Starting phenix.real_space_refine on Sat Mar 16 20:42:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ad9_11721/03_2024/7ad9_11721_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ad9_11721/03_2024/7ad9_11721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ad9_11721/03_2024/7ad9_11721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ad9_11721/03_2024/7ad9_11721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ad9_11721/03_2024/7ad9_11721_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ad9_11721/03_2024/7ad9_11721_updated.pdb" } resolution = 3.5 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= 0.002 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 115 5.16 5 C 9810 2.51 5 N 2605 2.21 5 O 3010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15560 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "H" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "I" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "Q" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "S" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.94, per 1000 atoms: 0.57 Number of scatterers: 15560 At special positions: 0 Unit cell: (99.22, 91.96, 191.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 115 16.00 P 15 15.00 Mg 5 11.99 O 3010 8.00 N 2605 7.00 C 9810 6.00 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.83 Conformation dependent library (CDL) restraints added in 2.9 seconds 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH O 6 " pdb=" CB DTH P 6 " pdb=" CB DTH Q 6 " pdb=" CB DTH R 6 " pdb=" CB DTH S 6 " Number of C-beta restraints generated: 3640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 15 sheets defined 47.1% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 56 through 64 removed outlier: 3.607A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLY B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.775A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.985A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 261 removed outlier: 4.861A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.650A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 333 through 336 removed outlier: 4.559A pdb=" N LYS B 336 " --> pdb=" O PRO B 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 333 through 336' Processing helix chain 'B' and resid 338 through 348 removed outlier: 3.782A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 359 through 365 removed outlier: 3.531A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 56 through 64 removed outlier: 3.608A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLY D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.774A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.985A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 261 removed outlier: 4.862A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 296 removed outlier: 4.650A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 333 through 336 removed outlier: 4.559A pdb=" N LYS D 336 " --> pdb=" O PRO D 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 333 through 336' Processing helix chain 'D' and resid 338 through 348 removed outlier: 3.783A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 359 through 365 removed outlier: 3.531A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'L' and resid 3 through 15 Processing helix chain 'H' and resid 45 through 47 No H-bonds generated for 'chain 'H' and resid 45 through 47' Processing helix chain 'H' and resid 56 through 64 removed outlier: 3.608A pdb=" N LYS H 61 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLY H 63 " --> pdb=" O GLN H 59 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE H 64 " --> pdb=" O SER H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 91 Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 137 through 145 removed outlier: 3.775A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 182 through 196 removed outlier: 3.985A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU H 195 " --> pdb=" O LYS H 191 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 216 Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 252 through 261 removed outlier: 4.862A pdb=" N CYS H 257 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 264 through 267 Processing helix chain 'H' and resid 274 through 283 Processing helix chain 'H' and resid 287 through 296 removed outlier: 4.651A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 305 Processing helix chain 'H' and resid 309 through 320 Processing helix chain 'H' and resid 333 through 336 removed outlier: 4.560A pdb=" N LYS H 336 " --> pdb=" O PRO H 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 333 through 336' Processing helix chain 'H' and resid 338 through 348 removed outlier: 3.783A pdb=" N SER H 348 " --> pdb=" O SER H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 352 No H-bonds generated for 'chain 'H' and resid 350 through 352' Processing helix chain 'H' and resid 359 through 365 removed outlier: 3.530A pdb=" N GLU H 364 " --> pdb=" O GLN H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 371 Processing helix chain 'E' and resid 3 through 15 Processing helix chain 'F' and resid 45 through 47 No H-bonds generated for 'chain 'F' and resid 45 through 47' Processing helix chain 'F' and resid 56 through 64 removed outlier: 3.607A pdb=" N LYS F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLY F 63 " --> pdb=" O GLN F 59 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE F 64 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.775A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 196 removed outlier: 3.985A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 252 through 261 removed outlier: 4.861A pdb=" N CYS F 257 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 287 through 296 removed outlier: 4.651A pdb=" N LYS F 291 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ASP F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 305 Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 333 through 336 removed outlier: 4.560A pdb=" N LYS F 336 " --> pdb=" O PRO F 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 333 through 336' Processing helix chain 'F' and resid 338 through 348 removed outlier: 3.783A pdb=" N SER F 348 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 359 through 365 removed outlier: 3.531A pdb=" N GLU F 364 " --> pdb=" O GLN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 371 Processing helix chain 'G' and resid 3 through 15 Processing helix chain 'I' and resid 45 through 47 No H-bonds generated for 'chain 'I' and resid 45 through 47' Processing helix chain 'I' and resid 56 through 64 removed outlier: 3.608A pdb=" N LYS I 61 " --> pdb=" O GLU I 57 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLY I 63 " --> pdb=" O GLN I 59 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE I 64 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 91 Processing helix chain 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'I' and resid 113 through 125 Processing helix chain 'I' and resid 137 through 145 removed outlier: 3.775A pdb=" N LEU I 142 " --> pdb=" O ALA I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 182 through 196 removed outlier: 3.985A pdb=" N THR I 194 " --> pdb=" O MET I 190 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU I 195 " --> pdb=" O LYS I 191 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG I 196 " --> pdb=" O ILE I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 216 Processing helix chain 'I' and resid 223 through 232 Processing helix chain 'I' and resid 252 through 261 removed outlier: 4.862A pdb=" N CYS I 257 " --> pdb=" O ARG I 254 " (cutoff:3.500A) Proline residue: I 258 - end of helix Processing helix chain 'I' and resid 264 through 267 Processing helix chain 'I' and resid 274 through 283 Processing helix chain 'I' and resid 287 through 296 removed outlier: 4.650A pdb=" N LYS I 291 " --> pdb=" O ILE I 287 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASP I 292 " --> pdb=" O ASP I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 305 Processing helix chain 'I' and resid 309 through 320 Processing helix chain 'I' and resid 333 through 336 removed outlier: 4.559A pdb=" N LYS I 336 " --> pdb=" O PRO I 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 333 through 336' Processing helix chain 'I' and resid 338 through 348 removed outlier: 3.782A pdb=" N SER I 348 " --> pdb=" O SER I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 352 No H-bonds generated for 'chain 'I' and resid 350 through 352' Processing helix chain 'I' and resid 359 through 365 removed outlier: 3.531A pdb=" N GLU I 364 " --> pdb=" O GLN I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 367 through 371 Processing sheet with id= A, first strand: chain 'B' and resid 17 through 21 removed outlier: 3.959A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.026A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= D, first strand: chain 'D' and resid 17 through 21 removed outlier: 3.959A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.025A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= G, first strand: chain 'H' and resid 17 through 21 removed outlier: 3.959A pdb=" N THR H 106 " --> pdb=" O CYS H 10 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASN H 12 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 297 through 300 removed outlier: 6.025A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER H 300 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU H 153 " --> pdb=" O SER H 300 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 238 through 241 Processing sheet with id= J, first strand: chain 'F' and resid 17 through 21 removed outlier: 3.958A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASN F 12 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.026A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'I' and resid 17 through 21 removed outlier: 3.958A pdb=" N THR I 106 " --> pdb=" O CYS I 10 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASN I 12 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 297 through 300 removed outlier: 6.026A pdb=" N ILE I 151 " --> pdb=" O VAL I 298 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N SER I 300 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU I 153 " --> pdb=" O SER I 300 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 238 through 241 570 hydrogen bonds defined for protein. 1545 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: 4.55 Time building geometry restraints manager: 7.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4914 1.34 - 1.46: 3557 1.46 - 1.58: 7199 1.58 - 1.70: 15 1.70 - 1.82: 200 Bond restraints: 15885 Sorted by residual: bond pdb=" CA ILE D 151 " pdb=" C ILE D 151 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.19e-02 7.06e+03 2.49e+01 bond pdb=" CA ILE F 151 " pdb=" C ILE F 151 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.19e-02 7.06e+03 2.46e+01 bond pdb=" CA ILE H 151 " pdb=" C ILE H 151 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.19e-02 7.06e+03 2.45e+01 bond pdb=" CA ILE I 151 " pdb=" C ILE I 151 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.19e-02 7.06e+03 2.44e+01 bond pdb=" CA ILE B 151 " pdb=" C ILE B 151 " ideal model delta sigma weight residual 1.522 1.464 0.058 1.19e-02 7.06e+03 2.41e+01 ... (remaining 15880 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.90: 523 105.90 - 113.67: 8851 113.67 - 121.45: 8378 121.45 - 129.22: 3688 129.22 - 136.99: 105 Bond angle restraints: 21545 Sorted by residual: angle pdb=" N VAL F 54 " pdb=" CA VAL F 54 " pdb=" C VAL F 54 " ideal model delta sigma weight residual 108.12 115.88 -7.76 1.44e+00 4.82e-01 2.91e+01 angle pdb=" N VAL B 54 " pdb=" CA VAL B 54 " pdb=" C VAL B 54 " ideal model delta sigma weight residual 108.12 115.86 -7.74 1.44e+00 4.82e-01 2.89e+01 angle pdb=" N VAL I 54 " pdb=" CA VAL I 54 " pdb=" C VAL I 54 " ideal model delta sigma weight residual 108.12 115.85 -7.73 1.44e+00 4.82e-01 2.88e+01 angle pdb=" N VAL D 54 " pdb=" CA VAL D 54 " pdb=" C VAL D 54 " ideal model delta sigma weight residual 108.12 115.84 -7.72 1.44e+00 4.82e-01 2.87e+01 angle pdb=" N VAL H 54 " pdb=" CA VAL H 54 " pdb=" C VAL H 54 " ideal model delta sigma weight residual 108.12 115.84 -7.72 1.44e+00 4.82e-01 2.87e+01 ... (remaining 21540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.01: 9330 29.01 - 58.02: 195 58.02 - 87.02: 15 87.02 - 116.03: 5 116.03 - 145.04: 10 Dihedral angle restraints: 9555 sinusoidal: 3880 harmonic: 5675 Sorted by residual: dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.04 -145.04 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.02 -145.02 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O1B ADP H 401 " pdb=" O3A ADP H 401 " pdb=" PB ADP H 401 " pdb=" PA ADP H 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.01 -145.01 1 2.00e+01 2.50e-03 4.37e+01 ... (remaining 9552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1303 0.057 - 0.115: 760 0.115 - 0.172: 218 0.172 - 0.230: 80 0.230 - 0.287: 39 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE I 151 " pdb=" CA ILE I 151 " pdb=" CG1 ILE I 151 " pdb=" CG2 ILE I 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB ILE H 151 " pdb=" CA ILE H 151 " pdb=" CG1 ILE H 151 " pdb=" CG2 ILE H 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 2397 not shown) Planarity restraints: 2725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 11 " -0.028 2.00e-02 2.50e+03 5.73e-02 3.29e+01 pdb=" CG ASP D 11 " 0.099 2.00e-02 2.50e+03 pdb=" OD1 ASP D 11 " -0.036 2.00e-02 2.50e+03 pdb=" OD2 ASP D 11 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP I 11 " -0.028 2.00e-02 2.50e+03 5.73e-02 3.28e+01 pdb=" CG ASP I 11 " 0.099 2.00e-02 2.50e+03 pdb=" OD1 ASP I 11 " -0.036 2.00e-02 2.50e+03 pdb=" OD2 ASP I 11 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 11 " -0.028 2.00e-02 2.50e+03 5.71e-02 3.26e+01 pdb=" CG ASP H 11 " 0.099 2.00e-02 2.50e+03 pdb=" OD1 ASP H 11 " -0.036 2.00e-02 2.50e+03 pdb=" OD2 ASP H 11 " -0.034 2.00e-02 2.50e+03 ... (remaining 2722 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 30 2.39 - 3.02: 9941 3.02 - 3.65: 23182 3.65 - 4.27: 39325 4.27 - 4.90: 61397 Nonbonded interactions: 133875 Sorted by model distance: nonbonded pdb=" CD1 TRP R 3 " pdb=" SG CYS R 7 " model vdw 1.765 3.620 nonbonded pdb=" CD1 TRP P 3 " pdb=" SG CYS P 7 " model vdw 1.765 3.620 nonbonded pdb=" CD1 TRP S 3 " pdb=" SG CYS S 7 " model vdw 1.765 3.620 nonbonded pdb=" CD1 TRP O 3 " pdb=" SG CYS O 7 " model vdw 1.765 3.620 nonbonded pdb=" CD1 TRP Q 3 " pdb=" SG CYS Q 7 " model vdw 1.766 3.620 ... (remaining 133870 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' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.020 Extract box with map and model: 6.770 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 44.090 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.017 0.093 15885 Z= 1.089 Angle : 1.608 10.129 21545 Z= 0.979 Chirality : 0.082 0.287 2400 Planarity : 0.011 0.057 2725 Dihedral : 12.960 145.040 5915 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.30 % Allowed : 0.30 % Favored : 99.39 % Cbeta Deviations : 0.27 % 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: -0.26 (0.19), residues: 1900 helix: -1.30 (0.15), residues: 880 sheet: 0.22 (0.33), residues: 225 loop : 1.47 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.005 TRP H 340 HIS 0.031 0.007 HIS F 40 PHE 0.053 0.008 PHE B 124 TYR 0.063 0.007 TYR B 143 ARG 0.020 0.004 ARG I 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 438 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 ASN cc_start: 0.7662 (t0) cc_final: 0.6847 (t0) REVERT: B 82 MET cc_start: 0.9072 (tpt) cc_final: 0.8852 (tpt) REVERT: B 190 MET cc_start: 0.7943 (mtp) cc_final: 0.7630 (mtp) REVERT: B 305 MET cc_start: 0.8823 (mmm) cc_final: 0.8482 (mmt) REVERT: B 326 LYS cc_start: 0.8131 (tptt) cc_final: 0.7749 (tttt) REVERT: D 113 LYS cc_start: 0.7920 (mttt) cc_final: 0.7673 (mtmt) REVERT: D 115 ASN cc_start: 0.8415 (t0) cc_final: 0.8187 (t0) REVERT: D 119 MET cc_start: 0.8350 (ttp) cc_final: 0.8139 (ttm) REVERT: D 151 ILE cc_start: 0.8854 (mt) cc_final: 0.8583 (mt) REVERT: H 44 MET cc_start: 0.7546 (mtp) cc_final: 0.7341 (mtm) REVERT: H 115 ASN cc_start: 0.8445 (t0) cc_final: 0.8082 (m-40) REVERT: F 305 MET cc_start: 0.8620 (mmm) cc_final: 0.8213 (mmt) REVERT: I 154 ASP cc_start: 0.8289 (t0) cc_final: 0.7895 (t70) REVERT: I 225 ASN cc_start: 0.8338 (m-40) cc_final: 0.7865 (m110) REVERT: I 274 ILE cc_start: 0.8022 (pt) cc_final: 0.7808 (tt) REVERT: I 283 MET cc_start: 0.8566 (mmp) cc_final: 0.8354 (mmt) outliers start: 5 outliers final: 0 residues processed: 441 average time/residue: 0.3013 time to fit residues: 188.6793 Evaluate side-chains 202 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 172 optimal weight: 0.2980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN D 40 HIS H 59 GLN H 121 GLN H 353 GLN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN F 121 GLN I 128 ASN I 314 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15885 Z= 0.175 Angle : 0.618 8.299 21545 Z= 0.305 Chirality : 0.046 0.153 2400 Planarity : 0.004 0.047 2725 Dihedral : 11.122 113.982 2250 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.55 % Allowed : 7.78 % Favored : 89.67 % 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: 0.98 (0.19), residues: 1900 helix: 0.24 (0.17), residues: 840 sheet: 0.33 (0.34), residues: 235 loop : 1.54 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 340 HIS 0.004 0.001 HIS B 101 PHE 0.034 0.002 PHE D 375 TYR 0.015 0.001 TYR H 294 ARG 0.007 0.001 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 257 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8914 (tpt) cc_final: 0.8703 (tpt) REVERT: B 123 MET cc_start: 0.7251 (mmm) cc_final: 0.6913 (mmm) REVERT: B 325 MET cc_start: 0.6628 (mtm) cc_final: 0.6269 (mtt) REVERT: B 326 LYS cc_start: 0.8106 (tptt) cc_final: 0.7824 (tttt) REVERT: D 119 MET cc_start: 0.8239 (ttp) cc_final: 0.7963 (ttm) REVERT: D 179 ASP cc_start: 0.8274 (m-30) cc_final: 0.8069 (m-30) REVERT: L 11 GLU cc_start: 0.7621 (tp30) cc_final: 0.7395 (tp30) REVERT: H 115 ASN cc_start: 0.8064 (t0) cc_final: 0.7838 (m-40) REVERT: H 128 ASN cc_start: 0.7822 (m-40) cc_final: 0.7450 (t0) REVERT: H 289 ILE cc_start: 0.8610 (mm) cc_final: 0.8370 (mm) REVERT: E 6 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8008 (mm) REVERT: F 157 ASP cc_start: 0.8211 (t70) cc_final: 0.7977 (t0) REVERT: F 305 MET cc_start: 0.8631 (mmm) cc_final: 0.8230 (mmt) REVERT: F 335 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7773 (mtm180) REVERT: G 1 MET cc_start: 0.6036 (ptt) cc_final: 0.4942 (ptm) REVERT: G 9 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7256 (ttpp) REVERT: I 289 ILE cc_start: 0.8421 (mm) cc_final: 0.8129 (mm) REVERT: I 375 PHE cc_start: 0.8211 (t80) cc_final: 0.7953 (t80) outliers start: 42 outliers final: 17 residues processed: 281 average time/residue: 0.2622 time to fit residues: 110.7105 Evaluate side-chains 206 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 80 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 143 optimal weight: 0.0670 chunk 117 optimal weight: 0.0010 chunk 47 optimal weight: 0.7980 chunk 172 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 171 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 overall best weight: 0.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN F 115 ASN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15885 Z= 0.148 Angle : 0.560 9.829 21545 Z= 0.268 Chirality : 0.044 0.161 2400 Planarity : 0.004 0.052 2725 Dihedral : 9.531 95.576 2250 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.19 % Allowed : 9.73 % Favored : 88.09 % 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: 1.41 (0.20), residues: 1900 helix: 0.72 (0.18), residues: 835 sheet: 0.25 (0.34), residues: 235 loop : 1.71 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 340 HIS 0.003 0.001 HIS B 40 PHE 0.019 0.001 PHE D 375 TYR 0.011 0.001 TYR H 294 ARG 0.005 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 206 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8909 (tt) REVERT: B 154 ASP cc_start: 0.7890 (t0) cc_final: 0.7555 (t70) REVERT: B 202 THR cc_start: 0.7112 (p) cc_final: 0.6206 (m) REVERT: B 326 LYS cc_start: 0.8125 (tptt) cc_final: 0.7884 (tttt) REVERT: D 119 MET cc_start: 0.8227 (ttp) cc_final: 0.7886 (ttm) REVERT: D 202 THR cc_start: 0.7832 (p) cc_final: 0.7515 (p) REVERT: D 205 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6622 (mp0) REVERT: D 352 PHE cc_start: 0.9118 (t80) cc_final: 0.8763 (t80) REVERT: H 289 ILE cc_start: 0.8623 (mm) cc_final: 0.8339 (mm) REVERT: E 7 ILE cc_start: 0.8554 (mm) cc_final: 0.8251 (mm) REVERT: E 8 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7464 (mtmt) REVERT: F 283 MET cc_start: 0.8538 (mmp) cc_final: 0.8156 (mmt) REVERT: F 305 MET cc_start: 0.8726 (mmm) cc_final: 0.8431 (mmt) REVERT: F 335 ARG cc_start: 0.8284 (mtm-85) cc_final: 0.8008 (mtm180) REVERT: G 9 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7301 (ttmm) REVERT: I 283 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8349 (mmt) REVERT: I 289 ILE cc_start: 0.8442 (mm) cc_final: 0.8118 (mm) outliers start: 36 outliers final: 17 residues processed: 232 average time/residue: 0.2607 time to fit residues: 92.2196 Evaluate side-chains 204 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain H residue 59 GLN Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 283 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 7.9990 chunk 129 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 116 optimal weight: 0.2980 chunk 173 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 161 HIS ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 HIS ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15885 Z= 0.210 Angle : 0.571 9.566 21545 Z= 0.273 Chirality : 0.045 0.164 2400 Planarity : 0.004 0.053 2725 Dihedral : 8.283 96.544 2250 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.10 % Allowed : 10.09 % Favored : 86.81 % 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: 1.56 (0.20), residues: 1900 helix: 1.01 (0.19), residues: 805 sheet: 0.20 (0.33), residues: 235 loop : 1.63 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 79 HIS 0.003 0.001 HIS F 40 PHE 0.012 0.002 PHE I 223 TYR 0.012 0.001 TYR H 294 ARG 0.004 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 194 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8939 (tt) REVERT: B 154 ASP cc_start: 0.8142 (t0) cc_final: 0.7804 (t70) REVERT: D 119 MET cc_start: 0.8264 (ttp) cc_final: 0.7997 (ttm) REVERT: D 340 TRP cc_start: 0.8380 (t60) cc_final: 0.8133 (t60) REVERT: D 352 PHE cc_start: 0.9096 (t80) cc_final: 0.8683 (t80) REVERT: H 119 MET cc_start: 0.8757 (ttm) cc_final: 0.8430 (ttm) REVERT: H 194 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8782 (p) REVERT: H 352 PHE cc_start: 0.8789 (t80) cc_final: 0.8550 (t80) REVERT: E 6 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8211 (mt) REVERT: E 8 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7625 (mtmt) REVERT: F 335 ARG cc_start: 0.8447 (mtm-85) cc_final: 0.8168 (mtm-85) REVERT: G 9 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7341 (ttmm) REVERT: I 141 SER cc_start: 0.8601 (m) cc_final: 0.8315 (m) REVERT: I 289 ILE cc_start: 0.8506 (mm) cc_final: 0.8173 (mm) outliers start: 51 outliers final: 33 residues processed: 228 average time/residue: 0.2550 time to fit residues: 89.3258 Evaluate side-chains 215 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 177 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 111 ASN Chi-restraints excluded: chain I residue 194 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 101 HIS ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 15885 Z= 0.496 Angle : 0.722 8.313 21545 Z= 0.356 Chirality : 0.051 0.186 2400 Planarity : 0.005 0.058 2725 Dihedral : 8.134 103.662 2250 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.40 % Allowed : 11.00 % Favored : 85.59 % 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: 0.69 (0.19), residues: 1900 helix: 0.40 (0.18), residues: 835 sheet: -0.20 (0.28), residues: 310 loop : 1.15 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 79 HIS 0.007 0.002 HIS F 88 PHE 0.025 0.002 PHE L 10 TYR 0.018 0.002 TYR I 53 ARG 0.004 0.001 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 163 time to evaluate : 1.685 Fit side-chains revert: symmetry clash REVERT: B 289 ILE cc_start: 0.8833 (mm) cc_final: 0.8517 (mt) REVERT: D 132 MET cc_start: 0.8142 (tmm) cc_final: 0.7826 (tmm) REVERT: D 202 THR cc_start: 0.8652 (p) cc_final: 0.8043 (p) REVERT: D 205 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: D 248 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8713 (pt) REVERT: D 325 MET cc_start: 0.7106 (ttm) cc_final: 0.6852 (ttm) REVERT: H 119 MET cc_start: 0.8888 (ttm) cc_final: 0.8612 (ttm) REVERT: H 194 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8905 (p) REVERT: H 289 ILE cc_start: 0.8723 (mm) cc_final: 0.8420 (mm) REVERT: E 1 MET cc_start: 0.7076 (ptt) cc_final: 0.6860 (ptt) REVERT: E 8 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7864 (mtmt) REVERT: F 313 MET cc_start: 0.8826 (tpp) cc_final: 0.8456 (ttm) REVERT: G 5 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8535 (p0) REVERT: G 9 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7524 (ttpp) REVERT: I 132 MET cc_start: 0.8939 (pmm) cc_final: 0.8332 (pmm) REVERT: I 289 ILE cc_start: 0.8644 (mm) cc_final: 0.8331 (mm) outliers start: 56 outliers final: 36 residues processed: 204 average time/residue: 0.2341 time to fit residues: 75.0498 Evaluate side-chains 199 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 111 ASN Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 250 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15885 Z= 0.180 Angle : 0.551 7.466 21545 Z= 0.263 Chirality : 0.045 0.162 2400 Planarity : 0.004 0.051 2725 Dihedral : 7.188 74.240 2250 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.07 % Allowed : 12.58 % Favored : 85.35 % 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 (0.20), residues: 1900 helix: 0.91 (0.19), residues: 805 sheet: -0.09 (0.33), residues: 235 loop : 1.25 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 340 HIS 0.003 0.001 HIS D 161 PHE 0.014 0.001 PHE F 255 TYR 0.011 0.001 TYR H 294 ARG 0.004 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 2.123 Fit side-chains REVERT: D 248 ILE cc_start: 0.8855 (tt) cc_final: 0.8492 (pt) REVERT: D 325 MET cc_start: 0.6986 (ttm) cc_final: 0.6720 (ttm) REVERT: H 119 MET cc_start: 0.8759 (ttm) cc_final: 0.8527 (ttm) REVERT: H 289 ILE cc_start: 0.8669 (mm) cc_final: 0.8447 (mm) REVERT: E 8 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7767 (mtmt) REVERT: F 313 MET cc_start: 0.8691 (tpp) cc_final: 0.8396 (ttm) REVERT: G 9 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7442 (ttmm) REVERT: I 82 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8368 (mmm) REVERT: I 132 MET cc_start: 0.8890 (pmm) cc_final: 0.8312 (pmm) REVERT: I 289 ILE cc_start: 0.8376 (mm) cc_final: 0.8077 (mm) REVERT: I 325 MET cc_start: 0.7026 (tpp) cc_final: 0.6648 (mtp) outliers start: 34 outliers final: 24 residues processed: 198 average time/residue: 0.2416 time to fit residues: 74.8041 Evaluate side-chains 187 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 194 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15885 Z= 0.229 Angle : 0.564 6.427 21545 Z= 0.269 Chirality : 0.045 0.165 2400 Planarity : 0.004 0.054 2725 Dihedral : 7.073 71.384 2250 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.07 % Allowed : 13.19 % Favored : 84.74 % 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 (0.20), residues: 1900 helix: 1.00 (0.19), residues: 805 sheet: -0.13 (0.33), residues: 235 loop : 1.17 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 340 HIS 0.003 0.001 HIS F 88 PHE 0.016 0.001 PHE F 375 TYR 0.011 0.001 TYR H 294 ARG 0.003 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 1.771 Fit side-chains REVERT: B 44 MET cc_start: 0.7038 (mmm) cc_final: 0.6724 (mmm) REVERT: D 248 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8521 (pt) REVERT: D 325 MET cc_start: 0.7047 (ttm) cc_final: 0.6796 (ttm) REVERT: H 119 MET cc_start: 0.8770 (ttm) cc_final: 0.8525 (ttm) REVERT: H 289 ILE cc_start: 0.8647 (mm) cc_final: 0.8366 (mm) REVERT: H 355 MET cc_start: 0.8025 (mtp) cc_final: 0.7725 (mtt) REVERT: E 8 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7722 (mtmt) REVERT: F 313 MET cc_start: 0.8709 (tpp) cc_final: 0.8396 (ttm) REVERT: G 9 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7479 (ttmm) REVERT: I 289 ILE cc_start: 0.8405 (mm) cc_final: 0.8109 (mm) REVERT: I 325 MET cc_start: 0.7201 (tpp) cc_final: 0.6799 (mtp) outliers start: 34 outliers final: 24 residues processed: 188 average time/residue: 0.2362 time to fit residues: 69.6616 Evaluate side-chains 183 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 194 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 0.0980 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 166 optimal weight: 0.5980 chunk 175 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15885 Z= 0.155 Angle : 0.528 6.661 21545 Z= 0.250 Chirality : 0.044 0.158 2400 Planarity : 0.004 0.050 2725 Dihedral : 6.793 72.361 2250 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.76 % Allowed : 13.62 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.30 (0.20), residues: 1900 helix: 1.09 (0.19), residues: 810 sheet: -0.13 (0.33), residues: 235 loop : 1.21 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 340 HIS 0.003 0.001 HIS D 161 PHE 0.012 0.001 PHE F 255 TYR 0.009 0.001 TYR H 294 ARG 0.003 0.000 ARG F 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.821 Fit side-chains REVERT: B 44 MET cc_start: 0.7072 (mmm) cc_final: 0.6814 (mmm) REVERT: D 132 MET cc_start: 0.8593 (ppp) cc_final: 0.8268 (tmm) REVERT: D 248 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8432 (pt) REVERT: D 325 MET cc_start: 0.6907 (ttm) cc_final: 0.6594 (ttm) REVERT: H 119 MET cc_start: 0.8745 (ttm) cc_final: 0.8499 (ttm) REVERT: H 355 MET cc_start: 0.7935 (mtp) cc_final: 0.7638 (mtt) REVERT: E 8 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7706 (mtmt) REVERT: F 313 MET cc_start: 0.8645 (tpp) cc_final: 0.8377 (ttm) REVERT: G 9 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7616 (ttmm) REVERT: I 95 ARG cc_start: 0.7950 (mmm160) cc_final: 0.7278 (mmt180) REVERT: I 289 ILE cc_start: 0.8341 (mm) cc_final: 0.8043 (mm) REVERT: I 325 MET cc_start: 0.6950 (tpp) cc_final: 0.6691 (mtp) outliers start: 29 outliers final: 22 residues processed: 182 average time/residue: 0.2627 time to fit residues: 75.1313 Evaluate side-chains 184 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 194 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 154 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN I 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15885 Z= 0.165 Angle : 0.534 7.675 21545 Z= 0.252 Chirality : 0.044 0.158 2400 Planarity : 0.004 0.052 2725 Dihedral : 6.693 74.010 2250 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.88 % Allowed : 13.86 % Favored : 84.26 % 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: 1.33 (0.20), residues: 1900 helix: 1.13 (0.19), residues: 810 sheet: -0.14 (0.33), residues: 235 loop : 1.22 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 340 HIS 0.003 0.001 HIS D 161 PHE 0.013 0.001 PHE F 375 TYR 0.009 0.001 TYR H 294 ARG 0.003 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.919 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.7196 (mmm) cc_final: 0.6942 (mmm) REVERT: B 325 MET cc_start: 0.6738 (ptp) cc_final: 0.6536 (ptp) REVERT: D 132 MET cc_start: 0.8647 (ppp) cc_final: 0.8300 (tmm) REVERT: D 248 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8440 (pt) REVERT: D 325 MET cc_start: 0.6910 (ttm) cc_final: 0.6585 (ttm) REVERT: H 119 MET cc_start: 0.8748 (ttm) cc_final: 0.8506 (ttm) REVERT: H 355 MET cc_start: 0.7953 (mtp) cc_final: 0.7640 (mtt) REVERT: E 8 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7684 (mtmt) REVERT: F 313 MET cc_start: 0.8610 (tpp) cc_final: 0.8382 (ttm) REVERT: G 1 MET cc_start: 0.5516 (ptm) cc_final: 0.5034 (ptm) REVERT: G 9 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7647 (ttmm) REVERT: I 289 ILE cc_start: 0.8334 (mm) cc_final: 0.8022 (mm) outliers start: 31 outliers final: 23 residues processed: 179 average time/residue: 0.2479 time to fit residues: 69.0569 Evaluate side-chains 181 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 187 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15885 Z= 0.249 Angle : 0.570 7.120 21545 Z= 0.272 Chirality : 0.046 0.162 2400 Planarity : 0.004 0.053 2725 Dihedral : 6.817 71.911 2250 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.82 % Allowed : 13.68 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.23 (0.20), residues: 1900 helix: 1.06 (0.19), residues: 810 sheet: -0.23 (0.33), residues: 235 loop : 1.16 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 340 HIS 0.004 0.001 HIS F 88 PHE 0.018 0.002 PHE D 375 TYR 0.011 0.001 TYR H 294 ARG 0.009 0.000 ARG D 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 168 time to evaluate : 1.896 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.7053 (mmm) cc_final: 0.6525 (mmm) REVERT: B 289 ILE cc_start: 0.8671 (mm) cc_final: 0.8423 (mt) REVERT: B 325 MET cc_start: 0.6827 (ptp) cc_final: 0.6623 (ptp) REVERT: B 360 GLN cc_start: 0.8738 (tp40) cc_final: 0.8360 (tp-100) REVERT: D 132 MET cc_start: 0.8597 (ppp) cc_final: 0.8267 (tmm) REVERT: D 248 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8523 (pt) REVERT: D 325 MET cc_start: 0.6969 (ttm) cc_final: 0.6685 (ttm) REVERT: H 119 MET cc_start: 0.8778 (ttm) cc_final: 0.8498 (ttm) REVERT: H 289 ILE cc_start: 0.8640 (mm) cc_final: 0.8322 (mm) REVERT: H 355 MET cc_start: 0.8064 (mtp) cc_final: 0.7769 (mtt) REVERT: E 8 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7705 (mtmt) REVERT: F 313 MET cc_start: 0.8649 (tpp) cc_final: 0.8423 (ttm) REVERT: G 1 MET cc_start: 0.5626 (ptm) cc_final: 0.5170 (ptm) REVERT: G 9 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7525 (ttmm) REVERT: I 289 ILE cc_start: 0.8461 (mm) cc_final: 0.8117 (mm) outliers start: 30 outliers final: 24 residues processed: 189 average time/residue: 0.2404 time to fit residues: 70.9083 Evaluate side-chains 181 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 187 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.0040 chunk 150 optimal weight: 4.9990 chunk 63 optimal weight: 0.0870 chunk 155 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN B 115 ASN B 246 GLN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN I 115 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.091726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.081221 restraints weight = 31143.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.083680 restraints weight = 15435.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.085263 restraints weight = 9244.916| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15885 Z= 0.229 Angle : 0.562 7.222 21545 Z= 0.268 Chirality : 0.045 0.160 2400 Planarity : 0.004 0.052 2725 Dihedral : 6.815 71.376 2250 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.95 % Allowed : 14.10 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.20), residues: 1900 helix: 1.08 (0.19), residues: 810 sheet: -0.22 (0.33), residues: 235 loop : 1.09 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 340 HIS 0.004 0.001 HIS D 161 PHE 0.015 0.001 PHE F 375 TYR 0.010 0.001 TYR H 294 ARG 0.009 0.000 ARG D 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2818.13 seconds wall clock time: 52 minutes 22.63 seconds (3142.63 seconds total)