A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TRP A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N CYS A 180 " --> pdb=" O TRP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.509A pdb=" N ARG A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 216 Processing helix chain 'A' and resid 225 through 240 removed outlier: 4.388A pdb=" N PHE A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.804A 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 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 342 through 362 removed outlier: 4.332A pdb=" N LYS A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.808A pdb=" N GLU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 510 through 533 Processing helix chain 'A' and resid 538 through 562 Processing helix chain 'B' and resid 7 through 21 removed outlier: 3.703A pdb=" N PHE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 40 removed outlier: 4.253A pdb=" N VAL B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 66 through 74 Processing helix chain 'B' and resid 80 through 93 removed outlier: 3.939A pdb=" N GLU B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) removed outlier: 4.580A 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: 3.591A 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 142 Processing helix chain 'C' and resid 149 through 180 removed outlier: 3.590A pdb=" N THR C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 161 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N CYS C 180 " --> pdb=" O TRP C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.509A pdb=" N ARG C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 216 Processing helix chain 'C' and resid 225 through 240 removed outlier: 4.389A pdb=" N PHE C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET C 238 " --> pdb=" O GLN C 234 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 4.804A 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 339 No H-bonds generated for 'chain 'C' and resid 337 through 339' Processing helix chain 'C' and resid 342 through 362 removed outlier: 4.332A pdb=" N LYS C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 385 removed outlier: 3.808A pdb=" N GLU C 385 " --> pdb=" O CYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 394 Processing helix chain 'C' and resid 510 through 533 Processing helix chain 'C' and resid 538 through 562 Processing helix chain 'D' and resid 7 through 21 removed outlier: 3.703A pdb=" N PHE D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 40 removed outlier: 4.253A pdb=" N VAL D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 66 through 74 Processing helix chain 'D' and resid 80 through 93 removed outlier: 3.939A pdb=" N GLU D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.580A 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: 3.591A 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 142 Processing helix chain 'E' and resid 149 through 180 removed outlier: 3.589A pdb=" N THR E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TRP E 158 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE E 161 " --> pdb=" O PHE E 157 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY E 179 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N CYS E 180 " --> pdb=" O TRP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 removed outlier: 3.509A pdb=" N ARG E 195 " --> pdb=" O LEU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 216 Processing helix chain 'E' and resid 225 through 240 removed outlier: 4.389A pdb=" N PHE E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET E 238 " --> pdb=" O GLN E 234 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A) removed outlier: 4.804A 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 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' Processing helix chain 'E' and resid 342 through 362 removed outlier: 4.333A pdb=" N LYS E 362 " --> pdb=" O LYS E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 385 removed outlier: 3.808A pdb=" N GLU E 385 " --> pdb=" O CYS E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 394 Processing helix chain 'E' and resid 510 through 533 Processing helix chain 'E' and resid 538 through 562 Processing helix chain 'F' and resid 7 through 21 removed outlier: 3.703A pdb=" N PHE F 20 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 40 removed outlier: 4.253A pdb=" N VAL F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU F 40 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 54 Processing helix chain 'F' and resid 66 through 74 Processing helix chain 'F' and resid 80 through 93 removed outlier: 3.939A pdb=" N GLU F 84 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG F 91 " --> pdb=" O ARG F 87 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) removed outlier: 4.580A 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: 3.591A 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 142 Processing helix chain 'G' and resid 149 through 180 removed outlier: 3.590A pdb=" N THR G 153 " --> pdb=" O ALA G 149 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE G 157 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE G 161 " --> pdb=" O PHE G 157 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY G 179 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N CYS G 180 " --> pdb=" O TRP G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 195 removed outlier: 3.509A pdb=" N ARG G 195 " --> pdb=" O LEU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 216 Processing helix chain 'G' and resid 225 through 240 removed outlier: 4.389A pdb=" N PHE G 232 " --> pdb=" O ARG G 228 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET G 238 " --> pdb=" O GLN G 234 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU G 239 " --> pdb=" O ILE G 235 " (cutoff:3.500A) removed outlier: 4.803A 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 339 No H-bonds generated for 'chain 'G' and resid 337 through 339' Processing helix chain 'G' and resid 342 through 362 removed outlier: 4.333A pdb=" N LYS G 362 " --> pdb=" O LYS G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 385 removed outlier: 3.808A pdb=" N GLU G 385 " --> pdb=" O CYS G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 391 through 394 Processing helix chain 'G' and resid 510 through 533 Processing helix chain 'G' and resid 538 through 562 Processing helix chain 'H' and resid 7 through 21 removed outlier: 3.703A pdb=" N PHE H 20 " --> pdb=" O ALA H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 40 removed outlier: 4.253A pdb=" N VAL H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 54 Processing helix chain 'H' and resid 66 through 74 Processing helix chain 'H' and resid 80 through 93 removed outlier: 3.939A pdb=" N GLU H 84 " --> pdb=" O THR H 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 4.580A 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: 3.591A pdb=" N ARG H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 146 Processing sheet with id= A, first strand: chain 'B' and resid 100 through 102 Processing sheet with id= B, first strand: chain 'D' and resid 100 through 102 Processing sheet with id= C, first strand: chain 'F' and resid 100 through 102 Processing sheet with id= D, first strand: chain 'H' and resid 100 through 102 960 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: 11.05 Time building geometry restraints manager: 27.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15628 1.03 - 1.22: 36 1.22 - 1.42: 7000 1.42 - 1.61: 9200 1.61 - 1.81: 160 Bond restraints: 32024 Sorted by residual: bond pdb=" CAT I0S G 701 " pdb=" SBF I0S G 701 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CAT I0S A 705 " pdb=" SBF I0S A 705 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CAT I0S E 701 " pdb=" SBF I0S E 701 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CAT I0S C 701 " pdb=" SBF I0S C 701 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CBE I0S E 701 " pdb=" SBF I0S E 701 " ideal model delta sigma weight residual 1.717 1.584 0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 32019 not shown) Histogram of bond angle deviations from ideal: 96.55 - 104.05: 146 104.05 - 111.55: 34525 111.55 - 119.04: 8813 119.04 - 126.54: 13797 126.54 - 134.04: 251 Bond angle restraints: 57532 Sorted by residual: angle pdb=" OAQ I0S E 701 " pdb=" SAI I0S E 701 " pdb=" OAR I0S E 701 " ideal model delta sigma weight residual 119.45 103.60 15.85 3.00e+00 1.11e-01 2.79e+01 angle pdb=" OAQ I0S C 701 " pdb=" SAI I0S C 701 " pdb=" OAR I0S C 701 " ideal model delta sigma weight residual 119.45 103.61 15.84 3.00e+00 1.11e-01 2.79e+01 angle pdb=" OAQ I0S A 705 " pdb=" SAI I0S A 705 " pdb=" OAR I0S A 705 " ideal model delta sigma weight residual 119.45 103.62 15.83 3.00e+00 1.11e-01 2.79e+01 angle pdb=" OAQ I0S G 701 " pdb=" SAI I0S G 701 " pdb=" OAR I0S G 701 " ideal model delta sigma weight residual 119.45 103.62 15.83 3.00e+00 1.11e-01 2.79e+01 angle pdb=" CA I0S G 701 " pdb=" N I0S G 701 " pdb=" CAG I0S G 701 " ideal model delta sigma weight residual 121.42 107.76 13.66 3.00e+00 1.11e-01 2.07e+01 ... (remaining 57527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.18: 14644 34.18 - 68.36: 300 68.36 - 102.55: 28 102.55 - 136.73: 24 136.73 - 170.91: 8 Dihedral angle restraints: 15004 sinusoidal: 8088 harmonic: 6916 Sorted by residual: dihedral pdb=" CBB I0S E 701 " pdb=" CAZ I0S E 701 " pdb=" OBA I0S E 701 " pdb=" CBC I0S E 701 " ideal model delta sinusoidal sigma weight residual -1.02 -171.93 170.91 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CBB I0S A 705 " pdb=" CAZ I0S A 705 " pdb=" OBA I0S A 705 " pdb=" CBC I0S A 705 " ideal model delta sinusoidal sigma weight residual -1.02 -171.92 170.90 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CBB I0S G 701 " pdb=" CAZ I0S G 701 " pdb=" OBA I0S G 701 " pdb=" CBC I0S G 701 " ideal model delta sinusoidal sigma weight residual -1.02 -171.91 170.89 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 15001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1886 0.062 - 0.124: 476 0.124 - 0.186: 82 0.186 - 0.248: 12 0.248 - 0.310: 4 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CB VAL E 308 " pdb=" CA VAL E 308 " pdb=" CG1 VAL E 308 " pdb=" CG2 VAL E 308 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB VAL A 308 " pdb=" CA VAL A 308 " pdb=" CG1 VAL A 308 " pdb=" CG2 VAL A 308 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CB VAL G 308 " pdb=" CA VAL G 308 " pdb=" CG1 VAL G 308 " pdb=" CG2 VAL G 308 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 2457 not shown) Planarity restraints: 4672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 174 " -0.009 9.50e-02 1.11e+02 1.92e-02 8.10e+00 pdb=" NE ARG G 174 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG G 174 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG G 174 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 174 " -0.006 2.00e-02 2.50e+03 pdb="HH11 ARG G 174 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG G 174 " -0.020 2.00e-02 2.50e+03 pdb="HH21 ARG G 174 " -0.032 2.00e-02 2.50e+03 pdb="HH22 ARG G 174 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 174 " 0.010 9.50e-02 1.11e+02 1.91e-02 8.01e+00 pdb=" NE ARG C 174 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 174 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 174 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 174 " 0.006 2.00e-02 2.50e+03 pdb="HH11 ARG C 174 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG C 174 " 0.020 2.00e-02 2.50e+03 pdb="HH21 ARG C 174 " 0.031 2.00e-02 2.50e+03 pdb="HH22 ARG C 174 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 174 " 0.010 9.50e-02 1.11e+02 1.91e-02 7.95e+00 pdb=" NE ARG A 174 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 174 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 174 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 174 " 0.006 2.00e-02 2.50e+03 pdb="HH11 ARG A 174 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 174 " 0.020 2.00e-02 2.50e+03 pdb="HH21 ARG A 174 " 0.031 2.00e-02 2.50e+03 pdb="HH22 ARG A 174 " -0.039 2.00e-02 2.50e+03 ... (remaining 4669 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.38: 13356 2.38 - 3.07: 88977 3.07 - 3.76: 106317 3.76 - 4.45: 167372 4.45 - 5.14: 255155 Nonbonded interactions: 631177 Sorted by model distance: nonbonded pdb=" O TRP E 120 " pdb=" H VAL E 124 " model vdw 1.694 1.850 nonbonded pdb=" O TRP G 120 " pdb=" H VAL G 124 " model vdw 1.694 1.850 nonbonded pdb=" O TRP C 120 " pdb=" H VAL C 124 " model vdw 1.695 1.850 nonbonded pdb=" O TRP A 120 " pdb=" H VAL A 124 " model vdw 1.695 1.850 nonbonded pdb=" OD1 ASP C 564 " pdb="HH21 ARG E 562 " model vdw 1.700 1.850 ... (remaining 631172 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: 0.760 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: 0.470 Extract box with map and model: 4.950 Check model and map are aligned: 0.490 Set scattering table: 0.280 Process input model: 103.410 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.133 16372 Z= 0.903 Angle : 0.985 15.849 22140 Z= 0.534 Chirality : 0.057 0.310 2460 Planarity : 0.005 0.053 2756 Dihedral : 14.782 170.912 5996 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.27 (0.16), residues: 1936 helix: -1.28 (0.11), residues: 1488 sheet: None (None), residues: 0 loop : -1.62 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP E 379 HIS 0.006 0.002 HIS C 126 PHE 0.023 0.003 PHE A 332 TYR 0.025 0.003 TYR A 299 ARG 0.007 0.001 ARG E 243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 658 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 658 time to evaluate : 2.557 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 133 VAL cc_start: 0.9067 (p) cc_final: 0.8434 (p) REVERT: A 519 ARG cc_start: 0.8604 (ttm-80) cc_final: 0.8385 (ttt90) REVERT: B 29 THR cc_start: 0.7227 (m) cc_final: 0.7017 (p) REVERT: B 85 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7796 (tp30) REVERT: B 100 TYR cc_start: 0.8639 (m-80) cc_final: 0.8424 (m-10) REVERT: B 113 LEU cc_start: 0.7854 (mt) cc_final: 0.7391 (tp) REVERT: B 145 MET cc_start: 0.7921 (ttp) cc_final: 0.7310 (tmm) REVERT: C 133 VAL cc_start: 0.9038 (p) cc_final: 0.8557 (p) REVERT: C 519 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8402 (ttt90) REVERT: C 547 GLN cc_start: 0.8588 (mt0) cc_final: 0.7787 (mt0) REVERT: C 562 ARG cc_start: 0.6759 (tpt170) cc_final: 0.6544 (tpt90) REVERT: D 29 THR cc_start: 0.7214 (m) cc_final: 0.7006 (p) REVERT: D 85 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7784 (tp30) REVERT: D 100 TYR cc_start: 0.8659 (m-80) cc_final: 0.8427 (m-10) REVERT: D 113 LEU cc_start: 0.7846 (mt) cc_final: 0.7394 (tp) REVERT: D 145 MET cc_start: 0.7933 (ttp) cc_final: 0.7309 (tmm) REVERT: E 133 VAL cc_start: 0.9086 (p) cc_final: 0.8561 (m) REVERT: E 519 ARG cc_start: 0.8617 (ttm-80) cc_final: 0.8384 (ttt90) REVERT: F 29 THR cc_start: 0.7234 (m) cc_final: 0.7027 (p) REVERT: F 85 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7769 (tp30) REVERT: F 100 TYR cc_start: 0.8649 (m-80) cc_final: 0.8424 (m-10) REVERT: F 108 HIS cc_start: 0.8373 (t-90) cc_final: 0.7963 (t-90) REVERT: F 113 LEU cc_start: 0.7915 (mt) cc_final: 0.7461 (tp) REVERT: F 145 MET cc_start: 0.7898 (ttp) cc_final: 0.7311 (tmm) REVERT: G 133 VAL cc_start: 0.9013 (p) cc_final: 0.8420 (p) REVERT: G 382 TYR cc_start: 0.7264 (t80) cc_final: 0.6914 (t80) REVERT: G 519 ARG cc_start: 0.8594 (ttm-80) cc_final: 0.8391 (ttt90) REVERT: H 29 THR cc_start: 0.7217 (m) cc_final: 0.7013 (p) REVERT: H 100 TYR cc_start: 0.8670 (m-80) cc_final: 0.8427 (m-10) REVERT: H 113 LEU cc_start: 0.7882 (mt) cc_final: 0.7438 (tp) REVERT: H 145 MET cc_start: 0.7910 (ttp) cc_final: 0.7171 (tmm) outliers start: 0 outliers final: 0 residues processed: 658 average time/residue: 0.8436 time to fit residues: 751.8343 Evaluate side-chains 434 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 174 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 GLN A 386 ASN B 144 GLN C 240 HIS C 356 GLN C 386 ASN D 144 GLN E 386 ASN F 144 GLN G 386 ASN H 144 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16372 Z= 0.169 Angle : 0.506 4.824 22140 Z= 0.274 Chirality : 0.034 0.114 2460 Planarity : 0.003 0.041 2756 Dihedral : 15.122 176.552 2372 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.55 % Allowed : 10.38 % Favored : 89.08 % 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: -0.10 (0.18), residues: 1936 helix: 0.37 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.20 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 176 HIS 0.007 0.001 HIS G 240 PHE 0.017 0.001 PHE F 20 TYR 0.013 0.001 TYR C 545 ARG 0.004 0.001 ARG C 518 *********************** 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 472 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 463 time to evaluate : 2.704 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: A 537 ASP cc_start: 0.7062 (p0) cc_final: 0.6655 (p0) REVERT: B 28 ILE cc_start: 0.6178 (mm) cc_final: 0.5753 (tp) REVERT: B 29 THR cc_start: 0.7156 (m) cc_final: 0.6903 (p) REVERT: B 100 TYR cc_start: 0.8666 (m-80) cc_final: 0.8264 (m-10) REVERT: B 145 MET cc_start: 0.7927 (ttp) cc_final: 0.7450 (tmm) REVERT: C 519 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.8421 (ttt90) REVERT: C 537 ASP cc_start: 0.7028 (p0) cc_final: 0.6644 (p0) REVERT: C 562 ARG cc_start: 0.6693 (tpt170) cc_final: 0.6492 (tpt90) REVERT: D 28 ILE cc_start: 0.6173 (mm) cc_final: 0.5746 (tp) REVERT: D 29 THR cc_start: 0.7158 (m) cc_final: 0.6897 (p) REVERT: D 75 ARG cc_start: 0.6314 (ttp-110) cc_final: 0.5956 (ptp-170) REVERT: D 100 TYR cc_start: 0.8687 (m-80) cc_final: 0.8292 (m-10) REVERT: D 145 MET cc_start: 0.7938 (ttp) cc_final: 0.7452 (tmm) REVERT: E 519 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8356 (ttt90) REVERT: E 531 GLN cc_start: 0.8160 (mt0) cc_final: 0.7883 (pt0) REVERT: E 537 ASP cc_start: 0.6960 (p0) cc_final: 0.6640 (p0) REVERT: F 28 ILE cc_start: 0.6166 (mm) cc_final: 0.5733 (tp) REVERT: F 29 THR cc_start: 0.7157 (m) cc_final: 0.6913 (p) REVERT: F 100 TYR cc_start: 0.8685 (m-80) cc_final: 0.8269 (m-10) REVERT: F 145 MET cc_start: 0.7923 (ttp) cc_final: 0.7490 (tmm) REVERT: G 537 ASP cc_start: 0.7111 (p0) cc_final: 0.6740 (p0) REVERT: H 28 ILE cc_start: 0.6186 (mm) cc_final: 0.5740 (tp) REVERT: H 29 THR cc_start: 0.7159 (m) cc_final: 0.6909 (p) REVERT: H 100 TYR cc_start: 0.8712 (m-80) cc_final: 0.8307 (m-10) outliers start: 9 outliers final: 8 residues processed: 470 average time/residue: 0.7927 time to fit residues: 505.0477 Evaluate side-chains 429 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 421 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 386 ASN Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain G residue 105 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 173 optimal weight: 0.0980 chunk 59 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 GLN D 144 GLN F 144 GLN G 547 GLN H 144 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16372 Z= 0.327 Angle : 0.544 4.700 22140 Z= 0.300 Chirality : 0.037 0.118 2460 Planarity : 0.004 0.044 2756 Dihedral : 14.539 173.375 2372 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.40 % Allowed : 11.59 % Favored : 87.01 % 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: 0.46 (0.19), residues: 1936 helix: 0.75 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.96 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 176 HIS 0.007 0.001 HIS G 240 PHE 0.018 0.002 PHE G 332 TYR 0.019 0.002 TYR C 299 ARG 0.006 0.001 ARG H 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 451 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 428 time to evaluate : 2.420 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: B 28 ILE cc_start: 0.6387 (mm) cc_final: 0.5907 (tp) REVERT: B 29 THR cc_start: 0.7286 (m) cc_final: 0.7051 (p) REVERT: B 100 TYR cc_start: 0.8832 (m-80) cc_final: 0.8316 (m-10) REVERT: B 127 ARG cc_start: 0.9081 (ptm-80) cc_final: 0.8824 (tmm-80) REVERT: B 141 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8462 (pt0) REVERT: B 145 MET cc_start: 0.7782 (ttp) cc_final: 0.7419 (tmm) REVERT: C 519 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8468 (ttm110) REVERT: C 562 ARG cc_start: 0.6694 (tpt170) cc_final: 0.6392 (tpt90) REVERT: D 28 ILE cc_start: 0.6401 (mm) cc_final: 0.5902 (tp) REVERT: D 29 THR cc_start: 0.7286 (m) cc_final: 0.7038 (p) REVERT: D 100 TYR cc_start: 0.8846 (m-80) cc_final: 0.8321 (m-10) REVERT: D 127 ARG cc_start: 0.9090 (ptm-80) cc_final: 0.8828 (tmm-80) REVERT: D 145 MET cc_start: 0.7839 (ttp) cc_final: 0.7481 (tmm) REVERT: F 28 ILE cc_start: 0.6377 (mm) cc_final: 0.5887 (tp) REVERT: F 29 THR cc_start: 0.7292 (m) cc_final: 0.7062 (p) REVERT: F 100 TYR cc_start: 0.8847 (m-80) cc_final: 0.8319 (m-10) REVERT: F 127 ARG cc_start: 0.8954 (ptm-80) cc_final: 0.8725 (ttp80) REVERT: F 145 MET cc_start: 0.8017 (ttp) cc_final: 0.7659 (ttp) REVERT: H 28 ILE cc_start: 0.6407 (mm) cc_final: 0.5894 (tp) REVERT: H 29 THR cc_start: 0.7294 (m) cc_final: 0.7049 (p) REVERT: H 100 TYR cc_start: 0.8860 (m-80) cc_final: 0.8331 (m-10) REVERT: H 127 ARG cc_start: 0.9078 (ptm-80) cc_final: 0.8837 (tmm-80) outliers start: 23 outliers final: 18 residues processed: 440 average time/residue: 0.7485 time to fit residues: 453.8201 Evaluate side-chains 412 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 394 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 386 ASN Chi-restraints excluded: chain E residue 540 ASP Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 122 CYS Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain G residue 540 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: 1.9990 chunk 83 optimal weight: 20.0000 chunk 117 optimal weight: 0.2980 chunk 175 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN C 386 ASN E 386 ASN ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16372 Z= 0.245 Angle : 0.500 4.511 22140 Z= 0.273 Chirality : 0.036 0.114 2460 Planarity : 0.003 0.041 2756 Dihedral : 14.301 175.926 2372 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.09 % Allowed : 12.86 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.92 (0.19), residues: 1936 helix: 1.09 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.83 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 176 HIS 0.007 0.001 HIS G 240 PHE 0.016 0.001 PHE H 20 TYR 0.014 0.001 TYR G 299 ARG 0.009 0.000 ARG E 519 *********************** 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 442 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 424 time to evaluate : 2.826 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: B 29 THR cc_start: 0.7390 (m) cc_final: 0.7148 (p) REVERT: B 100 TYR cc_start: 0.8805 (m-80) cc_final: 0.8225 (m-10) REVERT: B 127 ARG cc_start: 0.9146 (ptm-80) cc_final: 0.8850 (tmm-80) REVERT: C 519 ARG cc_start: 0.8684 (ttm-80) cc_final: 0.8237 (ttm110) REVERT: C 562 ARG cc_start: 0.6782 (tpt170) cc_final: 0.6411 (tpt90) REVERT: D 29 THR cc_start: 0.7393 (m) cc_final: 0.7149 (p) REVERT: D 100 TYR cc_start: 0.8814 (m-80) cc_final: 0.8225 (m-10) REVERT: D 127 ARG cc_start: 0.9152 (ptm-80) cc_final: 0.8853 (tmm-80) REVERT: E 519 ARG cc_start: 0.8713 (ttm110) cc_final: 0.8481 (ttm-80) REVERT: F 29 THR cc_start: 0.7471 (m) cc_final: 0.7246 (p) REVERT: F 100 TYR cc_start: 0.8821 (m-80) cc_final: 0.8230 (m-10) REVERT: F 127 ARG cc_start: 0.9010 (ptm-80) cc_final: 0.8757 (tmm-80) REVERT: F 145 MET cc_start: 0.8016 (ttp) cc_final: 0.7744 (ttp) REVERT: H 29 THR cc_start: 0.7389 (m) cc_final: 0.7152 (p) REVERT: H 100 TYR cc_start: 0.8826 (m-80) cc_final: 0.8246 (m-80) outliers start: 18 outliers final: 17 residues processed: 433 average time/residue: 0.7818 time to fit residues: 483.4048 Evaluate side-chains 423 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 406 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain H residue 80 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16372 Z= 0.388 Angle : 0.572 5.664 22140 Z= 0.313 Chirality : 0.039 0.126 2460 Planarity : 0.004 0.073 2756 Dihedral : 14.410 175.972 2372 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.00 % Allowed : 14.56 % Favored : 83.43 % 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: 0.59 (0.19), residues: 1936 helix: 0.87 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -1.02 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 176 HIS 0.007 0.001 HIS A 240 PHE 0.020 0.002 PHE E 296 TYR 0.021 0.002 TYR G 299 ARG 0.008 0.001 ARG H 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 473 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 440 time to evaluate : 2.704 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: A 210 MET cc_start: 0.8176 (mtp) cc_final: 0.7883 (mtp) REVERT: B 28 ILE cc_start: 0.6380 (mm) cc_final: 0.5958 (tp) REVERT: B 29 THR cc_start: 0.7517 (m) cc_final: 0.7284 (p) REVERT: B 100 TYR cc_start: 0.8884 (m-80) cc_final: 0.8087 (m-10) REVERT: B 127 ARG cc_start: 0.9080 (ptm-80) cc_final: 0.8834 (tmm-80) REVERT: B 141 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8497 (pt0) REVERT: C 519 ARG cc_start: 0.8711 (ttm-80) cc_final: 0.8293 (ttm110) REVERT: C 562 ARG cc_start: 0.6904 (tpt170) cc_final: 0.6385 (tpt90) REVERT: D 28 ILE cc_start: 0.6388 (mm) cc_final: 0.5959 (tp) REVERT: D 29 THR cc_start: 0.7527 (m) cc_final: 0.7284 (p) REVERT: D 100 TYR cc_start: 0.8878 (m-80) cc_final: 0.8118 (m-80) REVERT: D 127 ARG cc_start: 0.9093 (ptm-80) cc_final: 0.8846 (tmm-80) REVERT: E 519 ARG cc_start: 0.8745 (ttm110) cc_final: 0.8479 (ttm110) REVERT: F 29 THR cc_start: 0.7518 (m) cc_final: 0.7294 (p) REVERT: F 100 TYR cc_start: 0.8875 (m-80) cc_final: 0.8172 (m-80) REVERT: F 127 ARG cc_start: 0.8998 (ptm-80) cc_final: 0.8751 (tmm-80) REVERT: H 28 ILE cc_start: 0.6368 (mm) cc_final: 0.5937 (tp) REVERT: H 29 THR cc_start: 0.7496 (m) cc_final: 0.7267 (p) REVERT: H 100 TYR cc_start: 0.8886 (m-80) cc_final: 0.8117 (m-80) REVERT: H 127 ARG cc_start: 0.9264 (ttp80) cc_final: 0.8976 (tmm-80) outliers start: 33 outliers final: 28 residues processed: 457 average time/residue: 0.7133 time to fit residues: 461.9658 Evaluate side-chains 453 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 425 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 386 ASN Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 122 CYS Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 80 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: 0.5980 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16372 Z= 0.178 Angle : 0.481 5.911 22140 Z= 0.259 Chirality : 0.035 0.122 2460 Planarity : 0.003 0.054 2756 Dihedral : 14.023 176.247 2372 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.70 % Allowed : 15.11 % Favored : 83.19 % 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: 1.22 (0.19), residues: 1936 helix: 1.29 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.63 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 176 HIS 0.006 0.001 HIS C 240 PHE 0.016 0.001 PHE H 20 TYR 0.010 0.001 TYR G 545 ARG 0.007 0.000 ARG H 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 466 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 438 time to evaluate : 2.596 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: A 210 MET cc_start: 0.8134 (mtp) cc_final: 0.7856 (mtp) REVERT: B 29 THR cc_start: 0.7593 (m) cc_final: 0.7354 (p) REVERT: B 73 MET cc_start: 0.6173 (mmm) cc_final: 0.5933 (mmm) REVERT: B 100 TYR cc_start: 0.8785 (m-80) cc_final: 0.8024 (m-10) REVERT: B 127 ARG cc_start: 0.9085 (ptm-80) cc_final: 0.8828 (tmm-80) REVERT: C 138 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8392 (tt) REVERT: C 516 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8285 (p) REVERT: C 520 MET cc_start: 0.8637 (mtm) cc_final: 0.8355 (mpp) REVERT: C 562 ARG cc_start: 0.6951 (tpt170) cc_final: 0.6427 (tpt90) REVERT: D 29 THR cc_start: 0.7576 (m) cc_final: 0.7339 (p) REVERT: D 100 TYR cc_start: 0.8824 (m-80) cc_final: 0.7980 (m-10) REVERT: D 127 ARG cc_start: 0.9104 (ptm-80) cc_final: 0.8847 (tmm-80) REVERT: E 519 ARG cc_start: 0.8736 (ttm110) cc_final: 0.8509 (ttm110) REVERT: E 555 ARG cc_start: 0.8330 (ttm110) cc_final: 0.7736 (mtp180) REVERT: F 29 THR cc_start: 0.7559 (m) cc_final: 0.7328 (p) REVERT: F 100 TYR cc_start: 0.8783 (m-80) cc_final: 0.8080 (m-10) REVERT: F 127 ARG cc_start: 0.8988 (ptm-80) cc_final: 0.8685 (tmm-80) REVERT: H 29 THR cc_start: 0.7580 (m) cc_final: 0.7349 (p) REVERT: H 100 TYR cc_start: 0.8837 (m-80) cc_final: 0.8049 (m-10) outliers start: 28 outliers final: 23 residues processed: 450 average time/residue: 0.6978 time to fit residues: 443.4581 Evaluate side-chains 446 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 421 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 80 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16372 Z= 0.233 Angle : 0.510 6.927 22140 Z= 0.274 Chirality : 0.036 0.134 2460 Planarity : 0.003 0.064 2756 Dihedral : 13.911 175.832 2372 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.06 % Allowed : 15.29 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.21 (0.19), residues: 1936 helix: 1.28 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.67 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 379 HIS 0.006 0.001 HIS G 240 PHE 0.016 0.001 PHE H 20 TYR 0.017 0.001 TYR G 382 ARG 0.012 0.000 ARG C 519 *********************** 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 465 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 431 time to evaluate : 2.843 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: A 210 MET cc_start: 0.8148 (mtp) cc_final: 0.7856 (mtp) REVERT: A 555 ARG cc_start: 0.7564 (mmm160) cc_final: 0.6554 (ttm110) REVERT: B 29 THR cc_start: 0.7614 (m) cc_final: 0.7383 (p) REVERT: B 73 MET cc_start: 0.6195 (mmm) cc_final: 0.5902 (mmm) REVERT: B 100 TYR cc_start: 0.8786 (m-80) cc_final: 0.7977 (m-10) REVERT: B 127 ARG cc_start: 0.9101 (ptm-80) cc_final: 0.8856 (tmm-80) REVERT: B 141 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8492 (pt0) REVERT: C 138 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8382 (tt) REVERT: C 555 ARG cc_start: 0.7293 (ttm110) cc_final: 0.6943 (ttm110) REVERT: C 562 ARG cc_start: 0.6966 (tpt170) cc_final: 0.6303 (tpt90) REVERT: D 29 THR cc_start: 0.7598 (m) cc_final: 0.7366 (p) REVERT: D 85 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7778 (mm-30) REVERT: D 100 TYR cc_start: 0.8807 (m-80) cc_final: 0.7962 (m-80) REVERT: D 127 ARG cc_start: 0.9103 (ptm-80) cc_final: 0.8855 (tmm-80) REVERT: E 519 ARG cc_start: 0.8775 (ttm110) cc_final: 0.8518 (ttm110) REVERT: E 555 ARG cc_start: 0.8248 (ttm110) cc_final: 0.7667 (mtp180) REVERT: F 29 THR cc_start: 0.7579 (m) cc_final: 0.7365 (p) REVERT: F 100 TYR cc_start: 0.8803 (m-80) cc_final: 0.7993 (m-10) REVERT: G 138 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8437 (tt) REVERT: H 29 THR cc_start: 0.7555 (m) cc_final: 0.7331 (p) REVERT: H 100 TYR cc_start: 0.8826 (m-80) cc_final: 0.7977 (m-80) outliers start: 34 outliers final: 28 residues processed: 444 average time/residue: 0.7496 time to fit residues: 469.3523 Evaluate side-chains 448 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 418 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain D residue 20 PHE Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 122 CYS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 80 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 117 optimal weight: 0.5980 chunk 126 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16372 Z= 0.249 Angle : 0.520 7.593 22140 Z= 0.278 Chirality : 0.036 0.149 2460 Planarity : 0.003 0.053 2756 Dihedral : 13.487 175.688 2372 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.25 % Allowed : 15.17 % Favored : 82.58 % 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: 1.18 (0.19), residues: 1936 helix: 1.26 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.69 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 379 HIS 0.006 0.001 HIS A 240 PHE 0.017 0.002 PHE C 296 TYR 0.026 0.001 TYR A 382 ARG 0.011 0.001 ARG C 519 *********************** 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 469 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 432 time to evaluate : 2.632 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: A 138 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8451 (tt) REVERT: A 210 MET cc_start: 0.8137 (mtp) cc_final: 0.7858 (mtp) REVERT: B 29 THR cc_start: 0.7577 (m) cc_final: 0.7340 (p) REVERT: B 73 MET cc_start: 0.6183 (mmm) cc_final: 0.5872 (mmm) REVERT: B 100 TYR cc_start: 0.8810 (m-80) cc_final: 0.8002 (m-80) REVERT: B 127 ARG cc_start: 0.9086 (ptm-80) cc_final: 0.8862 (tmm-80) REVERT: C 138 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8378 (tt) REVERT: C 555 ARG cc_start: 0.7252 (ttm110) cc_final: 0.6969 (ttm110) REVERT: C 562 ARG cc_start: 0.6986 (tpt170) cc_final: 0.6283 (tpt90) REVERT: D 29 THR cc_start: 0.7560 (m) cc_final: 0.7326 (p) REVERT: D 85 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7806 (mm-30) REVERT: D 100 TYR cc_start: 0.8855 (m-80) cc_final: 0.8001 (m-80) REVERT: D 125 MET cc_start: 0.8779 (ttt) cc_final: 0.8514 (ttp) REVERT: D 127 ARG cc_start: 0.9093 (ptm-80) cc_final: 0.8849 (tmm-80) REVERT: E 138 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8392 (tt) REVERT: E 519 ARG cc_start: 0.8842 (ttm110) cc_final: 0.8558 (ttm110) REVERT: E 555 ARG cc_start: 0.8333 (ttm110) cc_final: 0.7834 (mmm160) REVERT: F 29 THR cc_start: 0.7625 (m) cc_final: 0.7401 (p) REVERT: F 85 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7747 (mm-30) REVERT: F 100 TYR cc_start: 0.8801 (m-80) cc_final: 0.7983 (m-80) REVERT: G 138 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8439 (tt) REVERT: H 29 THR cc_start: 0.7646 (m) cc_final: 0.7411 (p) REVERT: H 37 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7652 (mpp) REVERT: H 100 TYR cc_start: 0.8869 (m-80) cc_final: 0.8029 (m-80) outliers start: 37 outliers final: 29 residues processed: 447 average time/residue: 0.6856 time to fit residues: 435.1198 Evaluate side-chains 448 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 414 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 552 LEU Chi-restraints excluded: chain E residue 556 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 122 CYS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 171 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.6210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16372 Z= 0.223 Angle : 0.498 5.879 22140 Z= 0.273 Chirality : 0.035 0.112 2460 Planarity : 0.003 0.087 2756 Dihedral : 12.826 175.820 2372 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.94 % Allowed : 15.53 % Favored : 82.52 % 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: 1.25 (0.19), residues: 1936 helix: 1.31 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.63 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 379 HIS 0.007 0.001 HIS C 240 PHE 0.017 0.001 PHE B 20 TYR 0.029 0.001 TYR C 382 ARG 0.013 0.001 ARG C 519 *********************** 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 453 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 421 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: A 138 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8446 (tt) REVERT: A 210 MET cc_start: 0.8130 (mtp) cc_final: 0.7833 (mtp) REVERT: B 29 THR cc_start: 0.7629 (m) cc_final: 0.7378 (p) REVERT: B 73 MET cc_start: 0.6170 (mmm) cc_final: 0.5861 (mmm) REVERT: B 100 TYR cc_start: 0.8832 (m-80) cc_final: 0.8038 (m-80) REVERT: B 125 MET cc_start: 0.8864 (ttt) cc_final: 0.8606 (ttp) REVERT: B 127 ARG cc_start: 0.9035 (ptm-80) cc_final: 0.8812 (tmm-80) REVERT: B 141 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8520 (pt0) REVERT: C 138 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8351 (tt) REVERT: C 562 ARG cc_start: 0.7015 (tpt170) cc_final: 0.6280 (tpt90) REVERT: D 29 THR cc_start: 0.7606 (m) cc_final: 0.7352 (p) REVERT: D 85 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7776 (mm-30) REVERT: D 100 TYR cc_start: 0.8812 (m-80) cc_final: 0.7959 (m-80) REVERT: D 125 MET cc_start: 0.8808 (ttt) cc_final: 0.8559 (ttp) REVERT: D 127 ARG cc_start: 0.9075 (ptm-80) cc_final: 0.8833 (tmm-80) REVERT: E 138 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8388 (tt) REVERT: E 519 ARG cc_start: 0.8849 (ttm110) cc_final: 0.8529 (ttm110) REVERT: E 555 ARG cc_start: 0.8336 (ttm110) cc_final: 0.7826 (mmm160) REVERT: F 29 THR cc_start: 0.7666 (m) cc_final: 0.7436 (p) REVERT: F 85 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7786 (mm-30) REVERT: F 100 TYR cc_start: 0.8833 (m-80) cc_final: 0.8039 (m-80) REVERT: G 138 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8435 (tt) REVERT: H 29 THR cc_start: 0.7637 (m) cc_final: 0.7387 (p) REVERT: H 100 TYR cc_start: 0.8901 (m-80) cc_final: 0.8077 (m-80) outliers start: 32 outliers final: 27 residues processed: 438 average time/residue: 0.7504 time to fit residues: 472.7722 Evaluate side-chains 435 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 404 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 122 CYS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 291 SER Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 117 optimal weight: 0.0870 chunk 93 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16372 Z= 0.166 Angle : 0.483 5.839 22140 Z= 0.262 Chirality : 0.035 0.123 2460 Planarity : 0.003 0.065 2756 Dihedral : 12.300 176.025 2372 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.70 % Allowed : 15.59 % Favored : 82.71 % 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: 1.57 (0.19), residues: 1936 helix: 1.52 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : -0.49 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 379 HIS 0.006 0.001 HIS A 240 PHE 0.017 0.001 PHE F 20 TYR 0.025 0.001 TYR A 382 ARG 0.014 0.000 ARG C 519 ********************** 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 448 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 420 time to evaluate : 2.723 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: A 138 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8432 (tt) REVERT: A 210 MET cc_start: 0.8106 (mtp) cc_final: 0.7843 (mtp) REVERT: B 29 THR cc_start: 0.7660 (m) cc_final: 0.7437 (p) REVERT: B 73 MET cc_start: 0.6086 (mmm) cc_final: 0.5755 (mmm) REVERT: B 100 TYR cc_start: 0.8807 (m-80) cc_final: 0.8016 (m-80) REVERT: B 125 MET cc_start: 0.8844 (ttt) cc_final: 0.8595 (ttp) REVERT: B 127 ARG cc_start: 0.9032 (ptm-80) cc_final: 0.8804 (tmm-80) REVERT: B 141 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8511 (pt0) REVERT: C 138 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8352 (tt) REVERT: C 382 TYR cc_start: 0.7572 (t80) cc_final: 0.7371 (t80) REVERT: C 562 ARG cc_start: 0.6991 (tpt170) cc_final: 0.6347 (tpt90) REVERT: D 29 THR cc_start: 0.7596 (m) cc_final: 0.7360 (p) REVERT: D 85 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7769 (mm-30) REVERT: D 100 TYR cc_start: 0.8792 (m-80) cc_final: 0.7944 (m-80) REVERT: D 127 ARG cc_start: 0.9054 (ptm-80) cc_final: 0.8826 (tmm-80) REVERT: E 138 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8365 (tt) REVERT: F 29 THR cc_start: 0.7693 (m) cc_final: 0.7462 (p) REVERT: F 85 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7745 (mm-30) REVERT: F 100 TYR cc_start: 0.8826 (m-80) cc_final: 0.8010 (m-80) REVERT: G 138 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8428 (tt) REVERT: H 29 THR cc_start: 0.7696 (m) cc_final: 0.7482 (p) REVERT: H 100 TYR cc_start: 0.8825 (m-80) cc_final: 0.8056 (m-80) outliers start: 28 outliers final: 23 residues processed: 435 average time/residue: 0.6793 time to fit residues: 418.0679 Evaluate side-chains 436 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 409 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 105 HIS Chi-restraints excluded: chain G residue 122 CYS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 46 optimal weight: 0.3980 chunk 140 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.164455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.107003 restraints weight = 76197.994| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.39 r_work: 0.3225 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16372 Z= 0.250 Angle : 0.518 6.159 22140 Z= 0.283 Chirality : 0.036 0.140 2460 Planarity : 0.003 0.067 2756 Dihedral : 12.356 175.390 2372 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.00 % Allowed : 15.41 % Favored : 82.58 % 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: 1.36 (0.19), residues: 1936 helix: 1.39 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.60 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 379 HIS 0.010 0.001 HIS A 240 PHE 0.017 0.001 PHE C 296 TYR 0.024 0.001 TYR E 382 ARG 0.014 0.001 ARG E 519 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9653.67 seconds wall clock time: 170 minutes 37.35 seconds (10237.35 seconds total)